Server output explanation

Output explanation

The servers use WHAT IF, and thus you get WHAT IF-like output. For regular WHAT IF users that output makes sense, but that might not be the case for you. We therefore explain here some of the output formats that are often used.

Residue numbers

When WHAT IF lists a residue number, it gives a lot of information. E.g.:

3 LYS  (   5 ) A 12

Means from left to right:

This is the third residue in the PDB file.
It is a lysine
The number in brackets is the number found in the PDB file. This example strongly suggests that the first two residues could not be seen by the crystallographer or NMR spectroscopist.
The character A is the chain identifier.
The number 12 indicates that this residue sits in 12-th NMR model.

Explanation for the atomic output per residue

The servers use WHAT IF, and thus you get WHAT IF-like output. The WHAT IF option for displaying all possible information is called LISTA. A typically LISTA output is given below.

The first line gives about the information for one residue. Prp is the residue property value, this value will be zero in the output on most servers. A few servers calculate a value for every residue. This result is stored in this so-called residue property value.

The second line is just a header. Between these first two lines more information can be given in case this residue is member of a family or a cluster (and if this server uses families or clusters), or in case WHAT IF has corrected or mutated this residue.

Residue:    37 ASP  (  37 ) E     (Prp= 0.00)
Atom    X     Y     Z   Acc   B   WT   VdW  Colr   AtOK  Val
 N    18.2  59.6  -5.1  0.0 16.7  1.0  1.7  340     +    0.00
 CA   17.0  58.8  -5.2  1.7 16.0  1.0  1.8  240     +    0.00
 C    16.9  57.7  -4.1  1.6 23.4  1.0  1.8  240     +    0.00
 O    16.1  56.9  -4.2  2.7 19.6  1.0  1.4  120     +    0.00
 CB   16.8  58.2  -6.6  3.5 16.8  1.0  1.8  240     +    0.00
 CG   16.6  59.3  -7.6  4.0 43.8  1.0  1.8  240     +    0.00
 OD1  16.0  60.4  -7.1  7.6 41.3  1.0  1.4  120     +    0.00
 OD2  17.0  59.2  -8.7  6.0 42.4  1.0  1.4  120     +    0.00
  *1    *2    *2    *2   *3   *4   *5   *6   *7    *8      *9

The last line (the one with *1 *2 etc., on it) is not part of the output but added here to guide you to the column by column explanation given below.

The atom names.
The coordinates in Ångstrom
The accessible molecular surface area (only zeros indicates buried or not calculated yet, that depends on which server you used).
The B-factor. >60 means this atom is for sure not here....
Weight. This is almost always 1.0. If 0.0 the coordinates were modeled. If between 0.0 and 1.0, alternative conformations have been observed.
The Van der Waals' radius for this atom. (Using the WHAT IF defaults:C:1.8 Ångstrom; O:1.4 Ångstrom; N:1.7 Ångstrom; S:2.0 Ångstrom.).
The colour for this atom. (Only used by servers that also produce graphics output).
Is-atom-OK flag. Atoms that are wrong (or missing) according to WHAT IF get a minus in this column.
The atomic value. Several servers calculate values for each atom. Those values are displayed in this so-called atomic value column.

Sometimes some colums are added to the type of output described above. For example, the vacuum accessibility server produces output like:

Residue:    46 ASN  (  46 )       (Prp= 0.00)
 Phi=-112.9 Psi= 162.3 Omega= 178.4
Atom    X     Y     Z   Acc   B   WT   VdW Colr   OK  Use  Vac.   %
  N    14.0   6.5  13.7  0.0  5.8  1.0  1.7 340    +   -   0.8   0.0
  CA   13.5   5.4  12.9  1.0  6.2  1.0  1.8 240    +   -   1.2  85.7
  C    13.3   5.9  11.5  2.3  6.6  1.0  1.8 240    +   -  12.9  17.6
  O    13.7   6.9  11.0  0.7  7.2  1.0  1.4 120    +   -   8.8   8.4
  CB   12.3   4.8  13.5  0.5  7.3  1.0  1.8 240    +   -   9.4   5.6
  CG   12.5   4.3  14.9  0.0  8.0  1.0  1.8 240    +   -   2.4   0.0
  OD1  12.0   4.8  15.9  3.4 11.0  1.0  1.4 120    +   -   8.9  38.1
  ND2  13.4   3.3  15.0  9.7 10.3  1.0  1.7 340    +   -  15.4  62.6
                        17.6                              59.9  29.4

But in such cases the extra output is trivial. Here the right two columns do of course give you the accessibility in vacuum and the ratio between normal and vacuum accessibility as a percentage. The extra numbers on the bottom are residue wide summaries.

Ensemble tables

In tables that run over ensembles you always get to see for each determined variable:

AVE, SDEV, VALMIN, POSMIN, VALMAX, POSMAX
where
AVE      = average of this parameter in all MODELs in the ensemble
SDEV     = standard deviation
VALMIN   = minimal value for this parameter in all MODELs in the ensemble
POSMIN   = number of the MODEL in which the minimum was observed
VALMAX   = maximal value for this parameter in all MODELs in the ensemble
POSMAX   = number of the MODEL in which the maximum was observed

Headers per PDB file

A typical header per PDB file in a table looks like:

PDB identifier ........................ :1hue
Number of the file .................... : 1
This is most likely an NMR structure.
Number of MODELs read from PDB file ... : 9
Number of MODELs present in PDB file .. : 25

In which:

Line 1 indicates the 4 letter PDB identifier.
Line 2 indicates the serial number of this PDB file in the list of files that was fed to WHAT IF.
Line 3 tell you whether WHAT IF thinks that this is a structure solved by NMR or by Xray. WHAT IF takes this decision after reading the SCALE matrix in the PDB file.
Line 4 indicates how many models were read in case the PDB file is an NMR ensemble. In case of Xray files this line is not printed. WHAT IF stops reading the PDB file when it thinks that reading the next MODEL would overflow its capacity. WHAT IF can read maximally 500 molecules, 4000 amino acids and 32000 atoms.
Line 5 is only printed if WHAT IF did not read all MODELS from a PDB file that holds an NMR ensemble.