$Id: PARAMS.FIG 7056 2010-01-01 16:16:31Z vriend $
This is the WHAT IF internal parameter file. This file holds
many different parameters that are internally used for different
purposes. If you are smart you can change this file to make
WHAT IF behave differently. If you are smart, you do not touch
this file, other than to read it, and use the SETWIF command
to change parameters on the fly. That is less permanent. If you
work with web-services then, no matter how smart you are, you
will need to read this file if you want to modify WHAT IF parameters.
The format of this file is as follows:
- This top 90% is only a description. But, as this description is used
to tell the user what the parameter means, and what it's useful
values are, etc., it is strongly suggested you use EXACTLY the
format as used sofar. Also, please make sure no line gets longer
than 80 characters.
The first 5 columns should hold the parameter number, and nothing
else.
- The bottom 10 holds the actual parameter data.
In this bottom part the first five columns should hold the parameter
number, the actual value should be in the columns 6 till 80.
Parameters not mentioned in the second part are initialized at zero.
- An asterisk in column 1 indicates the beginning of the real data.
Be aware that a few parameters are re-initialized in a machine
dependent manner in subroutine WIF023 in the module ini.f. If you use
web-services, a series of parameters is reinitialized anyway. Parameter
1072 is, for obvious reasons, always set at 1, no matter what you try.
This rigid file format is required for WHAT IF's HELP facility.
Any line that is empty in the columns 1-5 is regarded by WHAT IF
as comments, and thus skipped.
Search for FREE if you need one single free WIFPAR, or otherwise,
stay in your own block of reserved parameters.
1 One or three letter code flag for listing amino acids
= 0 1 letter code
= 1 3 letter code
2 Amount of sequence information
= 0 only sequence
= 1 sequence + aa frequency
= 2 sequence + frequency + neighbor matrix
3 Scale factor for arrows (*100)
4 The number of the database file indicated to work with
5 Output in DEBUMP flag
= 0 Do not give output (unless other flag says to do so)
= 1 Do always give output
= 2 Only give final output per residue
6 Precision of accessibility calculation
= 0 Very course
= 1 Course
= 2 Normal (default)
= 3 Fine
= 4 Very fine ion
7 Repeat angle for property moment calculations
default = 100 (helix)
8 Moving average box width in property moment calculations
default = 17
9 Property number for property moment calculations
default = 19 (hydrophobic moment)
10 Text in TOPTXT indicates error.
= 0 No, normal text
= 1 Yes there is an error
11 Use protons in FCONATI etc routines
= 0 Use protons
= 1 Do NOT use protons
12 Use the database etc
= 0 Open all data base files upon startup of WHAT IF
= 1 Do NOT open any data base files upon startup of WHAT IF
13 Set NUMGRV to zero in character output
= 0 Set NUMGRV every time to zero in CHR000 (default)
= 1 Do NOT set NUMGRV to zero in CHR000
14 Automatic looping flag for SUPPOS (3SSP)
= 0 Prompt user where ever needed
= 1 Always compare M1 with M2 automatically (for 3SSP)
15 Display protons in graphics options
= 0 Yes, display them if possible (Default)
= 1 No, never display them
16 Number of degrees per step in automatic density fitting
17 Number of steps per try in automatic density fitting
18 Number of hits below which sleeping proteins will be used
too in the SCNSEL option of the SCAN3D menu.
19 Use sequence information for 2 residues in DGINSS
= 0 Use only for 1 residue
= 1 Use it for two residues
20 Width of the stick of an arrow in Angstroms (*100)
Default=0.5
21 Length of the stick of an arrow in Angstroms (*100)
Default=2.5
22 Width of the point of an arrow in Angstroms (*100)
Default=0.5
23 Length of the point of an arrow in Angstroms (*100)
Default=1.0
24 Number of sides of an arrow
Default=6
25 Colour of an arrow
Default=170
26 Use nearest neighbour in BUMPS and CONTAC runs, etc.
= 0 Use them
= 1 Dont use them (deauflt)
27 Graphics flag in BUMPS and CONTAC runs
= 0 Do not show dashed lines for contacts and bumps
<>0 Show dashed lines for contacts and bumps (default)
28 Draw non-hydrogen bonded hydrogens in HB2GRA
= 0 Draw them (default)
= 1 Dont draw them
29 Radius of the water probe. Default = 1.4 A. (*100)
30 Update PRO/GLY backbone in BLDPIR
= 0 Update the backbone coordinates (default)
= 1 Dont update the backbone coordinates
31 Colour of DSSP determined 'H ' residue
32 Colour of DSSP determined '3' residue
33 Colour of DSSP determined 'S' residue
34 Colour of DSSP determined 'B' residue
35 Colour of DSSP determined 'T' residue
36 Colour of DSSP determined 'C' residue
37 UPLOW when creating DGEOM boundaries from real atoms
38 Lowest colour in colour ranges
39 Highest colour in colour ranges
40 Flag to tell MUTATE that 'self' mutations should be done
= 0 Dont self mutate
= 1 Do self mutate (mainly meant to add protons...)
41 Flag to determine how to grow in the BUILD menu
= 0 Default extension (roughly sheetish)
= 1 Use special angles (see below)
42 Phi-angle in case parameter 41 is set to 1
43 Psi-angle in case parameter 41 is set to 1
44 Omega-angle in case parameter 41 is set to 1.
In case of a N-terminal residue the phi-angle is applied
to the next residue. In case of a C-terminal residue, the
omega- and psi-angle are applied to the previous residue.
45 Salt bridge atomic distance *100.0 (5.0)
46 Debug flag for WALSER
= 0 No debug output
= 1 Some debug output
= 2 More debug output
47 Flag to determine whether only to prompt for the middle
residue or for the whole stretch in the SCAN3D contact
options SCNCON, SCNGRN, SCNGRL, etc.
= 0 Only prompt for the middle one of a stretch length five
= 1 Prompt for the whole stretch of predefined length
48 Internal parameter holding the group number for the group
presently being set. This parameter can not be set by the
user.
49 Error limit for DGCONT hits to accepted, default is 4.0 A.
50 Use default when asking for MOL-object
= 0 Use as default the first empty MOL-object
= 1 Don't use a default
51 Length of groups to search for
= 1 Search for single amino acids
= 2 Search for pairs of amino acids
...
52 100 * the maximal allowed error in Calpha position in
DGLOOP fitting.
53 100 * the allowed RMS error in the total fit in DGLOOP
fitting.
54 Number of hits by DGLOOP
55 Number of DGLOOP hits to be searched (default = 80).
56 100 * The Van der Waals radius overlap limit (Default = 0.25 A)
57 Default B-factor when no B-factor is present upon reading
Default value is 12
58 Warn for bad C-terminal residues
= 0 Yes, warn the normal way
= 1 No, work silently in the background
59 Allowed accessible surface for `buried` residue or atom
Default value is 2 squared Angstrom
60 Use only same set name in bump analysis
= 0 Use everything
= 1 Only look for bumps with residues that are in same set
61 Warn for big errors (e.g. > 10.0 sigma) in REFI.
= 0 Warn for these big errors
= 1 Suppress all REFI error warnings but the summary per step
= 2 Suppress all REFI error warnings
62 Did we pick something since last looking at this parameter
= 0 No, nothing got picked
<>0 Yes, something got picked
63 Number of the group in a movie under DOS. (See also 66).
64 Additional backbone fit flag in DG-replace options.
= 0 Do not perform the additional fit.
= 1 Perform additional fit on N, Ca, C.
= 2 Perform additional fit on N, Ca, C, O.
= 3 Perform additional fit on N, Ca, C, O, Cb (if present)
65 Maximal allowed difference between original and fitted
Ca position (thus after real 3D superposition) *100.0
66 Number of hits in movie group. (See also 63).
67 Should we return from WHATIF_LOOP
= 0 WHATIF_LOOP runs an infinite loop
= 1 WHATIF_LOOP executes RETURN after next/this command
68 Number of dots on the dots sphere (formerly IQB).
Do not modify: will be set by WIF083. Change WIFPAR(6)
instead.
69 Determines whether HEADER cards read from a PDB file
will be shown upon reading or not.
= 0 Do not show them (default).
= 1 Do show them.
70 Number of anchor amino acids at either end of an insertion
or deletion in the DG**** menu /options. Default=3.
71 Default color for lines drawn at the graphics
72 Mode for lines drawn at the graphics
= 0 Continuous lines
= N In N dashes (15=default)
73 Steps per 360 degrees in debumping. Default=3.
74 Do we use pull_down menus
= 0 Yes we do
= 1 No we dont
75 Skip first occurence of FULLST
= 0 Just execute FULLST normally
= n Skip FULLST n times before executing it
76 Number of sigma steps above which REFI gives output
77 Special flag for SCNGRN in the SCAN3D menu.
= 0 Write MOL-ITEMS always to the graphics
= 1 Do not write MOL-items to the graphics, but to a file
78 Use secondary structure in REFI or not?
= 0 Default. Do not use backbone forces for secondary structure.
= N Use N*default force towards LOCHST given secondary structure.
79 Mode for accessibility calculation
= 0 (Default) give contact surface
= 1 Give accessible surface
80 Type of gif file output
= 0 Mono pictures 512*512 pixels
= 1 Stereo pictures 1024*512 pixels for cross-eye
= 2 Stereo pictures 1024*512 pixels for parallel viewing
81 Minimal length of stretch in auto suppos (default=15)
82 Maximal individual error in auto suppos (default=100*5.0)
83 Maximal RMS error in auto suppos (default=100*3.0)
84 Do we use hydrogens?
= 0 No
= 1 Yes
85 Lowest residue of range that can be picked
86 Highest residue of range that can be picked
87 Write bad atoms in WIF508 or not?
= 0 Yes, write everything
= 1 No, skip ISATOK=FALSE atoms
88 Suppress output during sequence reading
= 0 Print everything
= 1 Suppress output during sequence reading
89 Where do we open WALIGN.BIG
= 0 In the local directory
= 1 On /usr/tmp/
90 TRA015 MUST use SYNC_OUT.PDB or not
= 0 No, prompt the user
= 1 Yes, use SYNC_IN.PDB
= 2 Yes, use SYNC_OUT.PDB
91 Background colour for fly files
= 0 Black
= 1 White
92 Sphere for PLUTO pictures (default=0.5(*100))
93 Thickness of PLUTO bonds (default=0.1(*100))
94 Number of lines in PLUTO bonds (default=20)
95 Square mode flag in diagonal plots
= 0 Square side length is function of number of atoms in residue
= 1 All square side lengths will be identical
96 Read symmetry information in GETDBF
< 0 Dont read it, dont prompt the user
= 0 Prompt the user
> 0 Dont prompt the user, but read it
97 MINIMAL NUMBER OF NON-HELICAL RESIDUES IN MOTIF FRAGMENTS
98 OUTPUT IN 3SSP OPTION TO LOGFILE OR UNIT 6
= 0 DO NOT PRODUCE OUTPUT
= 1 DO PRODUCE OUTPUT
99 Should MOL004 write the C-alpha 1 - i+3 torsion angles or not
= 0 No, don't; default
<>0 Yes write them as a REMARK card
100 Number of symmetry matrix for MAKMOL
101 Has a function in contact analysis
102 Colour of frame in contact analysis
103 colour of sequences written in contact analysis frame
104 Colour of neighbour residues in contact analysis
105 Should WIF508 (MAKMOL) write non polar protons? (For Flexx)
= 0 Just write what is in the soup
= 1 Skip non-polar protons in MAKMOL
106 FLAG FOR PUTTING CA-CROSSES IN RESIDUE SQUARES IN ANACON
= 0 DO NOT PUT OUT CA CROSSES (DEFAULT)
= 1 DO PUT OUT CA CROSSES
107 THREE LETTER CODE IN FRAME FLAG
= 0 USE ONE LETTER CODE (DEFAULT)
= 1 USE THREE LETTER CODE
108 Use protons or not in WIF507
109 USE ONLY TOP HALF OF PLOT FLAG
= 0 USE FULL PLOT (DEFAULT)
= 1 USE ONLY TOP HALF
110 COLOUR OF CA CROSSES IN RESIDUE SQUARES IN CONTACT ANALYSIS
111 Skip MOL200A in MOL101
= 0 Normally run MOL200A
= 1 Skip MOL200A to prevent infinite looping
112 ANCHOR FLAG IN REFINE
= 0 DO NOT ANCHOR THE ENDS OF A REFINEMENT STRETCH
= 1 ANCHOR THE ENDS OF A REFINEMENT STRETCH
113 Fix-force in REFI
114 Print Donor/Acceptor status in SHOIAA
= 0 No, don't
= 1 yes, do
115 Refine chain breaks after BLDPIR?
= 0 Dont close gaps (default)
= 1 Close gaps after modelling
116 Last picked point from second pick list
117 Use CAVITY (MAP006) interactively or not
= 0 Use defaults everywhere in MAP006
= 1 Use it interactively
118 Input status after WIFGRN (needed to separate erroneous
input from user input of 0 (zero).
= 0 Input was error free
= 1 Input contained an error
119 Cutoff for cavity in order to be called cavity
120 Only accept second picklist
= 0 Accept all picks
= 1 Accept only second picklist (and menus)
121 Use dashed bonds in graphics flag
= 0 Do not use dashed bonds
= 1 Use dashed bonds
122 Use double bonds in graphics flag
= 0 Do not use double bonds
= 1 Use double bonds
123 User kept one or more cavities in MAP006
= 0 Multiple cavities, so ask to select by picking
= 1 Only one cavity, so take just that one
124 Number of cycles in REFI
125 Number of iterations per cycle in REFI
126 Prompt for ranges in COLATV. ACCESS also uses this for the env!
= 0 Prompt for the ranges
<>0 Do NOT prompt for the ranges, but keep what we have
127 Old or new contour lines in Ramachandran plot?
= 0 New contour lines
= 1 Old contour lines
128 Size of GRACHI crosses (*100)
129 Colour of GRACHI crosses
130-131 Parameters reserved for the MAPEDIT module
130 In use
131 In use
132 Was TEXONE called from the TEXALL option in DOSELF
= 0 TEXONE was called from the menu
= 1 TEXONE was called from the TEXALL loop
133 Skip backbone in WIF041I or not
= 0 Look at backbone too
= 1 Skip backbone
134 Should MAKMOL write a 4 letter code in columns 73-76?
= 0 No, leave 73-76 empty
= 1 Yes, write 4 letter code inthere
135 Maximal acceptable length for a bond to be drawn (*100)
136 Atom moved in Bertje's menu
137 Select cavities or not
= 0 Ask user (depending on other flags)
= 1 Keep all cavities
138 Dirty hack for proton klonking
= 0 No dirty hack.
= 1 Tell klonk to dream up empty protons
139 Intended number of sequences per page in pretty plot
140 Intended number of amino acids per line in pretty plot
141 FAMTYP of residue requested in WIFGAA
= 0 Undetermined residue type, accept what user gives
= N Only accept residue types that have this FAMTYP
142 Special character for CHR001
143 Cutoff for reporting deviations in the INP* routines (*100)
144 Parameter to avoid recursion in REF_BOND_FIX_NOK
145 Bertje's MOVEAT X-coordinate*1000
146 Bertje's MOVEAT Y-coordinate*1000
147 Bertje's MOVEAT Z-coordinate*1000
148 Call HB2SPN between HB2INI and HB2NET in HBONDS
= 0 No, don't
= 1 Yes, do
149 100*scalefactor for characters
150 Number of equivalent residues required for pretty-boxing.
151 Lower residue of Bertje's range
152 Higher residue of Bertje's range
153 Have we ever been in bertje?
= 0 No, bertje was never executed
= 1 Yes, bertje has at least once been used
154 If not zero run MOL200 later 'again'
155 Plot file output type
= 0 Postscript
= 1 HPGL
= 2 Robjes stuff to directly write Xfig
= 3 Write FLY format (pre-GIF)
156 Range in SHAKE
157 Range in SHAKE
158 Force structure inversion in the REFI flip routine
= 0 Ask the user if coordinates need hand inversion
= 1 Invert the hand when needed. Dont ask anything.
159 Echo the results of REF_DIST in REFI
= 0 No, don't
<>0 Yes, do
160 Use sigma in CORMUT or not
= 0 Use sigma in CORMUT
= 1 Dont use sigma in CORMUT
161 Use X11clip or not
= 0 Yes, use it normally
= 1 No dont, we are in PAUSE or other guaranteed loop mode
162 Correct atom names in case many start with A, or B, or C, etc.
= 0 Yes, make these corrections
<>0 No, keep the wrong atom names.
163 Is JURSAV active
= 0 No, BCK coord space can freely be used
= 1 Yes, BCK coord space is in use by JURSAV
164 100*RMS Z-score on distances in REFI
165 100*RMS Z-score on angles in REFI
166 Are we adding protons?
= 0 No, we are not adding protons
<>0 Yes, we are adding protons
167 RMS Z-score on chiral volumes in REFI
168 Execute MOL200A (sometimes dangerous because of looping)
= 0 Normally execute MOL200A
= 1 Skip MOL200A when called
= 2 Execute GVSKIL if MOL200A is called
169 LOCK continuous coordinate updates
= 0 Background SOUP updates are allowed
= 1 Background SOUP updates are not allowed
170 Do an update round for < WIFPAR(171) sequences in walser
= 0 Dont do any profile updating
= 1 Do an UPDPRF round in WLS050 (GPCMA*) (default)
= 2 Do an UPAPRF round in WLS050 (GPCMA*)
171 Number of sequences below which 170 can activate UPAPRF
172 Get one range or multiple in HITRNG in SCN*
= 0 Get just one range
= 1 Get multiple ranges
173 Give output in FLUSHAHEAD or not
= 0 Yes, give normal output
<>0 No, skip printing unexecuted input
174 Make only FT and FTFT files in GPCMA*
= 0 GPCMA* does normally everything
<>0 GPCMA* skips everything after the FT and FTFT files
175 Should T54EQUAL fiddle around with O1 and O2?
= 0 Yes, equivalence permutations of terminal oxygens
<>0 No, stricktly equivalence the characters only
176 Percentage of hits in DEL3SP required for a residue to survive.
177 Build models in GPCMA* or not
= 0 Skip the models
= 1 Build the models
178 Did user (Bertje) use middle and right button at the same time
= 0 No he did not
= 1 Yes he did
179 BLOCK mode in XRAGMX
= 0 No Block mode
<>0 Distance relative to atom stored in WIFPAR(180) and WIFPAR(181) as ra
180 Atom relative to which forces are calculated for BLOCK in XRAGMX
181 Radius over which forces are calculated in BLOCK in XRAGMX
182 Lower residue of PLUTO range in XRAGMX
183 Lower residue of PLUTO range in XRAGMX
184 GOPULL works in debug mode
= 0 GOPULL works normal
= 1 GOPULL only reads the stationary file
185 Show ATTVAL or ATTVL2 in SHOIAA
= 0 ATTVAL
= 1 ATTVAL
= 2 ATTVL2
186 Number of atoms in GROMACS file in XRAGMX
187 Sort neighbours by distance in FCONATI (shortest first)
= 0 Don't sort
<>0 Yes, do sort
188 COLF is active in XRAGMX
= 0 Not active
= 1 Active
189 Escape flag for the infinite loop of GOPULL in XRAGMX
= 0 Keep looping
<>0 Terminate loop in next round
190 PARMAP is called from the screen in GOPULL
= 0 PARMAP is called normally
<>0 PARMAP is called by GOPULL in XRAGMX
191 MAKMOL should write CRYST from present default map
= 0 MAKMOL writes normally requested CRYST
= 1 MAKMOL writes MAPNOW header in CRYST line
192 What do we write in GOPULL continuous update
= 0 GRA1AA
= 1 GRA1CA
= 2 GRA1BB
= 3 GRA1AA + GRA1SS
193 In use
194 Print OXT-in-the-middle warning or not
= 0 Do not warn if an OXT is attached inside a chain
= 1 Do warn if an OXT is attached inside a chain
195 Proton nomenclature debug flag
= 0 Don't print any debug output
= 1 Print some proton nomenclature debug output
= 2 Print a lot of proton nomenclature debug output
196 Should standard rotamers be added in DGM003 or not?
= 0 Yes, add standard rotamers
<> 0 No, don't add standard rotamers
197 Should PRF004 print number of profiles left
= 0 Yes it should (default)
<>0 No it should not
198 Number of ALTATM 'errors' detected by GETMOL
199 LAST RESIDUE TO BE SHOWN IN status
200 Van der Waals radius of C
201 Van der Waals radius of N
202 Van der Waals radius of O
203 Van der Waals radius of S
204 Van der Waals radius of P
205 Van der Waals radius of I
206 Van der Waals radius of Z
207 Van der Waals radius of A
208 Van der Waals radius of Fe
209 Van der Waals radius of 1-6
210 Van der Waals radius of unknown atom type
211 Van der Waals radius of 'Water
212 Van der Waals radius of H, D, M, Q
213 Van der Waals radius of ...
214 Van der Waals radius of ...
215 Van der Waals radius of ...
216 Van der Waals radius of ...
217 Van der Waals radius of ...
218 Van der Waals radius of ...
219 Van der Waals radius of ...
220 EVATON parameter in XRAY menu
= 0 Do not write TABLE in EVA* options
<>0 Do write TABLE in EVA* options
221-231 Parameters reserved for the execution of program GRIN
232-250 Parameters reserved for the execution of program GRID
251 Weight on radial direction of residues in modelling
252 Free size around the map in Angstroms (=3)
253 Should FULCHK change coordinates
= 0 No, it shouldn't
= 1 Yes, flip Asn, Gln, His
= 2 Additionally, do REFI
= 3 Additionally, do CORALL
= 4 Additionally, move waters around
= 5 Additionally, remove 'strange' waters
254 Flag for automatic usage of MASMAP options
= 0 Prompt user for all input parameters
= 1 Take default or preset parameter for every input parameter
255 Remoteness value for MAS002 (Default=10)
256 Minimal value for map values upon scaling (=0)
257 Maximal value for map values upon scaling (=100)
258 Number of cycles in smoothing (MAS006)
259 Draw lines in WIF704 (DEBUMP) or not
= 0 Default. Do not draw lines.
= 1 Draw the lines that connect bumping atoms.
260 Print all vectors in GRAMOL
= 0 Dont print
= 1 Print them at the screen
261 We are calibrating map densities in EVACAL
262 Atom set to be used in MAKMOL output (default 1; range 1-4)
263 Spread in EMBED3
264 Refresh counter in IRI000
265 Colour of top identifier bar
266 Colour of top identifier text
267 Initial atom colours. (-1 means colour by atom type).
268 Colour of help text in pop up help boxes.
269 Status of input in drug understanding
= 0 Update all drugs with davadrug if needed
= 1 We are still reading things in, skip davadrug for now
270 ATOM-TO-USE FLAG FOR GRA1DB
= 0 DRAW ALL ATOMS FOR THIS DATABASE AMINO ACID.
= 1 DRAW ONLY THE SIDE CHAIN ATOMS FOR THIS DATABASE AMINO ACID
= 2 DRAW ONLY THE MAIN CHAIN ATOMS FOR THIS DATABASE AMINO ACID
= 3 DRAW ONLY THE TAGGED ATOMS FOR THIS DATABASE AMINO ACID
271 PART-OF-HIT TO SHOW FLAG FOR SCNGRN HITS
= 0 SHOW CENTER PLUS TWO NEIGBOURS
= 1 SHOW FULL HIT
= 2 SHOW CENTER PLUS BACKBONE OF FULL HIT
= 3 SHOW ONLY ATOMS TO BE USED FOR SUPPOS
= 4 SHOW ONLY SIDE CHAIN OF HIT
272 COLOUR DATABASE HIT FLAGS
= 0 USE UNIFORM COLOUR
= 1 USE INDIVIDUAL ATOMIC COLOURS
273 MAKE WHOLE RESIDUE OR JUST C-ALPHAS PICKABLE IN MOVIE
= 0 ONLY C-ALPHAS
= 1 WHOLE RESIDUES
274 100*Resolution cutoff in SFCALC (default=2.0)
275 Number of residue most recently popped
Remember (KILed residues are NOT stored in 275)
276 NUMBER OF ENTRIES FOUND IN THE TOPOLOGY FILE
277 SKIP DNA/RNA UPON READING PDB FILE
= 0 DO NOT SKIP DNA/RNA
= 1 SKIP DNA/RNA
278 USE ORIGINAL OR WHAT IF HST DETERMINATIONS
= 0 CONVERT DSSP HST DETERMINATIONS INTO WHAT IF NOMENCLATURE
= 1 MAINTAIN THE ORIGINAL DSSP NOMENCLATURE
279 Are we in PDB-CHECK modus?
=-1 We want no check output whatsoever
= 0 NO, we are in normal modus
= 1 YES we are in check modus
280 - 289 PARAMETERS RESERVED FOR QUALITY BOXES
280 LEVEL OF OUTPUT FLAG IN QUALITY CONTROL
= 0 ONLY SHOW INFORMATION AT A RESIDUE LEVEL
= 1 SHOW INFORMATION ABOUT RESIDUE AND ATOM LEVEL
= 2 SHOW INFORMATION AT DEBUG LEVEL
281 This flag tells MOL200 that we are in USEDD (against recursion)
= 0 Default, MOL200 should call USEDD1
<> We are in USEDD1, so MOL200 should not call USEDD1 again.
282 Should MAKMOL write GROMACS atom names
= 0 Write SOUP names
<>0 Write GROMACS names
283 VAN DER WAALS RADIUS OF ATOM UPON CONVOLUTING ATOMIC SPACE
WITH QUALITY CONTROL BOX. DEFAULT=1.8 (*100.0)
284 FLAG TO SKIP BACKBONE OF NEIGBOUR RESIDUES
= 0 DON'T SKIP ANY ATOM AT ALL.
= 1 SKIP MAIN CHAIN ATOMS OF COVALENT NEIGHBOUR RESIDUES
285 FLAG TO DETERMINE CONTACT VALUATION MODE
= 0 USE WHOLE NEIGHBOUR IN CASE OF CONTACT
= 1 USE ONLY CONTACTING ATOM
286 FLAG TO DETERMINE IF CB WILL BE SHOWN IN BB OPTION
= 0 DO SHOW CB (IF NOT GLY)
= 1 DO NOT SHOW CB
287 Ask for all atoms or explicitly one atom in WIFGAT
= 0 ALL, SIDE, ETC., is valid input too
<>0 Only one real atom name can be given
288 Mode of ALTATM resolving
= 0 Just take the lowest altatm indicator.
= 1 Take the highest occupancy, resolve with altatm indicator
= 2 Take the highest occupancy, resolve with B-factor
289 Use scaling in FLY
= 0 Yes, scale vectors in FLY
<>0 No, use previous scale in FLY
290 Molecule number of water group we are presently working with
291 Skip flag for residues in SSP007 - SSP009
= 0 Skip nothing
<>0 Skip all residues with PRPVAL equal to WIFPAR(291)
292 Print messages in WIF004
= 0 Yes, print what should be printed
<>0 No, print nothing is WIF004
293 Correlation normalization flag
= 0 Old-fashioned, do NOT normalize
= 1 Normalize correlations against a random score
294 Value of WIFPAR(276) directly after reading topology file
295 Colour of dots in ellips drawing options
296 Maximal allowed number of lines to be read from a PDB file
= 0 Skip nothing
<>1 Skip the whole file if it holds more than WIFPAR(296) lines
297 Give error message when MODEL 0 is encountered
= 0 Yes, give error message upon MODEL 0
= 1 No, accept MODEL 0 (mainly for wheatsheaf)
298 FLAG FOR WRITING ACCESSIBILITIES IN PDB FILE OR NOT
= 0 DO NOT WRITE ACCESSIBILITIES
= 1 DO WRITE ACCESSIBILITIES
299 NOCC read from profile in HSSP file
300 - 370 RESERVED FOR GROMOS AND PRE-GROMOS.
300 LEVEL OF USAGE FLAG.
= 0 CREATE INPUT/JOB FILES, DO NOT EDIT THEM, RUN JOB
= 1 CREATE INPUT/JOB FILES, EDIT INPUT, RUN JOB (DEFAULT)
= 2 CREATE INPUT/JOB FILES, EDIT INPUT/JOB, RUN JOB.
301 100*Minimal required structure factor intensity (default 0.01)
302 WATER FLAG
= 0 RUN IN VACUUM
= 1 USE CRYSTAL WATERS IF AVAILABLE (DEFAULT)
= 2 RUN IN WATER BOX RECTANGULAR
= 3 RUN IN WATER BOX MONOCLINIC
= 4 RUN IN WATER BOX OCTAHEDRAL
303 100*sigma of map as contour level(s)
304 Map-width in MENIRI8
305 Map-origin in X in MENIRI8
306 Map-origin in Y in MENIRI8
307 Map-origin in Z in MENIRI8
308 Overruling for special object 1 (917)
= 0 Whatever the rest of WHAT IF thinks
<>0 Off, no matter what the rest of WHAT IF thinks
309 Overruling for special object 2 (918)
= 0 Whatever the rest of WHAT IF thinks
<>0 Off, no matter what the rest of WHAT IF thinks
310 Overruling for special object 3 (919)
= 0 Whatever the rest of WHAT IF thinks
<>0 Off, no matter what the rest of WHAT IF thinks
311 NUMBER OF ENERGY MINIMIZATION STEPS
312 Overruling for special object 4 (920)
= 0 Whatever the rest of WHAT IF thinks
<>0 Off, no matter what the rest of WHAT IF thinks
313 Factor on cutoff for SPC map 1 (*100)
314 Factor on cutoff for SPC map 2 (*100)
315 Factor on cutoff for SPC map 3 (*100)
316 Factor on cutoff for SPC map 4 (*100)
317 Step-factor in map-contouring
318 Are we calling PDBOUT from checking or PDBSCO
= 0 Normal, we call PDBOUT from checking
<>0 We call PDBOUT, by accident, from PDBSCO
319 TEMPERATURE DURING MD RUN IN DEGREES KELVIN
320 Keep waters in a GROMACS trajectory or not
= 0 No, do not write (bulk) waters in trajectory file
= 1 Yes, I like my disk very full, so write all waters
321 FIX BY B-FACTOR FLAG (FIXMAN)
= 0 B-FACTORS ARE MEANINGLESS FOR GROMACS
= 1 B-FACTORS RELATE TO THE DAMPING FORCE
322 NUMBER OF X PICOSECONDS IN A MD RUN
323 SHOULS GROMACS BE VERBOSE OR NOT
= 0 GROMACS SHOULD NOT BE VERBOSE
= 1 GROMACS SHOULD BE VERBOSE
324 ADDITIONAL BOND-CHECK IN GRA1AA, ETC.
= 0 DON'T CHECK BOND DISTANCES
= 1 DO CHECK ADDITIONAL BOND DISTANCES
325 TRA-routines are being called from CONCRD or not
= 0 TRA-routines are used normally
<>0 TRA-routines are being called from CONCRD
326 Use C-alphas only or all atoms in trajectory options
= 0 Use all atoms
<>0 Use C-alphas only
327 FLAG FOR FASTMD
= 0 ALL SUBROUTINES WORK NORMAL
= 1 ALL SUBROUTINES WORK FAST, NO QUESTIONS ARE ASKED
328 Use waters or not in trajectory related options
= 0 Don't use waters in trajectory related options
<>0 Use waters in trajectory related option
329 Alternate atom KLONK Debug flag
330 Background colour in WALSER pages
= 0 White
= 1 CMS-yellow
331 FIX ALPHA CARBONS FLAG (FIXCAS)
= 0 DO NOT FIX ALPHA CARBONS IN EM AND MD
<>0 DO FIX ALPHA CARBONS IN EM AND MD
332 Let SOUPNT point at the present # N (for USEDD*)
= 0 Do nothing (default)
<>0 Use highest present SETNAME upon reading drugs in davabug
333 Default value for next GVSFFI operatie
334 Do ALTATM checks or not
= 0 Yes, treat ALTATMs normally and check them
= 1 No, skip the whole ALTATM thing
335 SELECT FLAG FOR WEDTRA
= 0 USE ALL ATOMS
= 1 USE CA ONLY
= 2 USE CA + GEOMETRICAL CENTER OF SIDE CHAIN
= 3 USE CA + TERMINAL ATOM OF SIDE CHAIN
= 4 DIHEDRAL SPACE
336 PRINT FLAG IN ESSENTIAL DYNAMICS/WAD*
= 0 DON'T PRINT PLOTS
= 1 PRINT PLOTS
337 Should TRA011 open a new file or assume IUNIT to be the file
= 0 Open a new GROMACS-PDB file at IUNIT
<>0 Assume that the GROMACS-PDB file is already open on IUNIT
338 Use DNA in GPC* options
= 0 Yes, generate the cDNA entries
= 1 No, skip the cDNA stuf
= 2 Use pre-existing cDNA files only
339 Offset in TRA015 for syncing soup against GROMACS files
= 0 Default, don't use an offset
<>0 Add this number to INDEXG in TRA015
340 WRITE TRAJECTORIES TO A FILE OR NOT FLAG
= 0 DO NOT WRITE TRAJECTORIES
= 1 DO WRITE OUT TRAJECTORIES
341 NUMBER OF STEPS AFTER WHICH A TRAJECTORY IS WRITTEN
342 Should missed atoms be disabled in trajectory syncing?
= 0 Yes do.
<>0 No, do not.
343 Should PRP123 read the file if it exists locally as a .brk file?
= 0 Yes, PRP123 just reads everything
<>0 No, PRP123 skips files that exist as a local .brk copy
344 Number of residues with wrong chirality anywhere
345 PRODRUG verbosity flag
= 0 Minimal verbosity
> 1 Higher number, more verbosity
346 Maximal number of atoms allowed in PRODRUG
347 Should SCN502B give output or not
= 0 Yes, SCN502B gives all possible output
<>0 No, SCN502B doesn't print anything
348 Maximal number of drugs to be read from a MOL2 file
= 0 Read everything
= N read the first N only
349 Dirty hack in case MEN*** comes from a BUTTONSCRIPT
= 0 Do nothing
<>0 Set MENIRI at this value next time around
350 Use full map of cavities in Space in DB Drug flipping
= 0 Use cavities
<>0 Use full density
351 Type of charge to be read from PCHARGE.FIL
Allowed values are 1 - 4. The default is 4
352 Force field type in GROMACS run
=-1 We are not doing any GROMACS stuff
= 0 GROMACS GMX force field
= 1 OPLS force field (Default)
353 Do we want to skip mis-docked entries upon reading MOL2 files
= 0 No, read everything
<>0 Yes skip entries too far from a certain point
354 Display crosses for centres of gravity of ligands read from MOL2 file
= 0 Don't display
<>0 Yes, do display centres of gravity
355 GRID STEPS IN ANAVOL OPTION (DEFAULT=50)
356 GRID SPACING IN ANAVOL OPTION (*100) (DEFAULT=.25)
357 100 * X coordinate of center of molecule
358 100 * Y coordinate of center of molecule
359 100 * Z coordinate of center of molecule
360 Drug number in USEDD3
361 Number of last MW atom in TIP4 water in TRA015
362 IUNIT in SOG150
363 Output reducer flag for SOG menu
= 0 Don't reduce output
<>0 Reduce a series of outputs throughout WHAT IF
364 Overrule SOUPRESET
= 0 Don't
<>0 Do
365 Scaringly hard reduction to reading only one MODEL from NMR files
<=0 Read all, or let other parameters do the work
> 0 Read only till the first ENDMDL
366 MAKMOL is called from DSSP or not
= 0 MAKMOL is not called from DSSP, everything is normal
= 1 MAKMOL is called from DSSP
367 Should DMATCH do precise alignment?
= 0 Yes, do the precise alignment
<>0 No, assume the approximation is good enough
368 Predefined number of models to be read from an NMR file
=-1 Prompt the user what he/she wants (reading N models)
= 0 This is not possible with NMR structure
= 1 Read only the first model
= N Read N models
= 999 Read as many MODELs as possible
369 Automatically protect against soup-overloads
= 0 Prompt the user (default)
<>0 Simply avoid soup overloading at all cost
370 Number to be added to PDB file in MAKMOL in LSCRIP
371 Gap open penalty in walign
372 Gap elongation penalty in walign
373 Gap open penalty in aliprf
374 Gap elongation penalty in aliprf
375 Are we wheatsheafing or not?
= 0 We are not working with wheatsheaf
<>0 Yes, we are working with wheatsheaf
376 Should ITM007 (get item name) make a suggestion
= 0 Yes, ITM007 should suggest a MOL-item name
= 1 No, ITM007 should not suggest a MOL-item name
377 Skip MOL100 in MOL015
= 0 Normally execute MOL100 in MOL015
<>0 Skip MOL100 in MOL015
378 Debug flag for printing all menu commands in IRIMAINMENU
379 Number to be used in computed REMARK in PDB file output
380 100*Weight on backbone fit in homology building. RCONFI(1)
381 100*Weight on rotamer density in homology building RCONFI(2)
382 100*Weight on quality control in homology building RCONFI(3)
383 100*Weight on bumps in homology building RCONFI(4)
384 Skip HB2RED when called or not
= 0 Normally execute HB2RED
<>0 Skip HB2RED when called
385 H-bond MC cutoff RCONFI(6)
386 Number of round in EMBED3
387 Initial slab value RCONFI(9)
388 100*Weight on hydrogen bonds in homology building RCONFI(12)
389 Colour map contour lines by atom type
= 0 Colour them as indicated by PARMAP
= 1 Colour them as function of atom type
390 Are we running the tutorial?
= 0 No, we are not
= 1 Yes we are
391 Use the own set or more in contact determinations
= 0 Use everything
= 1 Only use the own set
392 GVFYON returns TRUE upon wrong input if script is active
= 0 No, script just eats up script file waiting for correct answer
<>0 Yes, GVFYON returns TRUE (most likely to GVSKIL) upon wrong input
393 Warn for A<>B already at 0.001 A instead of 0.1 A
= 0 Cell A and B may differ up to 0.1
<>0 Cell A and B may not differ at all
394 ITYPE of last read sequence
395 Dont paste in WIF004 (for GETDBF).
= 0 Paste everything
= 1 Dont paste everything.
396 First atom of chiral torsion angle quartet
397 Second atom of chiral torsion angle quartet
398 Third atom of chiral torsion angle quartet
399 Fourth atom of chiral torsion angle quartet
400 Output unit for BIGGET in OTHER
401 Distance cutoff in NETWAT option
402 Recursion flag for MOL200
403 FLAG FOR WATER USAGE IN SCREEN MENU ITEM NAYB
= 0 SHOW CONTACTS FROM RESIDUES TO NEIGHBOUR RESIDUES AND WATERS
AND FROM PICKED WATERS TO RESIDUES AND ENVIRONMENT WATERS
= 1 SHOW ONLY RESIDUE-RESIDUE CONTACTS
= 2 SHOW ONLY WATER WATER CONTACTS
404 Make new water group after water subset determinations?
= 0 Only list results, dont make group.
= 1 List results, and make new group out of listed waters.
405 Reject all output flag
= 0 Normally print all output
= 1 Reject (skip) output
406 Lower residue of flexible range in SHARNG
407 Upper residue of flexible range in SHARNG
408 Lower value in B-factor plot (GRA512) (if not zero)
409 Higher value in B-factor plot (GRA512) (if not zero)
410 FIXFRC for GROMACS FIX... options
= 0 No restraining (default)
= 1 Low restraining
= 2 Medium
= 3 High
411 Used in MASMAP as loop counter
412 DIFFERENCE IN SPIKER OPTION (MAS018)
413 ATTENUATION IN SPIKER OPTION (MAS018)
414 TRUNCATION LEVEL AND NEW VALUE IN FLATEN OPTION (MAS013)
415 Must be in output of HB2LIS
= 0 Default, neglect this parameter
416 HB2LIS only prints sidechain H-bonds of amino acid in 415
= 0 Default. print everything
<>0 Print only H-bonds with sidechain of residue in 415
417 Second colour of hits in 3SP display options
418 Colour of hits in 3SP display options, in case of monochrome
419 Colour mode for graphics hits in 3SP display options
420 Mode of display in SHO3SP
= 1 As movie
= 2 In one MOL-item
421 SEQUENCE OR PACKING FLAG
= 0 USE ALL RESIDUES IN SUPPOS REFINEMENT LOOPING
> 0 USE ONLY STRETCHES OF THE INDICATED LENGTH
422 SUPPOS CALLED FROM SPCIAL MENU FLAG
= 0 DEFAULT. SUPPOS IS USED NORMALLY
= 1 SUPPOS IS CALLED FROM SPCIAL TO MAKE 3SSP FILES
423 Used
424 Skip helices or not in MOTIF
425 Allow Angstroms extra for Met SD and Gly C=O in FCONRED
= 0 Dont
<>0 100 times the extra allowed distance
426 Do H-bond calculations in ions options or not
= 0 Yes, each time work out the whole network
<>0 No, skip the time-consuming H-bond stuff in ions-related options
427 Do Water-addition in ion options
= 0 No, don't
<>0 yes, do
428 Kill incomplete N-termini
= 0 No, just keep them
<>0 Yes, kill incomplete N-termini
429 Skip date writing in log-file for testsuite
= 0 Write date and time in log-file
<>0 Skip date and time writing in logfile
430 Old or new format in checkdb
= 0 Default. New format.
<>1 Old format.
431 Lower residue of horizontal contact range
432 Higher residue of horizontal contact range
433 Lower residue of vertical contact range
434 Higher residue of vertical contact range
435 PAUL flag in PDBCHECK
436 How to write the _ for missing data in DIFOUT
= 0 Just write _
= 1 Write $_
= 2 Write a blank
437 Should CDB013 write a TCH header?
= 0 Yes, write the ?H_* header
<>0 No, skip PDBTCH in CDB013
438 Include NMR files in the internal database
= 0 No. Default. Warn user when NMR files are detected.
<>0 Yes. Accept NMR files. Just take first from ensemble.
439 Use SYM=1 in CONTAC
= 0 (Default). Yes, also list contacts in the same molecule
<>0 Skip contacts for SYM=1
440 Bins in GHS027 (histog.f line-printer histogrammen) (Default=21)
441 Number of SDs to be tabulated in GHS027/GHS003 (default=5)
442 Superfluous water counter
443 Flipped residue count
444 HIDE01 in SEQ3D calls PDBSCO with ALL or LIM
= 0 Call with parameter ALL
= 1 Call with parameter LIM
445 'Previous value' for WIFPAR(6) when calculating dot-density
446 100*Z-score for latest checked ion
447 Run statistics or use statistics in ions options
= 0 Use statistics
<>0 Generate statistics
448 FOR3DM flag
= 0 Default, we are working normally
= 1 Switch on and of a series of options for the 3DM project
449 Are we doing IONS STEP-* or 'normal options'
= 0 Normal options
= 1 STEP-2 to gather statistics
450 We are doing things for ROBIE7 (i.e. dead-end structure improver)
= 0 No, everything is normal
<>0 Yes, we are running ROBIE7
451 Unit number for ROBIE7 output file
= 0 We don't write anything (not ROBIE7 execution)
<>0 This is the unit number
452 Output unit where some header records should be written upon GETMOL
= 0 Don't write any header record on any extra unit
<>0 Write the essential PDB header cards on this unit
453 Debug communication between tlssup and packing quality
454 100*Worst allowed resolution
= 0 Don't use this facility
455 Symmetry contacts with ion gained by applying symmetry
456 Explain ion-surroundings or not?
= 0 No
= 1 Yes, explain for every surrounding why it was (not) selected
457 Skip non-oxygens in ion calculations
= 0 Don't skip anything
= 1 Skip all but oxygens in ion-calculations
458 Tollerance in inter-ligand angles in ion menu (default=20 degree)
459 Top atom of bi-pyramid ion ligand packing
460 Bottom atom of bi-pyramid ion ligand packing
461 USE OWN MOLECULE IN ACCESSIBILITY CALCULATIONS OR NOT
= 0 DO USE THEM
= 1 DO NOT USE THEM
462 Counter for listing overlapping atoms in different residues
463 Maximal number of PDB files to evaluate in IONS menu
= 0 Take all of them
<>0 This is the maximal number
464 Print REMARK 280 or not
= 0 Don't
<>0 Write on unit with as number this parameter
465 Use 6-coordination normalizer or not
= 0 Don't use it, use only raw Vion scores
<>0 Use the Vion normalizer to normalize Vion scores for six ligands
466 EXPDTA last read: 0=X-ray; 1=CRYO-EM; 2=FIBER; 3=NEUTRON; 4=NMR;
5=NMR-AVERAGED; 9=OTHER;
= 0 Last PDB file read was X-ray
<>0 Last PDB file read was not X-ray
467 ION-related options tend to use symmetry. This flag can overrule.
= 1 Normally use symmetry in ION options
= 0 Don't use symmetry in ION options
468 Independent of any SYM flag, determine what is used by STEP-* in IONS
= 0 Use only intra molecular ion surroundings
= 1 Use intra and inter molecular ion surroundings
= 2 Use only symmetry completed ion surroundings
469 UNIT for intra-ion-menu communication
470 STEP-* of GR*ION calls the ion-tree?
= 0 STEP-* calls ION002 - ION109 (store stats)
= 1 GR*ION calls ION002 - ION109 (use stats)
471 Do we have a statistics file for this (latest) IONTYP
= 0 Yes we have
= 1 No we don't
472 Normally MOVWAT etc look around for 30 A for better positions
This parameter can overrule that. Don't overdo it, there are
no overflow protections left after this PANIC parameter was issued.
473 Skip eps-plot generatie in FULCHK etc
474 100* VION score that ion is allowed worse than second best in step-*
= 0 Don't use this option
<>0 Value is 100* allowed VION inferiority
475 Suppress SHOWIF
= 0 Don't; normally run SHOWIF
<>0 Suppress SHOWIF
476 Reduce MOL200 functionality.
= 0 Run the whole MOL200
<>0 Run a reduced MOL200 (no IRI000, no MOL200A)
477 Z-score statistics in ION* (*100)
478 Counter in ION007
479 MODEL/ENDMDL records found at last GETMOL
= 0 No, none were found
<>0 Yes, at least one of those was found at least once
480 Number of ions for which Vion can be done
481 MAXIMAL ALLOWED DONOR ACCEPTOR DISTANCE (3.5A) *100
482 NUMTYP overruling value in ION parameter setting
= 0 Use whatever ion data is available
<> Use only information for this number of ions
483 Level of detail in GROMACS debug output
484 MAXIMAL HYDROGEN ACCEPTOR DISTANCE (2.5A) *100
485 MAXIMAL ANGULAR ERROR OVER HYDROGEN (60)
486 MAXIMAL ANGULAR ERROR OVER ACCEPTOR (90)
487 H-BOND GRAPHICS FLAG
= 0 ERROR
= 1 SHOW HBONDS AT TERMINAL, BUT NOT AT PS300
= 2 SHOW HBONDS AS DONOR ACCEPTOR DOTTED LINES
= 3 SHOW HYDROGENS AND HBONDS
488 HBONDS debug flag
489 How many MODEL cards were encountered
490 Write punch-card numbers as 1, 2, 3, etc or as in input
= 0 Write them serially
<>0 Write them as read in
491 Present SOUNAM pointer
492 Suppress printing when working with web-services
= 0 Write everything just fine
<>0 Suppress output in web-services
494 FREE
495 FREE
496 FREE
497 FREE
498 FREE
499 FREE
500-520 Parameters for the NEURAL network module
501 NUMBER OF INPUT NODES (DEFAULT=3)
502 WIDTH OF THE HIDDEN LAYERS (DEFAULT=5)
503 NUMBER OF HIDDEN LAYERS (DEFAULT=3)
504 SOFT LIMIT FOR NEURON VALUES (DEFAULT=2)
505 HARD LIMIT FOR NEURON VALUES (DEFAULT=5)
506 MAXIMAL STEP SIZE*100 (DEFAULT=100*2.0)
507 WRITE TEACHING SET ECHO IN NEURAL TRAINING(1) OR NOT(0)
508 NUMBER OF PRESENT NEURAL NETWORK SAVE FILE
524 GROUP NUMBER FOR OPTIONS THAT USE GROUPS WITHOUT USER IO
525 SAVe-file number for SAVSOU and RESSOU options
526 SAVe-file number for SAVSHA and RESSHA options
531 LINE WIDTH FOR GRAPHICS
532 FLAG TO TELL WIF425 ETC. THAT WE HAVE A CA-ONLY RESIDUE
535 ENTRY POINT IN ADD MENU OF PERSONAL MENU
536 OBJECT NUMBER TO OVERRULE GRAMOLS QUESTIONS
537 NUMBER OF LAST CREATED OBJECT
538 DEBUG FLAG TO TRACE CENTERING PROBLEMS
539 HELIX TYPE FLAG IN DAVID THOMAS' RIBBON OPTION
= 0 DEFAULT HELICAL CYLINDERS
= 1 SPIRAL HELICES
540 NUMBER OF THREADS PER HALF ARROW (DEFAULT=5)
541 HELICAL CURVE WEIGHT (1.0=1000)
542 HELICAL SLOPE WEIGHT (0)
543 STRAND CURVE WEIGHT (1.0=1000)
544 STRAND SLOPE WEIGHT (0)
545 LOOP CURVE WEIGHT (0.001=1)
546 LOOP SLOPE WEIGHT (0.001=1)
547 LOOPS AS SPLINE OR CA-TRACE
= 0 SPLINE
= 1 CA-TRACE
548 CYLINDERS BLUNT OR ARROWED
= 0 BLUNT
= 1 ARROW HEADED
549 Should we read the Chebyshev parameters?
= 0 Yes, read them
<>0 No, forget about them this round
550 MULTIPLICATIVE FACTOR ON STRAND WIDTH (*100.0)
551 NUMBER OF THREADS IN A SPIRAL HELIX (DEF=2*3+1)
552 SCALEFACTOR FOR POSTSCRIPT OUTPUT
553 X-BIAS FOR POSTSCRIPT OUTPUT
554 Y-BIAS FOR POSTSCRIPT OUTPUT
555 Degree of OLGA interactivity in the GROMACS menu
= 0 Default. Run everything, show all scripts interactively.
= 1 Run everything, but don't show the OLGA scripts to the user.
556 USE ACCESSIBILITY IN DGLOOP FLAG
= 0 DEFAULT, DO NOT USE ACCESSIBILITY.
= 1 USE ACCESSIBILITY.
557 Lower limit of accessibility in DGLOOP (0)
558 Upper limit of accessibility in DGLOOP (1000)
559 FREE
560 CONTINUOUS SHOSOU FLAG
= 0 OPTION DE-ACTIVATED
= 1 DO NOT UPDATE IN IRI000
= 2 NEXT PASS THROUGH IRI000, UPDATE CONTINUOUS SHOSOU
561 INTEGRATED QUALITY CONTROL SCORE OVER RANGE
562 USE WIFGRN IN QUA028 FLAG
= 0 DO NOT LOOK AT WIFGRN IN QUA028
= 1 ONLY USE RESIDUES FOR WHICH WIFGRN=.TRUE. IN QUA028
564 NUMBER OF RELAX STEPS ALLOWED IN DGLOOP OPTIONS
565 AUTOMATIC MODE IN WALIGN (OPTION HIDE08) FLAG
= 0 WE ARE IN MANUAL MODE
= 1 WE ARE IN AUTOMATIC MODE
566 FILLED PLOT MODE IN STRAND OPTION
< 0 We are using the ribbon thing in a movie
= 0 WE ARE IN NORMAL MODE
= 1 WE ARE IN FILLED PST MODE
567 Distance between solute and edge of box in GROMACS run
568 Number of NAYB residue
569 RESTRICTED ROTATION FLAG
= 0 WE ARE IN NORMAL MODE
= 1 ROTATE AROUND X ONLY
= 2 ROTATE AROUND Y ONLY
570 NUMBER OF COMPLICATED FOLLOW ME SPHERE CENTRAL RESIDUE
571 Backup of 570 in case SPHR is toggled off
572-576 Toggle switches for continuous update tables at screen
577 Number of sequences for which there is a CMCODE
578 Number of NAYB atom
579 Debug output in COR*** data preparation (WAL020)
= 0 Dont print anything
<>0 Print the contents of all tables and arrays in WAL020
580 Are we calling MOL002 from MAKDB?
= 0 No we are calling it the 'normal' way
<>0 Yes we are calling it from MAKDB
581-584 PHI/PSI of IAA-1/IAA+1 for DGLOOP purposes
585 IAA on which DGLOOP works at the moment
586 TOO_MANY calls GVSKIL or not
= 0 Don't call GVSKIL
<>0 Call GVSKILL upon overflow
587 DO WE USE THE RUBBER BANDING OPTION
= 0 NO WE DO NOT USE RUBBERS
= 1 YES WE ARE USING RUBBERS
588 FIRST RESIDUE IN RUBBER BANDING MOLECULE
589 LAST RESIDUE IN RUBBER BANDING MOLECULE
590 - 600 RESERVED FOR ROB HOOFT
590 "USESYM": 1 = Use symmetry in options that can use it
591 "PCKSYM": 1 = Pick symmetry related atoms
592 "LCKSYM": 1 = Lock symmetry matrices. no changes allowed
593 Default maximum number of lines in a PDBOUT table pdbout
594 Are we multiplying H-bond potentials with a B-factor comp?
= 0 NO WE ARE NOT
= 1 YES WE ARE
595 Are we ignoring hydrogen bonds between water molecules?
= 0 NO WE ARE NOT
= 1 YES WE ARE
596 The number of HB2MCX runs to perform for an optimization
597 Should there be any terminal output
=0 Normal, yes
=1 Suppress everything in GVSTO6 and GVSTT6
598 Which water molecules count in NQA?
=0 All waters.
=50 Ignore water atoms with population below 0.50 [DEFAULT]
=1000 Ignore water atoms completely.
599 Are we running a check over the database?
This is to notify subroutines that stupid poly-UNK proteins
should be skipped
= 0 NO
= 1 YES
601 ARE WE RUNNING DGINS AT THE MOMENT
= 0 NO WE ARE NOT
= 1 YES WE ARE
602 ARE WE USING HBONDS IN DEBUMP AT THE MOMENT
= 0 NO WE ARE NOT
= 1 YES WE ARE
603 Are we skipping bumps in DGLOOP
= 0 No we are not (default)
= 1 Yes we are
604 Number of the residue being DGLOOP-ed
605 Trajectory in Angstroms or in nanometers
= 0 Nanometers
= 1 Angstroms
606 Debump against the full soup
= 0 No we are not
= 1 Yes we are
607 DO WE WANT IMPORTANCE UPDATES DURING MODELING
= 0 NO WE DO NOT
= 1 YES WE DO
608 DO WE WANT TO ALWAYS MODEL LYS/MET DURING MODELING
= 0 NO WE DO NOT
= 1 YES WE DO
609 Do we want to suppress output during modeling
= 0 NO WE DO NOT
= 1 YES WE DO
610 Should TAB016 ask the user, or use preset values for TABLES input
= 0 TAB016 will prompt user
<>0 TAB016 will use table and range from PARAMS
611 IFT1 in case TAB016 uses PARAMS
612 IFT2 in case TAB016 uses PARAMS
613 TABLE type in case TAB016 uses PARAMS
614 NUMBER OF MOL-OBJECT 1 FOR TOGGLING
615 NUMBER OF MOL-OBJECT 2 FOR TOGGLING
616 NUMBER OF STEPS DONE FOR TOGGLING
617 NUMBER OF STEPS PER STEP FOR TOGGLING
618 USE BENT HELICES IN SPLINE OPTION
= 0 YES WE DO (DEFAULT)
= 1 NO WE DO NOT
619 Colour of pick label (0 means use default)
620 NUMBER OF VECTORS IN MOVING MOL-ITEM
621 CRIPPLE mode for tutorials
= 0 No we are not cripple
= 1 Yes we are cripple
622 Delete overlapping residues upon reading coordinate files
= 0 Yes, automatically
= 1 Yes/No, but after a question
= 2 No, hands off, keep them
= 3 Keep them, but flag them to avoid too many bound_to's
623 Number of residue presently being HAND-checked
624 SHOULD NOMENCLATURE ERRORS BE WRITTEN IN CHECK SUMMARY
= 0 NO
= 1 YES
630 How to measure distance in WIF689B
= 0 Normal distance (default)
= 1 Distance in X direction only
= 2 Distance in Y direction only
= 3 Distance in Z direction only
631 Colour of toptxt (right top of screen messages).
632 Shift (in pixels) of default X coords of text window.
633 Shift (in pixels) of default Y coords of text window
634 Colour of bottom of screen button text
635 ZFUNCT parameter (operating system dependent)
636 Degrees error in phi and psi allowed in DG* options
637 Colour of the text in the status box
638 Maximal length of groups to be used in DGLOOP options
639 NMBLFT in PHYTRE for WALSER
640 Atom presently being bump-checked in DGLOOP
641 Atom that bumped with 640
642 Skip residue output in MOL003
= 0 List all residues in the GETMOL option
<>0 Suppress the output of residues in the GETMOL option
643 Skip or use inter-chain contacts in FCONATI
= 0 Use inter-chain contacts
<>0 Skip inter-chain contacts
644 Counts number of BOUND_TOs per molecule in MOL004A
645 Maximally allowed number of BOUND_TOs in MOL004A
646
647
648
649
650
651 Atom stack for the XRAGMX menu
652 Atom stack for the XRAGMX menu
653 Atom stack for the XRAGMX menu
654 Atom stack for the XRAGMX menu
655 Atom stack for the XRAGMX menu
656 Atom stack for the XRAGMX menu
657 Atom stack for the XRAGMX menu
658 Atom stack for the XRAGMX menu
659 Atom stack for the XRAGMX menu
660 Atom stack for the XRAGMX menu
661 Atom stack for the XRAGMX menu
662 Atom stack for the XRAGMX menu
663 Atom stack for the XRAGMX menu
664 Atom stack for the XRAGMX menu
665 Atom stack for the XRAGMX menu
666 Atom stack for the XRAGMX menu
667 Atom stack for the XRAGMX menu
668 Atom stack for the XRAGMX menu
669 Atom stack for the XRAGMX menu
670 Atom stack for the XRAGMX menu
701 SIMPLE MODE FLAG FOR QUICK LOOKING
= 0 NO WE DO NOT
= 1 YES WE DO
702 SIMPLE MODE SPACE FLAG
= 0 YES THERE WERE EMPTY OBJECT(S)
= 1 NO THERE WERE NO EMPTY OBJECT(S)
704 NUMBER OF TIMES WIF104 SHOULD SKIP OUTPUT
705 DID OPTION PRODUCE OUTPUT?
= 0 NO
= 1 YES
706 MINIMAL SEQUENCE IDENTITY IN GENPRF
707 MINIMAL PROFILE CONVOLUTION IN GENPRF
708 Length of arrays in WIF426
710 Ensure that we don't start looping in IRI_002 (in test scripts)
At many other places, it makes sure we do not prompt users.
= 0 Yes, allow normal looping; yes prompt the user
<>0 Loop at most one time in IRI_002; no dont prompt the user
711 INTERNAL HIDDEN RETURN VALUE: LAST HB2 HYDROGEN BOND VAL
713 LOWER RESIDUE OF STRUCTURE RANGE IN HOMOLOGY MODELING
714 HIGHER RESIDUE OF STRUCTURE RANGE IN HOMOLOGY MODELING
715 Skip big calculations in mutate
= 0 Do HAS003 etc., in WIF330
<>0 Skip big calculations like HAS003 in WIF330
716 Desired luminance of non-black colors
717 Expected luminance of red
718 Expected luminance of green
719 Expected luminance of blue
720 Maximal number of frames in many trajectory options
721 Number of trajectory steps read already
722 100*Z-score on distances in REFI
723 100*Z-score on bond angles in REFI
724 Secondary structure fixing in GROMACS (FIXHST)
= 0 No forces (Default)
<>1 Forces
725 Skip HB2NET upon proton addition (for MUTQUA and similar big loops)
= 0 Use HB2RED as defined by WIFPAR 339
<>1 Skip HB2RED
789 Number to tag on the end of GROMACS output files
= 0 Default, don't do anything
<>0 Put this number at the end of the GROMACS output file names
790 Colour number of the background on SG machines
791 As 790, but in RGB mode
792 LRGBRA uses GETGDE flag
= 0 Dont use GETGDE in LRGBRA
= 1 Do use GETGDE in LRGBRA
801 Minimal sequence length in BIGFILE
802 Minimal guaranteed OK sequence length in bigfile
803 The last file got opened formatted
= 0 Yes
= 1 No, unformatted
804 100*THE UPAPRF GAP UPDATE VALUE
806 If not zero, use BSEQ always.
807 Number of zero-able points into caves.
808 Overrules resolution in MAP006 (*100)
= 0 Do not overrule automatic resolution in MAP006
<>0 100 * the resolution to be used in MAP006 (CAVITY etc).
809 Type of file read by MOL003B,C,..
= 1 PDB (default)
= 2 GROMOS
= 3 Kinemage
= 4 DIANA
810 Debug flag for output in TOPOLOGY file reading
= 0 give no output
= 1 give debug output
811 Lower colour of range to shift out
812 Upper colour of range to shift out
813 Atom number in Nardy's special option
814 Use C-alphas or just 1 residue in suppos in SCNGRL
= 0 Use C-alphas
<>0 Use one residue (the WIFPAR(814)-th one)
815 Give debug output is HST_TAB
= 0 give no output
= 1 give debug output
816 Draw balls in ball-and-stick in SPL options
= 0 draw the balls
= 1 dont draw the balls
820 Residue number of drug to be docked
821 Number of most central atom in drug to be docked
822 Type of 'force field' used in docking
823 Flag for interactive force-field convolution in FBRT
824 Colour of H-bonds in GRAEXT SPL*** options
825 Use old or new quality control for mutate and modeling
= 0 Old
= 1 New
= 2 None of the above
826 Read also non-peptidic drugs and waters from database
= 0 yes, do read drugs and waters
= 1 no, don`t read drugs and waters
= 2 Read complete PDB files
827 Keep previous database list in 3SSP options or not.
= 0 Prompt the user each round for the database files to use
= 1 Do not prompt the user, just keep using those database files
that were selected the last time before this flag is set.
828 Used old or new secondary structure determination
= 0 Not (yet) known
= 1 DSSP
= 2 Robs stuff
829 Level of sophistication in REFI
= 0 No, do not debump in REFI
= 1 Use bumps as one term in REFI
= 2 Include hydrophobic contacts
= 3 Include hydrogen bonds
= 4
= 5 Include course debumping
830 Atomic sequence distance for usage in DGEOM4
831 50 * the spread between upper and lower distances in DGEOM4
832 Number of generated DG structures
833 Use REFI in DGEOM
= 0 Do not use REFI in DGEOM
= 1 Use REFI in DGEOM
834 Fix user given ranges in GROMOS
= 0 Dont prompt user for fix ranges
= 1 Ask user for ranges to be fixed
835 Flag to tell SW-file reader to fil SERVER.BIG
= 0 Dont write in SERVER.BIG
<>0 This flag is SERVER.BIG record number
836 Number of cycles in RANDOM option (default is 10)
837 Print totals in ANASRF option; allow ACCDIF
= 0 Print totals in ANASRF option; allow ACCDIF
= 1 Do not print totals in ANASRF option; dis-allow ACCDIF
838 Print results in quality control
= 0 Do print results in quality control
= 1 Do not print results in quality control
839 Print ATOM records in MAKMOL
= 0 Do not print ATOM records in MAKMOL
= 1 Do print ATOM records in MAKMOL
840 Minimally required identity percentage for alignment
841 Minimally required profile overlap score for alignment
842 Sigma score (*100) below which REFI stops
843 Are we everywhere below WIFPAR(842) in REFI
= 0 No we are not
= 1 Yes we are
844 Should WIFGRN detect clusters for WIFWTF.
= 0 WIFGRN is not called from WIFWTF
= 1 WIFGRN is called from WIFWTF
845 Is CHOOSE active
= 0 CHOOSE is not active
= 1 CHOOSE is active
846 Counter of MODEL records in input PDB file
847 Read one or all MODELs in NMR structures etc. This is a funny
parameter that should be set indirectly by setting parameter 368.
848 Debug statements for type-ahead output flag.
= 0 Dont give type ahead debug output
= 1 Give type ahead debug output
849 Number of lines in a PBM file.
850 Number of points per line in a PBM file.
851-858 Help is active in for MOL-object 850+I in TEACH mode
= 0 No HELP present
= 1 Yes, HELP is present
859 Number of characters used by GVFLFI or GVFLFR
860 Default lower residue of input range
861 Default upper residue of input range
862 Tells WIFGRN it is being called by WIFGRS
863 Lower residue of range wherein input residues should fall
864 Upper residue of range wherein input residues should fall
865 100*ROTANG for stereo
866 100*Ca-Ca distance in DIGIT.F
867 100*WGT for 3D score in DIGIT.F
868 Time in seconds for DEMO10 option
869 Skip .NOT.USEAT atoms in drawat
= 0 just draw everything
= 1 draw only those that have USEAT true
870 What score to use in WALIGN related options.
= 0 Use identities only.
= 1 Convolute with the Dayhof matrix.
871 10* percentage sequence identity after alignment
872 10* sequence convolution after alignment
873 Should we kill GROMACS files automatically upon entry
= 0 No, first prompt the user
<>0 Yes, kill without mercy
874 Should MAP006 calculate extremes, or use the 'old' ones
= 0 Default, recalculate MAP parameters
<>0 Use previously stored MAP parameters
875 Give useless output in NQA014
= 0 Yes make the screen dirty
= 1 No, behave intelligently
876 Value of WIFPAR(873) at the previous position
(this is in OTHER.F where 873 is accidentally used too)
877 Value of WIFPAR(874) at the previous position
(this is in OTHER.F where 873 is accidentally used too)
878 Use DEBUMP and REFI in BLDPIR
= 0 Use everything
<> 1 The higher, the less regularisation.
880 Error upon GETMOL flag
= 0 GETMOL executed error free
<>0 GETMOL encoutered unsolvable problems
881 Use two ranges in FBRT or not
= 0 Use only one range
<>0 Use two ranges
882 Do water corrections in file corrections or not
= 0 Yes do all water corrections
<>0 No, skip the water corrections
883 Add missing atoms in file corrections or not
= 0 Yes add missing atoms
<>0 No, leave missing atoms missing
884 Normalize bonds, angles and planarities in file correction, or not
= 0 Yes normalize geometries
<>0 No, don't normalize geometries
885 Optimize H-bond network in file corrections, or not
= 0 Yes, optimize H-bond networks
<>0 No, don't optimaize the H-bond network
897 dummy to fudge CVS
898 dummy to fudge CVS
899 dummy to fudge CVS
900-949 reserved for Rob
900 Number of X-Y-Z scale parameters to refine in digit.f
901 Number of residues to refine at the same time in POWELL
902 100*Minimal distance 1-3 Ca-Ca for digit.f
903 Should warnings be printed if the 2D-line isn't seen?
1 = Yes!
0 = No!
904 Should "" on the WHAT IF command line do a
screen update?
1 = Yes
0 = No
905 For D2D module: convergence is reached if the relative change
in the E value is less than 1/WIFPAR(905)
906 For D2D module: maximum number of iterations
907 For D2D module: 100*ETA
908 For Bumpcheck: 100*ALLOWED_BUMP. Default is 40, which allows
bumps of 0.40 Angstrom before complaining. Purpose: set to 0.0
when building a model.
909 Usage of HASHTABLE in NQA002
0: Do not use hashtable
-1: Initialize hashtable, then use it
1: Use hashtable
910 Number of NQA002 HASH hits
911 Number of NQA002 HASH misses
912 jack-knife value (i.e. present sequence ?!)
913 jack-knife mode
=0 Skip if MOD(ISEQ,WIFPAR(917)).EQ.WIFPAR(912)
=1 Skip if MOD(ISEQ,WIFPAR(917)).NE.WIFPAR(912)
914 Interrupt mode. What do we do in case of interrupts? (Control C)
=-1 Do not install an interrupt handler at all
=0 Ignore completely
=1 Break current operation
=2 Close WHAT IF conditionally
=3 Close WHAT IF unconditionally?
915 Loop a script over a list of files or the WHAT IF database
=-1 Looping over file of files (unit 70)
=0 Not looping
>0 Current internal database number
916 100*Gamma value for X11 color map generation
917 Jack-knife modulo.
918 Jack-knife which?
1=NQA
2=PDBC62
3=LSCRIP (WIF013)
919 Are we making a database, or doing 'normal' things
= 0 Normal operation
<>0 We are making a database (SEQ3D options)
920 Suppress PDB file output in SEQ3D loop
= 0 Normally print
<>0 Suppress the output
921 For olga only: Keep 4-th 'atom' in TIPTP4 waters.
= 0 Don't keep 4-th atom
<>0 Yes, keep 4-th atom
922 Sodium Chloride concentration in MD run in water
923 Has NQA been used?
0 = "No" or "yes, but we should re-initialize"
1 = "Yes, no initialization is needed"
924 Should NQA024 return separate results for each of the atom types?
0 = no
1 = yes
925 Should INF004 complain if it doesn't find the option?
0 = yes. the user asked for the option
1 = no. It was an automatically generated help call
926 Number of atoms read that were discarded because they
do not belong in this residue type
927 Number of atoms read that were discarded because it is
specified more than once
928 Line width for DIGIT.
929 Should an NQA map be scaled by "reverse accessibility"?
0 = No
>0 = Yes, but the scale should not be higher than WP(929)/100.0
930 Are the NQA datafiles present on the system?
0 = No
1 = Yes
931 Are the old QUA datafiles present on the system?
0 = No
1 = Yes
932 Should plots be created by SCTPRP?
0 = Make plots
1 = Suppress plots
933 HB2 debug level
0 = Normal
>0= More verbose
<0= Less verbose
934 MSDB01: 100*Cutoff radius to be used in polymericity determination
935 MSDB01: Number of contacts per 1000 residues to call it a dimer
936 Parameter for detected molecular overlap.
937 Involved in HBONDS
938 Scale factor on Dayhof matrix in NEWPRF (*100.0)
939 MSDB01: 100*weight for the 1-3 contacts in determining cluster.
940 MSDB01: Minimum chain length to consider something a protein
941 100* Resolution of last read PDB file.
942 PdbCheck badness counter
<0 disabled
=0 everything OK
1 one little oops encountered
>1 more than one little oops and/or more than zero big oopses
943 Number of NCS comparisons and plots allowed
944 Server mode: never read from stdin, but wait for kill and
continue by reading SERVER.SCR
945 Restrict MAKMOL output
=0 No
=1 Yes, do not output non-polar hydrogens
946 Mode in which GETLINE5 fails as soon as IU54 changes. For WIF002A.
950 Debug counter in DGLOOP
951 Debug counter in DGLOOP
952 Debug counter in DGLOOP
953 Debug counter in DGLOOP
954 Debug counter in DGLOOP
955 Debug counter in DGLOOP
956 Debug counter in DGLOOP
957 Debug counter in DGLOOP
958 Debug counter in DGLOOP
959 Debug counter in DGLOOP
960 Debug counter in DGLOOP
961 Debug counter in DGLOOP
962 Debug counter in DGLOOP
963 Debug counter in DGLOOP
964 Debug counter in DGLOOP
965 Debug counter in DGLOOP
966 Debug counter in DGLOOP
967 Debug counter in DGLOOP
968 Debug counter in DGLOOP
969 Debug counter in DGLOOP
970 If not zero, print the DGLOOP killer counters
971 REFI also bad atoms or not
=0 Do not refine bad atoms (bad as in ISATOK=FALSE)
=1 Refine everything in REFI
972 What should GPCMAL write out?
=0 Everything
=1 Just the control file
973 Skip weight update in profiles in GPCMA*
=0 Update the weigths normally
=1 Skip weigth updating
1001-1400 Reserved for Gert
1001 Energy term to be put in ATTVAL in GETETM
1002 Write all atoms in MAKMOL or only those TRUE in a ROW
=0 Write all atoms
=1 Write only those that are TRUE in a ROW
1003 Parameter to prevent recursion between WIF303 and WIF303X
1004 RMS in SUPOPT option (*100)
1005 REFI should also execute SHAKE
=0 Dont do SHAKE in REFI
=1 Run SHAKE in REFI
1007 Number of 'the best' molecule in NMR ensambles.
1008 100* multiplier for SHAKE shift in REFI
1009 Number of drug atoms in soup at time of KLONKUP
1010 Number of water atoms in soup at time of KLONKUP
1011 Colour of protons (0 means HA + 10)
1012 General debug flag (was ICONFI(12))
= 0 Correct all errors, don't dump core
= 1 Dump core at the smallest error
1013 Skip CHECK routine in SHAKE module
= 0 Skip the check routine
= 1 Execute the check facility
1014 Debug flag in SHABLD
= 0 No debug output
= 1 Some debug output
= 2 Lots of debug output
1015 Steps to skip (0-99) in WAD options
1016 100* Gap open penalty in new profiles
1017 100* Gap elongation penalty in new profiles
1018 Suppress all kinds of output in GPCMAL
= 0 Give normal output
= 1 Suppress output
1019 Use sequence weights in UPAPRF, etc.
= 0 Do not use them
= 1 Do use sequence weights
1020 Prompt or not in case SAVSOU file will be overwritten
= 0 Ask the user if he/she really wants to overwrite
= 1 Overwrite, no matter what (also choice if DEFALL was set)
1021 GPCSEL/GPCSPL sorts sequences into directories or not
= 0 do not sort
= 1 sort sequences over the directories if possible
1029 Robjes param uitgecommenteerd
1030 Number of atoms with missing WEIGHT and BFACT
1031 Predefined colour for Ala
1032 Predefined colour for Cys
1033 Predefined colour for Asp
1034 Predefined colour for Glu
1035 Predefined colour for Phe
1036 Predefined colour for Gly
1037 Predefined colour for His
1038 Predefined colour for Ile
1039 Predefined colour for Lys
1040 Predefined colour for Leu
1041 Predefined colour for Met
1042 Predefined colour for Asn
1043 Predefined colour for Pro
1044 Predefined colour for Gln
1045 Predefined colour for Arg
1046 Predefined colour for Ser
1047 Predefined colour for Thr
1048 Predefined colour for Val
1049 Predefined colour for Trp
1050 Predefined colour for Tyr
1052 Use of PRODRG
=0 Do not use PRODRG
=1 Use PRODRG automatically on appropriate incoming drugs
1053 Print subroutine usage in FULLST
=0 No, dont
=1 Yes, do
1054 100*SAVSOU version number
1055 How to use MUTATE
= 0 Ask user
= 1 Always use fast mode
= 2 Always use slow mode
1056 Fix whole backbone in REFI
= 0 Dont FIX anything special
= 1 Overrule FIX flag and FIX whole back bone
1057 MAKMOL should write DELPHI file
= 0 Write normal PDB file
= 1 Write Delphi-style PDB file
= 2 Also write UHBD parameter file
= 3 Write an AUTODOCK .PDBqt file
1058 Default DELPHI grid size.
Dependent on fill-percentage and resolution of the DelPhi map
Default: 65
1059 Default DELPHI grid-fill percentage
Dependent on grid size and resolution of the DelPhi map.
Default: 90
1060 How far around atoms should potentials be removed
1061 Remove DelPhi potential from 'impossible' locations
=0 Keep your hands of the DelPhi potential map
=1 'Clean' the map by removal of potential from where nothing can go
1063 Pointer into residue backup common block
1064 Echo SCRIPT parameters with SCRIPT>>>> etc.
=0 Yes do
=1 No, dont
1065 Did INF004 get its man?
= 0 Yes, HELP was found
= 1 No HELP was not (yet) found
1066 Use BE_SOCIAL or not.
= 0 Use BE_SOCIAL if nothing changed.
= 1 Loop continuously
1067 Number of silent loops per continuous loop if 153=1
1068 Value to reset 1067 with
1069 NUMGRO as read in from last open GROMOS file
1070 SC1015 should try to repair ALL atoms, not just middle of chain
= 0 Don't fix ecerything (mainly for PDBREPORT purposes)
<>0 Fix as much as possible (mainly for GROMACS purposes)
1071 Skip manual OXT corrections.
= 0 Just do normal OXT corrections
= 1 Skip OXT corrections
1072 Accept $ commands?
= 0 Yes, normally accept them
= 1 No, do not accept $ commands
1073 Use preset WRK1TF in HAS003
=0 No, ask for it or use given range
=1 Use WRK1TF as given by calling subroutine
1074 Are we building a model by homology
= 0 No, we are not
= 1 Yes we are
1075 Sequence number in PRETYP used for numbers on top of plot
1076 Number of aa already seen in PRETYP sequence in 1075
1077 Number of aa already seen in PRETYP sequence in total
1078 Greyness for dark shaded residues in PRETYP
1079 Greyness for light shaded residues in PRETYP
1080 Convolution radius*100 in ANIFLX
1081 Do we need to update the BOUND_TO administration
=0 No, we dont
<>0 Yes, update it in the next MOL200
1082 Number of hits in CHSMOV (hidden in other)
1083 Write date and time with every note in notebooks
=0 Yes, write date and time
<>0 No, do NOT write date and time
1085 Write original CRYST and SCALE cards in MAKMOL?
=0 Dont
<>0 Yes, do
1086 Use ARBnmb in PRETYP or not
= 0 No, don't use ARBnmb but WIFPARs 1075 - 1077
<>0 Yes, use ARBnmb for top line numbering in PRETYP
1087 Should whole colums be made gray, or only boxed ones in WALGRA
= 0 Whole columns
= 1 Only the boxed ones
1088 Numerical equivalent of NUMNAM to be used in MOL104A
1089 What can SCN110 give back?
= 0 Everything
= 1 At most protein
1090 Rotate rest of chain in CHI010
= 0 Yes, do.
<>0 No, Don't.
1091 Really complete ranges in WRK1TF_COMPLETE if requested
=-1 Always add, don't ask questions
= 0 Yes, do the completion, but ask the user
= 1 No just neglect calls to WRT1TF_COMPLETE
1092 Length of first comparison equivalence array in WHAT_MODQ
1093 Something in PSTPLT
1094 Something in PSTPLT
1095 Something in PSTPLT
1096 Something in PSTPLT
1097 Something in PSTPLT
1098 Last Character size in FLYPLT
1099 Are we in dash mode or not?
= 0 We are drawing solid lines
= 1 We are drawing dashed lines
1100 Delay nomenclature/chirality correction in GETMOL
= 0 Normally correct everything in MOL199
<>0 Do not correct in MOL199
1101 Length of second comparison equivalence array in WHAT_MODQ
1102 Are we checking structures or models
= 0 Structures
= 1 Models
1103 Write OXT or O in WIF509
= 0 Write O OXT
= 1 Write O O
= 2 Write O O2
= 3 Write O' O''
= 4 Write O1 O2
1104 FREE
1105 Are we running WHAT IF from a server
= 0 No we are not
= 1 Yes, we are running a server
1106 Optimise the view of FLY files
= 0 Yes do
= 1 No, don't
1107 Horizontal mouse error in fullscreen stereo on SGI.
1108 Vertical mouse error in fullscreen stereo on SGI.
1109 Vertical mouse error in other fullscreen stereo screen on SGI.
1110 Write out DE record in PHYTRE options
= 0 Yes do
= 1 No, don't
1111 Dont do stereo in FLY files but use wide screen anyway
= 0 Dont overrule anything
= 1 Dont do stereo in FLY files but use wide screen anyway
1112 Use or in GPCMAL HTML pages
= 0 Use
= 1 USE
1113 Are we doing SHAKE-like things
= 0 No, we are not
= 1 Yes we are
1114 Unit where phylogenetic tree option should write HTML code
= 0 Don't use this facility
<>0 Write to the unit indicated by this parameter value
1115 Number of hits in HLANDB
1116 Skip loops that contact with partner in dimer in GLA_loop search
= 0 No, don't
= 1 Yes, skip them
1117 Colour number of C in COLATM
1118 Colour number of N in COLATM
1119 Colour number of O in COLATM
1120 Colour number of S in COLATM
1121 Colour number of P in COLATM
1122 Colour number of other atoms in COLATM
1123 Debug parameter for SHAKE
1124 Yes in FBRT does normal yes or works on individual atoms.
= 0 After Yes, FBRT is accepted
= 1 After Yes, user is prompted for the part(s) that should move
1125 Only use bumps with backbone in LOOPS
= 0 Use all atoms
= 1 Only use BB-SS and SS-BB
= 2 Only use BB-BB
1401-1500 Reserved for Buggy Bertje and Dumb Daantje
1126 M1 or M2 is M1 or M2 in Glay's loop routines or not....
= 1 M1 / M2
= 2 M2 / M1
= 3 M1 / M1
= 4 M2 / M2
1127 We are executing the TOM module
= 0 No, we are not, everything is normal
= 1 Yes we are, so skip some output here and there, etc.
1128 Suppress symmetry information output
= 0 No, just show everything
= 1 Yes, suppress 'non-informative' symmetry messages
1129 Secondary structure type to be used in the loops module
= 2 Strand
= 4 Helix
= 6 Loop
1130 100* Accessibility cutoff in GLA_03
1131 Put delay after GVSSPL etc.
= 0 Don't waste any time
= 1 Put 5 seconds delay at end of GVSSPL to allow OS to relax a bit
1132 Maximal fragment length for splines
1133 SUMERR over the ANGLIST in refine
1134 Should equal use protons if possible
= 0 No, EQUAL always skips protons
= 1 Yes, EQUAL should use protons if present
1135 Recursion level in MOL105
1136 SUMERR over the PAIRLIST in refine
1137 100*Z-Score on bonds in last REFI round
1138 100*Z-Score on angles in last REFI round
1139 100*translational bump error in last REFI round
1140 100*distance misfit in last REFI round
1141 100*planar misfit in last REFI round
1142 100*in-plane misfit in last REFI round
1143 100*parallel misfit in last REFI round
1144 100*PO4-PO4 misfit in last REFI round
1145 Use external distances in REFI or not?
= 0 No, dont use external distances in REFI
= 1 Yes, do.
1146 Should ADDHYD put protons on GLU and Asp
= 0 No.
= 1 Yes.
1147 Should ALIPRF write the FT files
= 0 No
<>0 Yes
1148 Debug, use mutation data in ALIPRF
1150 100*The cut-off CUTOF1 in CONCRD/CONCOORD
1152 MINDIS in CONCRD (minimal number of constraints per atom)
1153 Use NOEs in CONCRD or not
= 0 No, dont use them
= 1 Yes, use them
1154 Number of structure requested in CONCRD
1155 Maximal number of iterations per step in CONCRD
1156 GROMACS works with PDB or XTC files
= 0 Normal, default, we use PDB-style files
<>0 Weird, we use XTC files
1157 Tolerance in sequence search in SELECT
1158 100*neighbour parallel misfit in last REFI round
1159 Last used GROUP number
1160 NUMAAF after reading PDB file in GLA_07
1161 Write TER or ENDMDL in SCNFIL
= 0 Write TER between the hits
= 1 Write ENDMDL between the hits
1162 Mode of operation in WLS050
= 0 Error
= 1 GPCMAL (Everything)
= 2 GPCMA1 (root + all branches)
= 3 GPCMA2 (branche + all roots)
= 4 GPCMA0 (Just this one branche)
1163 WIF303 should also list !!s for ROW1 hits
= 0 No, WIF303 is used normally
= 1 Yes WIF303 is called from the search module
1164 Cutoff printing proton only molecules in SHOSOU
Proton-only entities will be skipped when there are more
than this parameter. 99999 indicates "Skip them always".
1165 Will we print all proton only molecules in SHOSOU
= 0 Yes, print them
= 1 No don't print them
1166 Total number of proton-only molecules in the soup
1167 Next MOL-object number in DEMOS
1168 Next MOL-item number in DEMOS
1169 Second next MOL-object number in DEMOS
1170 Second next MOL-item number in DEMOS
1171
1172 Use Pseudo atoms?
= 0 No, reject them
= 1 Yes, try to read them in
1173
1174 NUMAAT at begin of MOL003
1175 NUMATF at begin of MOL003
1176 Flag to avoid that SOUP name administration option get active. Mainly for
use during the reading of molecules etc.
= 0 mol5 options are allowed to modify molecule and residue names
=<>0 mol5 options are not allowed to work
1177 Print all chirals in HNDCHK or not
= 0 No dont
= 1 Yes, print them
1178 INDICATES THAT MOL036 DETECTED A SEVERE PROBLEM
= 0 MOL036 is happy
= 1 MOL036 detected that the file is shit
1179 Should MOL200 be re-run afterwards
= 0 No, 1 time is enough
= 1 Yes, (e.g. after geklooi with OXT)
1180 MOL123 should call MOL200 yes or no
= 0 Yes, MOL123 should call MOL200
= 1 NO, MOL123 should not call MOL200 to avoid looping around
1182 Class we are working on in GPCMA
1183 SYMCUT should skip protons?
= 0 No, SYMCUT normally uses protons
= 1 Yes, SYMCUT should skip the protons
1185 Number of non-waters written on unit 13 in MOL003
1186 Number of skipped Q and M protons
1187 Number of bad angles printed by INP201D
1188 Are we making MOL-items without a window?
= 0 No, without window no graphics
= 1 Yes, make the .WPL file at all cost
1189 Sequence number in INFPCK options
1190 Highest IREC seen by INP106
1191 100*allowed bump in rotamers
1192 DGROTA should take same residue type or prompt user
= 0 Default, promt the user
= 1 Take the residue type that is already there.
1193 Prime every option with % if not found in own menu.
= 0 Do not prime with %
= 1 Yes, try every option primed with % upon failure to find it
1194 Suppress jokes? NOJOKE
= 0 No, show them
= 1 Yes, suppress them
1195 Do we use DELETE or DELENT
= 0 DELETE
= 1 DELENT
1196 Eliminate resetting of BOUND_TO in MOL200
= 0 Default, reset BOUND_TO when needed
= 1 MOL200 will (temporarily) not set BOUND_TOs
1197 If not 0, the unit where SUGLIST should write also
1198 Do we fudge the FlexX pocket generator by looking at drug?
= 0 No, use FlexX honestly
= 1 Yes, make the pocket file perfect
1199 Skip action if pdb file already exists locally in PRP001/INFPCK
= 0 Just always work
= 1 Dont do work double
1200 Due to 1199 something got skipped
= 0 1199 says "Do your work"
= 1 1199 says "Don't do double work"
1201 Header template file in MAKMOL, and prompt for REMARK
=-1 Always use DUMMY.HED and dont prompt for REMARK
= 0 Just default, ask the user and prompt for REMARK
> 0 Take the indicated action
1202 INFPCK flag
= 0 Everything is normal
= 1 What ever is being executed, be aware we came from INFPCK
1203 INFPCK IUNIT number
1204 Anti recursie parameter for MOL200
= 0-1 Nothing special going on
= 2 We are in MOL200 somewhere
1205 Skip database loading in RAMA options?
= 0 No, just normally load them every time
= 1 Yes, skip them to save time in some options
1206 Recursion memory for SHOIAA
1207 Advanced DEBUG flag for GETMOL with protons
1208 Advanced DEBUG flag for BOUND_TO checking and PRODRUG checking
1209 To prevent HAS001-HAS003 recursion
= 0 All is normal
= 1 HAS003 was called from HAS001
1210 Advanced DEBUG flag for proton nomenclature checking
1211 Advanced DEBUG flag for proton nomenclature checking
1212 Where was ACC006 called from?
= 0 Normally called from the menus.
= 1 Called from ACC005 (DIFACC option).
1213 Skip BUMPVAL in DGMUT
= 0 No, use the bump score
= 1 Yes, skip the bump score
1214 Counts how many lines have been KLONKed
1215 Should WIFPUSHSTK write what it does in a file?
= 0 No, don't write anything
= 1 Yes, write the whole diarhea
1216 Anti recursion flag for WIFPUSHSTK
1217 Interactively overrule OXT addition
= 0 Do whatever is default at the moment.
<>0 Never and nowhere add OXT, except for GROMOS
1218 Used somewhere in INFTLS
1219 Colour to overrule colours in PHYTRE
1220 100*Scale factor for PSTMOVE and PSTDRAW in FLY-mode
1221 Should the HSSP file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1222 Should the SEQUENCES file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1223 Should the SNAKES file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1224 Should the MVIEW file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1225 Should the PROFILE file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1226 Should the MSF file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1227 Should the CORMUT file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1228 Should the PHYTRE file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1229 Are we running the testsuite
= 0 No we are running interactively or as a server
= 1 Yes we are running the testsuite
1230 Print all texts in GVSCC6?
= 0 No, don't
= 1 Yes, do
1231 Write SWSQ line in WALFTADM
= 0 Yes, do write
= 1 No don't write
1232 Half-1 window length in REPEAT
1233 Cutoff score in REPEAT
1234 Stereo device parameter
1235 Eye separation in mm
1236 Viewing distance
1237 Set weigth in CNC002 or not
= 0 Yes, set weights according to range
<>0 No, assume weight was set already
1238 Damp factor for CONCRD/CONCOORD (*100). All distance
margins are multiplied with this value.
= 0 Nothing moves
= 1 Default
1239 Number of X-pixels in FLY output
1240 Number of Y-pixels in FLY output
1241 Should the PHYTRE80 file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1242 Should the PHYTRE60 file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1243 Should the PHYTRE40 file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1244 Should the PHYTRE20 file be written in 7TM control file
= 0 Yes, do
= 1 No, don't
1245 Reduction factor of VdW radii in CPK mode (*100) Default=0.45
Only used when 1249 is set to zero!
1246 Toggle in counting modules and NONEs in COUNTR
1247 Skip MOL200 at all. Very dangerous option!
1248 Thickness of bonds in ball-n-stick
1249 Fixed sphere radius (default is zero, meaning use 1245)
1250 Transparency of solied objects
= 0 totally transparent (invisible)
= 1 totally untransparent
1251 Transparency of surface maps
= 0 totally transparent (invisible)
= 1 totally untransparent
1252 100 * Aspect ratio of the screen.
1253 100 * Shininess of solid objects
1254 100 * Fog density
1255 Counter for atoms of which element cannot be determined
1256 Counter for atoms with correctable funny atom type
1257 FREE
1258 Minimally allowed distance between symmetry related copies
1259 Percentage noise in SF calculations
1260 Were all occupancies set at 1.0 forcefully
= 0 Occupancies were not touched
= 1 User/WHAT_CHECK fiddled with the occupancies.
1261 Keep cavity near one atom. 1261 is the atom number
1262 Debug parameter for FFT routines
= 0 Print NO debug information
<>0 Do print debug information
1263 Something in FFT
1264 Should SOUCOP give new group new set-name?
= 0 Yes, give a new set-name
= 1 No, give copied group same set-name as original
= 2 Yes, but let SOUCOP set new set-name
1265 Should one water be deleted if two are too close?
= 0 No, just warn and do nothing
<>0 Yes, delete the one furthest away from any protein
1266 Should topolified drugs be renumbered in GMO049C
= 0 Yes, they should normally be renumbered
<>0 No, skip them by giving them 'funny' numbers.
1269 Rippmann flag for writing REM290 in PDB file with MAKMOL
= 0 Don't write REM290
<>0 Write REM290 in PDB file
1270 Are we in GETMOL (for error messages in PRODRUG caller)
= 0 No, we finished GETMOL
<>0 Yes, we are executing GETMOL
1271 DBERLO handling flag for de boeren
= 0 Normal users
<>0 SEQ3D is in use by de boeren
1272 Speed factor in 3SSP (10-100). Default=80
1273 Run FULLSTOP at end of FULCHK
= 0 Don't stop after FULCHK
<>0 Terminate WHAT IF after FULCHK
1274 Type if HSTTAB should list only one type
= 0 Use all types
<>0 HSTTAB lists only fragments of this type
1275 Do we write the two layers of protein atoms in DAVADRUG or not?
= 0 No, only write the drug
<>0 Yes also write the local protein environment
1276 Number of atoms without Mendeleev symbol
1277 Debug flag in CMS and DEBUMP
= 0 CMS and DEBUMP do not print debug output
<>0 CMS and DEBUMP print debug output
1278 IHAC parameter in GRIN (default is 0)
= 0 Use defaults (suggested method)
= 1 Alternative (semiemperical method)
1279 MOVE PARAMETER IN GRIN (DEFAULT = 0)
= 0 Default
= 1 Writes more, including flexibility info
1280 DEEP parameter for GRID
1281 MOVG parameter for GRID
1282 POSI (actually number of POSI lines expected)
= 0 Default, GRID POSI command will not be used
> 0 Number of POSI lines expected from input and written for GRID
1283 100 * lowest cutoff in DRGMEN NAYB
1284 100 * second cutoff in DRGMEN NAYB
1285 100 * third cutoff in DRGMEN NAYB
1286 100 * highest cutoff in DRGMEN NAYB
1287 Colour of lines for bumps worse than 1283
1288 Colour of lines for bumps worse than 1284
1289 Colour of lines for bumps worse than 1285
1290 Colour of lines for bumps worse than 1286
1291 Resolution range high
= 0 Not in use
<>0 100 * Resolution range high value
1292 Resolution range low
= 0 Not in use
<>0 100 * Resolution range low value
1293 Total number of bumps reported in BMPCHK
1294 Bumps in PDBREPORT summary?
= 0 No
<>0 Yes
1295 List REMARK 3 refinement resolution ranges
= 0 No
<>0 Yes
1296 Are we working for GROMACS
= 0 No, we are normally going around our business
<>0 Yes, whatever we do, we are doing it for GROMACS
1297 Maximal number of CPUs to be used by GROMACS
1298 Number of points in Simulated Anealing
1299 Lower time in SA
1300 Higher time in SA
1301 Lower temperature in SA
1302 Higher temperature in SA
1303 Simulated Anealign type
= 1 Type is Single
1304 Residue used in DGROTA option in JMOL
1305 Should manually set B-factors of protons become 0.1 of their heavies
= 0 No, give them teh seme B-factor
<>0 Yes, divide their B-factor by 10 after manual setting
1306 100 * the cutoff parameter in JURRES / JURSAV default=25 (=0.25A)
1307 Should JURRES rotate all XH3s back to close where they came from
= 0 Yes, rotate all XH3s back to where they came from
<>0 No, only rotate CH3s back, but not NH3s
1308 Debug flag for ADDHYD
1309 Maximal number of entries to be used in NQA generation
1399 GERT gert Gert
1401-1450 Reserved for GROMACS
1403
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425 Which atoms to use in MAKMOL (ONESAT or GROATN)
= 0 Normal ONESAT atom names
<>0 Use GROATN resident atom names
1426 Still a bit in use in atom name type determination
1427 Should GRA1AA draw hydrogens?
= 0 Yes, draw them as usual
<>0 No, skip them
1428 Number of rotamers to be tested in DMG004A
= 0 Take local default
<>0 Take this parameter
1451-1500 Reserved for Elmar
1451 Twinset flag:
=0 This is the classic WHAT IF (default)
=1 This is the Twinset WHAT IF
=2 This is the Twinset YASARA
1452 Twinset MolObject transfer:
=0 Ask user for MolObject
=1 Put into MolObject 0
1453 Twinset REFI: Always sets WIFPAR(829) to 0
100 * Maximum allowed deviation Z-score in REFI, ignored if 0
1501-1600 Reserved for Rob
1454 Twinset skip MENDLV Update:
=0 Update MENDLV in MOL211 by copying the first two atom name characters
=1 Do not touch MENDLV
1501 Less than 0.001*WIFPAR(1501) from axis indicates special position
1502 Flag controlling the workings of FBONDI
=0: Find all bound atoms
>0: Find non-H atoms only
<0: Find H atoms only
1503 Guess whether we have an NMR structure here.
=0: probably X-ray structure
=1: NMR
1504 Soup change counter. Will be incremented by 1 every soup change.
To be used in routines to re-initialize themselves at soup changes.
1505 Should "Q" and "M" atoms be considered hydrogen atoms?
=0: yes
=1: no, not, skip them, as usual
1506 Are we reading a DNA residue? Automatically set in MOL003B
=0 no, we are reading an RNA residue
=1 yes, we are reading a DNA residue
=-1 yes, we have so far not seen that we will be reading RNA
1507 The class of the conventional cell different from the input cell?
=0 no, or we haven't checked [yet] (done in RCRYST1)
=1 yes
1508 Should we do SYMICMP to NUMAAF or to NUMAAT?
=0 to NUMAAF, water residues could be too big.
=1 to NUMAAT, water residues are small and close to the protein
1509 100*Minimum "weight" for water atoms to be marked usable by HBO010
1510 Did we have a soup overflow?
=0 No, not yet
=1 Yes, we did
1518 Debug parameter for stack-frame corruption in PUSH/POP PPP
1519 Do the user interaction in davadrug or not
= 0 Yes, ask the user if things are OK
= 1 No, just run through in davadrug, and don't ask the user anything
1520 Write HYDBND records with MAKMOL
= 0 Dont write HYDBND cards
= 1 Yes, write HYDBND cards
1521 Maximal CA displacement allowed in DGLOOP
1522 Use sequential serial numbers in MAKMOL, or ATTVAL as serial number
= 0 Use normal serial numbers
<>0 Use ATTVAL as serial number
1601-1700 Reserved for Robbie
1601 Weight of structure factors relative to geometry (*100)
default=0.3 (30 that is)
1602 Number of Refmac cycles
default=5
1801-2000 Reserved for Jens
1801 Number of standard deviations to include in Electrostatic Map
default=5
1802 Flag for assignment of charge and radius in electrostatic
calculations.
=0 No assignment made
=1 All assignments OK
=2 Radii assignments OK - charges missing
=3 Charge assignments OK - radii missing
=4 All assignments OK - but using altered charges
1803 pKa parameter valid flag
=0 No variables initialised
=1 Everything OK
1804 Holds the number titratable groups currently teated.
Default = 0
1805 DelPhi grid resolution * 100 (grds/A) - lattice spacing
Dependent on the grid fill-percentage and the grid size
Default: 2 grds/A
1806 DelPhi ionic strength * 1000
Default: 0.0 mM
1807 Ion radius (DelPhi) * 100
Default: 2.0 A
1808 Water probe radius (DelPhi) *100
Default: 1.4 A
1809 Boundary conditions (DelPhi)
Default: 2
=1 Potential is zero
=2 Approximated by the Debye/Huckel potential of the equivalent
dipole to the molecular charge distribution,
=3 Boundary conditions taken from previous run (focussing)
=4 Approximated by the sum of Debye-Huckel potentials of all
the charges.
1810 (N) Interior dielectric constant * 10
Default: 40
1811 (N) Exterior dielectric constant * 10
Default: 800
1812 Grid centering flag
=0 let DelPhi determine the grid center
=1 Set the grid center according to WIFPARs (1813-1815)
1813 X-center for DelPhi *100
1814 Y-center for DelPhi *100
1815 Z-center for DelPhi *100
1816 Map resolution byte or integer*2 (230 or 30000)
1817 (N) Should GETODM and OURELE set potentials inside atoms to 0 ?
0: No (Default)
1: Yes
1818 How should the resolution be specified in DelPhi runs
1: Grid fill percentage (default)
2: Grids per Angstroem
1819 Should GETODM ask for a filename and remove extremes
0: yes
1: No
1820 Should makmol use the ranges already in WRK1TF?
0: No
1: Yes
1821 Should CORELM remove values below -1900?
0: No
1: Yes
1822 Stupid flag for suppressing ADDHYDs second range request.
0: No effect
1: Addhyd will ask for ranges only once and use all atom in 2nd range
1823 Which kind of map file should DelPhi read?
0: DelPhi style
1: Insight style
2: GRASP style
1824 Should SAVMAP and RESMAP ask for filenames?
0: No
1: Yes
1825 Are we in pKa calculation mode ?
0: No
1: Yes
2: Yes, but with full debugging
1826 If non-zero, then this parameter holds the number of atoms to
get from ARGS that should have their ISATOK flag set to .FALSE.
in pKa calculations.
1827 CUTOFF value for finding strongly coupled groups in actsite *100 (in
Default: 100 (= 1 kT/e)
1828 Assign default charge (WIFPAR 1829) and default
radius (WIFPAR 1830) to unknown residues when
assigning radii and charges for DelPhi.
0: No
1: Yes
1829 Default charge*100 to assign to an unknown atom
when running DelPhi
1830 Default radius in A*100 to assign to an unknown atom
when running DelPhi
1831 What are we assigning now (for DelPhi interface)
0: Nothing 1: Charges 2: Radii
1832 Should SETSCG use charges in PROTSTAT?
0: No 1: Yes
1833 Are there any charges in PROTSTAT?
0: No 1: Yes
1834 What is in PKA()?
0:Nothing 1:WI pKas 2:Loaded pKas 3: pKas without reference to SOUP
1835 Does NUMTIT/TITCHA hold information on the corresponding groups
in TITRES/WIFPAR(1804)
0: No 1: Yes
1836 Should DelPhi calculate desolvation energies?
0: Yes 1: No
1837 Should we get DelPhi to calculate energies?
0: No 1: Yes
1838 Do we want to model insertions in BLDPIR?
0: No 1: Yes
1839 Number of residues to remodel on both sides of insertion. (FILGAP)
Default: 2
1840 Number of optimisation steps/100 for FILGAP. (Default 2)
1841 Maximum RMS allowed in FRNGE2*100 (Default 100)
1842 The value added to a grid point if a correlation is found.
1843 Does EDESOLV hold energies? 0: No 1: Yes
1844 Does EBACKGR hold energies? 0: No 1: Yes
1845 Does INTENE hold energies? 0: No 1: Yes
1846 Are we running the Linux version of DelPhi??
0: No 1: Yes
1847 Model pKa for Asp *100
1848 Model pKa for Glu *100
1849 Model pKa for His *100
1850 Model pKa for Lys *100
1851 Model pKa for Arg *100
1852 Model pKa for Tyr *100
1853 Model pKa for N-term *100
1854 Model pKa for C-term *100
1855 How should the pKa routines optimise Hbonds?
0: Not at all 1: Use the HB2 routines blindly 2: As fancy as possibl
1856 Cutoff energy for considering to titgrps a pair (in kT/e)*1000
1857 Should we consider pairwise interaction in detail? 0: No 1: yes
1858 Invoke the debump code when scoring hbonds? 0: No 1: Yes
1859 Make the TYR OH a very strong acceptor? 0: No 1: Yes
1860 If only 1/2 TYR should be a strong acceptor then 1860 holds its IAA
1861 If only 1/2 TYR should be a strong acceptor then 1861 holds its IAA
1862 Unused
1863 Use all charged/all neutral form of soup for desolvation energies?
0: Yes 1: No
1864 0: Use WHAT IF focussing values 1: Use Yang/Honig focussing
1865 1: Use the values in ATCOLR for determining the dielectric constant
1866 Is DelPhi buggy? (should we delete the ARCDAT file before each run?)
0: No 1: Yes - Default: 1
1867 The dielectric constant to use when calculating desolv+background int
if the criterium set by parameter 1877 is met.
Default: 16 (*10)
1868 The dielectric constant to use when calculating the charge-charge mat
the criterium set by parameter 1878 is met.
(See also parameter 1878)
Default: 60 (*10)
1869 The cutoff for cluster formation (in Bolztmann statistics) *100
Default: 20 (=0.2 kT/e)
1870 Model pKa for Cys *100
1871 Make the CYS SG a very strong acceptor? 0: No 1: Yes
1872 If one or two CYS should be strong acceptors then 1872 holds the IAA
1873 If one or two CYS should be strong acceptors then 1872 holds the IAA
1874 Residues with a QFINAL (in NUMROT) above this value/100 will keep the
1875 Residues with a B-factor below this value/10 will keep their colour.
1876 Ignore water molecules when assigning charges and radii?
0: No 1: Yes
1877 Cutoff for assigning alternative dielectric constant for desolv+backg
Default: 20
1878 Cutoff for assigning alternative dielectric constant for matrix
Default: 30
1879 Are we already trying a different focussing method?? (in GETPOTS)
0: No 1: Yes
1880 Residue 1 - for pKa routines.
1881 Residue 2 - for pKa routines.
1882 Use subroutine OPTIMISEGROUPS for optimising the Hbond network?
0: No 1: Yes
1883 Should RUNDEL run DelPhi (0), UHBD (1) or the internal PB-solver(2) D
This parameter also applies to GETODM...
1884 The pH range for GRAPKA plots
1885 The pH start for GRAPKA plots
1886 The minimum charge (*100) for GRAPKA plots
1887 The maximum charge (*100) for GRAPKA plots
1888 Do we have titration curves? 0: No, 1: Yes
1889 Model pKa value for Ser * 100
1890 Make the SER OG a very strong acceptor? 0: No 1: Yes
1891 If one or two SER should be strong acceptors then 1891 holds the IAA
1892 If one or two SER should be strong acceptors then 1892 holds the IAA
1893 List the amino acids added to a mol object in GRASHL?
1894 Should the pKa calculation routines ask for a pH range?
1895 Number of selection rounds for finding the autonomous cluster
1896 Model pKa value for Thr * 100
1897 Make the THR OG a very strong acceptor? 0: No 1: Yes
1898 If one or two THR should be strong acceptors then 1898 holds the IAA
1899 If one or two THR should be strong acceptors then 1899 holds the IAA
1900 In GRPINF, the group to start calculating for
1901 HAPPY factor 1
1902 HAPPY factor 2
1903 HAPPY factor 3
1904 HAPPY factor 4
1905 HAPPY factor 5
1906 HAPPY factor 6
1907 HAPPY correction factors on or off in DGM004A?
=0 Off
<>0 On
1908 Grid-size X for AutoDock Default = 40 A
1909 Grid-size Y for AutoDock Default = 40 A
1910 Grid-size Z for AutoDock Default = 40 A
1911 100* Grid spacing for AutoDock Default = 0.5 A
1912 100* Grid centre X for AutoDock
1913 100* Grid centre Y for AutoDock
1914 100* Grid centre Z for AutoDock
1915 AutoDock runs rigid docking or flexible docking
= 0 Rigid docking
= 1 Flexible docking
1916 A docked pose needs to have its centre within this radius from the
central point. Default 25 A.
2000 Not a parameter, just help text. Numbers absent in the list
below are set to their default value, which is zero.
Be aware that the two tables below are fixed format. The first number (the
parameter number) is fixed at five digits, and must be right justified. The
second number (the parameter value) is fixed at ten digits, and must also
be right justified:
five ten
....|.........|
* DON'T CHANGE THIS LINE
1 1
2 1
3 100
4 0
5 0
6 2
7 100
8 17
9 22
13 1
16 120
17 3
18 2
20 50
21 250
22 50
23 100
24 6
25 170
26 1
27 1
29 140
30 0
31 30
32 50
33 130
34 150
35 290
36 260
37 200
38 1
39 120
42 -150
43 150
44 180
45 500
49 400
51 5
52 70
53 30
55 80
56 25
57 12
59 2
60 1
61 0
64 3
65 70
70 3
71 270
72 15
73 3
74 0
76 10
81 15
82 500
83 300
87 1
88 0
89 0
91 0
92 50
93 10
94 20
95 1
97 5
101 1000
102 240
103 120
104 180
110 240
113 5
114 0
119 500
124 25
125 10
127 0
128 10
129 180
130 400
131 60
132 0
133 0
135 300
139 20
140 60
143 400
149 200
150 8
170 0
171 1000
176 75
199 2000
200 180
201 170
202 140
203 200
204 200
205 200
206 180
207 180
208 170
209 100
210 180
211 140
212 140
221 5
222 10
223 11
224 6
225 20
226 40
227 1000
228 0
229 2
230 0
231 600
232 5
233 10
234 20
235 6
236 4500
237 4000
238 80
239 20
240 5000
241 8000
242 1
243 30
244 1
245 1
247 1
248 1
250 1
251 200
252 5
255 10
257 100
258 2
261 2
262 1
263 100
265 7
266 1
267 -1
268 5
270 3
271 3
272 1
273 1
274 200
281 1
283 180
295 300
300 1
301 1
302 1
303 100
304 16
306 9000
307 1
308 0
309 0
310 0
311 100
312 0
313 75
314 100
315 133
316 200
317 1
318 0
319 300
320 0
321 0
322 100
324 1
329 0
331 0
332 0
335 1
337 0
340 1
341 25
346 100
351 1
352 1
353 2
355 50
356 25
371 1200
372 100
373 150
374 10
380 59
381 58
382 65
383 100
384 0
385 430
386 25
387 20
388 31
401 400
410 0
411 5
412 25
413 50
414 61
421 5
440 21
441 5
445 99
465 1
467 1
458 20
481 350
483 3
484 250
485 60
486 90
487 3
489 100
490 100
492 100
494 70
501 3
502 5
503 3
504 250
505 500
506 200
508 1
531 1
540 5
541 1000
543 1000
545 100
546 30
548 1
550 100
551 3
552 2500
553 30000
554 30000
555 0
558 99900
559 1
560 2
564 3
567 100
593 50
596 50
598 50
617 10
619 1
622 1
631 5
632 40
633 10
634 1
635 3
636 30
637 1
638 13
639 20
643 1
645 5
706 20
707 30
717 38
718 48
719 14
724 0
720 1000000
790 0
791 50
792 0
801 200
802 290
804 1
807 1000
808 100
809 1
811 130
812 200
813 1
816 1
824 60
825 1
826 0
830 100
831 50
832 20
836 10
840 25
841 35
842 50
847 -1
865 600
866 380
867 100000
868 10
901 3
902 520
904 1
905 100000
906 100
907 100
908 40
912 -1
914 1
916 180
917 10
928 3
929 0
933 -1
934 25
935 100
943 5
999 290
1008 100
1012 1
1015 19
1016 100
1017 10
1029 1
1031 230
1032 180
1033 120
1034 120
1035 240
1036 230
1037 30
1038 240
1039 30
1040 250
1041 180
1042 70
1043 230
1044 70
1045 30
1046 300
1047 300
1048 240
1049 240
1050 300
1052 1
1054 499
1058 65
1059 90
1060 10
1061 1
1067 10
1068 10
1075 1
1078 60
1079 90
1080 350
1082 1000
1085 0
1191 750
1104 2
1107 0
1108 0
1109 0
1115 1
1117 240
1118 340
1119 120
1120 180
1121 60
1122 300
1128 1
1129 6
1132 35
1150 400
1152 100
1154 25
1155 500
1164 10
1193 1
1216 1
1218 600
1219 250
1220 100
1232 2
1233 3
1235 65
1236 70
1237 0
1238 100
1245 30
1248 15
1250 100
1251 100
1252 127
1253 50
1254 50
1258 30
1272 80
1283 -100
1284 -75
1285 -50
1286 -25
1287 120
1288 150
1289 180
1290 220
1297 1
1298 0
1299 0
1300 50
1301 100
1302 300
1303 1
1306 25
1307 0
1308 0
1403 0
1407 99999
1408 1000
1409 1200
1410 5000
1411 2500
1412 5000
1413 5000
1414 50
1415 1
1416 650
1417 1
1418 0
1419 5000
1420 0
1421 1
1422 0
1423 0
1424 0
1501 5
1505 1
1509 50
1519 1
1521 70
1601 30
1602 5
1801 500
1802 0
1803 0
1804 0
1805 200
1806 0
1807 200
1808 140
1809 2
1810 40
1811 800
1812 0
1813 0
1814 0
1815 0
1816 30000
1817 0
1818 1
1819 0
1820 0
1821 0
1822 0
1823 0
1824 1
1825 0
1826 0
1827 100
1828 0
1829 0
1830 150
1831 0
1832 0
1833 0
1834 0
1835 0
1836 0
1837 1
1838 0
1839 2
1840 2
1841 100
1842 10
1843 0
1844 0
1845 0
1846 0
1847 400
1848 440
1849 630
1850 1040
1851 1300
1852 960
1853 800
1854 380
1855 0
1856 1000
1857 0
1858 0
1859 0
1860 0
1861 0
1862 0
1863 1
1864 0
1865 0
1866 1
1867 160
1868 600
1869 20
1870 870
1871 0
1872 0
1873 0
1874 75
1875 100
1876 0
1877 20
1878 30
1879 0
1880 0
1881 0
1882 0
1886 -999
1887 -999
1889 1500
1890 0
1891 0
1892 0
1893 0
1894 1
1895 2
1896 1500
1897 0
1898 0
1899 0
1900 1
1901 10
1902 30
1903 40
1904 10
1905 100
1906 133
1908 40
1909 40
1910 40
1911 50
1912 0
1913 0
1914 0
1915 0
1916 25
*END DON'T CHANGE THIS LINE, AND KEEP IT AS THE LAST ONE