Getting the servers installed and running on your own machine

If you want to have your own in-house WHAT IF - based servers, proceed as follows.
  1. Buy a version of WHAT IF
  2. Read the server installation notes and do as you are told.
I don't think the present set up will work with a Windows machine as server, but a real hacker can probably get it going by using the spirit of the installation notes rather than the literal implementation.

If you set up your own server, then you need

  1. Our permission
  2. Give proper credits and acknowledgements
  3. To be responsible for your servers and check all of them carefully by hand.

If you want to make the servers available to paying users, you need our written permission. Making servers available to the whole world, free of costs, go ahead, for that you have our permission already.

How to add an entry to your own server

To make your own server you need to understand WHAT IF, or have a VERY good connection with the WHAT IF team in Nijmegen (the going rate for servers is one bottle of single moult whiskey, 15 years or older per server).

In your server area you find the file This is the only file that you have to edit. Make a backup of this file first.

In you will find one description unit per server. I will describe the server that lists cysteine bridges and the server that draws a ramachandran plot.

Example 1

The description text for the cysteine bridges server looks like:
 1) listcys={
 2)     'name'   :"""Cysteines and cysteine bridges""",
 3)     'intro'  :"""This server will list cysteine bridges and free cysteines.""",
 4)     'methods':"""Two cysteines are called a bridged pair if the distance between
 5)                  their sulphurs is between 1.5 and 2.5 Ångstrom
 6)               """,
 7)     'input'  : [ ['&TWO1','Choose'] ],
 8)     'wifcom' :"""
 9) getmol &TWO1 set\n
10) soup\n
12) shocys\n
13)               """,
14)     'notes'  :""" """,
15)     'output' :"""The following cysteine bridges and free cysteines are present:""",
16)     'outnot' :""" """,
17)     'program':"""""",
18)     'picture':"""access-server.gif"""
19)     }
Ofcourse the first four character of each line should not be there (listcys, getmol, etc., that now start in column 5 should be left justified).
The format given above looks very rigid, but actually, there are only very few format aspects that are really fixed. Many blanks are allowed, things can be put on one line or many lines, etc. I prefer this rather rigid format because it makes me spot typographical errors more easily.
The text strings for 'name', 'intro', 'methods', 'notes', 'output' and 'outnot' are normal HTML, so all normal HTML text format commands such as A HREF=, STRONG, BR, P, etc., can be put in here, but please don't use global HTML commands such as HEAD, TITLE, etc., and try to be very careful with H1, H2, etc.
The general format of a server description is:
name={'option':'text', 'option':'text', 'option':'text', etc.}
If the text has to span multiple lines it should be enclosed in """ (triple double quotes rather than single quotes). Every 'option' should ofcourse have a different name.
Given this example, you should be able to make your own servers 'by homology', but we will explain them anyway, and we do that line by line. Explaining HTML in HTML is difficult because all these beautifully standard HTML browsers react differently on my attempts to use > and <, so i will not use these greater than and less than symbols around my HTML text in the explanation below.
  1. The first line holds the name of this server. Make sure the name is unique and I suggest that you make this name a function of the major option to be executed by the server. The ={ is obligatory, but extra spaces are allowed here.
  2. 'name' is associated with the title for the server in the list of servers per class. It is also the title of the server once you activate a server. I suggest that you try to keep this title at about 5 words.
  3. 'intro' is associated with the short text underneath the title in the list of servers per class, and it is the introduction text in the actual server page. I suggest you restrict this text to 1-3 lines of text (that is roughly up to 40 words).
  4. 'methods' is associated with the methods paragraph in the actual server. I suggest you explain here carefully what the server does, and try to give some explanation of any boundary conditions that you have put in the WHAT IF script. There are no limitations to the amount of text you can put here, but I suggest that if you use a construct like A HREF="my_text.html"click here"A and put the file my_text.html in the sever's html directory.
  5. 'methods' will most times extend over more than one line
  6. I put the closing tripple double quote always exactly underneath the opening one, but you can just as well put this """ at the end of the previos line. Don't forget the comma at the end of the """
  7. 'input' tells the server which boxes for input to put in the input form. The format of this line is
        'input' : '[ ['&NAME','text'], ['&NAME','text'], ['&NAME','text'], etc. ],
    in which &NAME should of course be different for each of them. The 'text's are the texts that will be put next to the input boxes in the input form. In this example, [ ['&TWO1','Choose'] ], &TWO1 will later be used in the WHAT IF script to get the name of the PDB file from the input form. the text 'Choose' will tell the input form that the user should get two boxes, one for a 4 letter PDB code and one for a file from the local directory. The three characters in the middle have a fixed meaning: The final digit should just sequentially run from 0 till 9.
  8. 'wifcom' is associated with the WHAT IF script. This is the most difficult part of the description file. I normally run WHAT IF in one window to test the commands, and run type them when they work in the 'wifcom' block in another window in parallel. In general, if WHAT IF can do it, a server can do it, but since servers cannot execute WHAT IF's GRAFIC command (because they cannot open an interactive window) some dirty tricks are needed. the following rules hold:
  9. This line executes GETMOL on the file that is obtained from the input form. The setname will be 'set'.
  10. This brings you in the SOUP menu.
  11. The command &STARTLOG\n opens the logfile
  12. this line executes the actual command we are interested in.
  13. Don't forgat to put """, at the end (this can also be put at the end of the previous line, but that is easier to forget.
  14. 'notes' are extra notes for the input form. Seldomly needed.
  15. 'output' is associated with the text that ends up on top of the output page that is returned to the user. Be aware that the user can not see the input form when looking at the results, so it does not hurt to repeat some of the key information in WHAT IF does not write an extensive table header or so. Sometimes it might be useful to put a pointer to a WHAT IF writeup chapter in the 'output' record.
  16. 'outnot' is associate with an extra note on the output page. Seldomly needed...
  17. 'program' is associated with the method of returning results to the user the following possibilities exist:
  18. 'picture' is associated with the gif that is shown in the top left corner of the page for this server. This is a rather unimportant keyword and this line can just as well read: 'picture':''
    Since this is the last line, no komma is needed at the end.
  19. } is needed to close the description of this server. This symbol can also be placed at the end of the previous line, but this way it is more difficult to forget it.
After you have created the server you need to register it in a class in the '_group' list. These classes are listed at the top of '' like (there are many more of course, but you can read that yourself):
          _groups = [{'name': 'model',
	     'title': 'Build/check/repair model',
	     'options': ['makemodel', 'fullcheck', 'modcheck', 
			 'corall', 'debump', 'compare']},

	    {'name': 'validate',
	     'title' :'Structure validation',
	     'options' :['namchk','oldqua','bndchk','structes','plnchk','newqua',
	    } ]  
The string you give in 'name' will be the name of the html-file for this class. The 'title' string will appear on the left hand side. In the option list you have put in the name of your new server. Note that you can register your server in more than one class.

Example 2

The server that makes a Ramachandran plot looks like:
 1) ramaplot={
 2) 'name'   :"""Ramachandran plot""",
 3) 'intro'  :"""This server will display a Ramachandran plot.""",
 4) 'methods':"""This server will display a coloured Ramachandran 
 5)              plot. Blue means helix, red means strand and green means turns and random coil.
 6)              The lines in the plot indicate prefered areas. The outer lines
 7)              encircle the area within which 90% of all crosses of the same
 8)              colour should be found; the inner lines indicate the 50% area.
 9)           """,
10) 'input'  :[ ['&TWO1','Choose'] ],
11) 'wifcom' :"""
12) getmol &TWO1 set
13) plotit nowind
14) gratwo
15) phipsi all 0 1 A
16) plotit setfly
17) pstplt
18) n
19) y
20) n
21) A 1.0 0
22) 0
23) Ramachandran-plot  
24)           """,
25) 'notes'  :""" """,
26) 'output' :"""The Ramachandran plot. Blue
27)              Some txt removed.
28)           """,
29) 'outnot' :""" """,
30) 'program':"""""",
31) 'group'  :"""graph2d""",
32) 'picture':"""access-server.gif""",
33) 'images' :["""PLOTR.101.gif""",]
34) }
All things that have been described in Example 1 will not be repeated here. Here I will only discuss the WHAT IF script (that is the text for the 'wifcom' command:
 1) getmol &TWO1 set
 2) plotit nowind
 3) gratwo
 4) phipsi all 0 1 A
 5) plotit setfly
 6) pstplt
 7) n
 8) y
 9) n
10) A 1.0 0
11) 0
12) Ramachandran-plot
  1. getmol &TWO1 set\n is the same as above, it reads a PDB file as indicated in the form
  2. plotit nowind\n is needed to tell WHAT IF that we are going to do some graphics. This is needed, because the server cannot open a graphics window, so some extra things must be done, like automatically centering the vectors that would be drawn at the screen otherwise. Also all kinds of WHAT IF savety mechanisms will be overruled with this command and the texts "Do you want a graphics window", "Second part of option not executed without graphics window" etc., are all skipped.
  3. gratwo gets us in the two dimensional graphics menu
  4. phipsi all 0 1 A\n makes a Ramachandran plot. 1 in the MOL-object number and A is the MOL-item name. The file A.WPL will be generated. This is a normal WHAT IF vector file, and if you can find this file on your system, you could even read it in and display it with the GETITM command in an interactive WHAT IF session.
  5. plotit setfly\n this gets us in the PLOTIT menu and tells WHAT IF that we don't want a PostScript file, but a gif file.
  6. pstplt normally makes a postscript file, but now a gif file
  7. n no stereo
  8. y yes we want colour
  9. n no, we do not want depth cueueing
  10. A 1.0 0 we want to put MOL-item A in the gif with 1 unit thick lines and dashing type 0 (that is no dashing)
  11. 0 no more MOL-items
  12. Ramachandran-plot we call the thing Ramachandran-plot, but nothing is done with this name (but don't forget it, there must be something here because WHAT If wants to read something).
In order to notify the web interface which plots to put in the output page put the names of the file in the 'images' list. You always have to put the images tag in if you make use of the class.
Email if you have questions.
(C) G.V. 1 Oct 2007