- Administration

It is impossible to fully automatically produce many millions of files without having an error, bug, or other problem here and there. If you suspect we goofed for some file, then please inspect that file′s ′sou′ entry.

These .sou file format is explained under the heading File content at the WHAT IF servers help page for output formats

The .sou Lists entries contain some additional information at the end of this line. E.g. 6o7y.sou looks like: 

 Molecule      Range              Type              Set name
     1    1 (    4)  183 (  186)A Protein           ORG                     1
     2  184 (  301)  184 (  301)A LRM               ORG        No topology  2
     3  185 (  302)  185 (  302)A SO4               ORG                     6
     4  186 (  303)  186 (  303)A SO4               ORG                     6
     5  187 ( HOH )  187 ( HOH )A water   (   68)   ORG                     5
 *END

At the WHAT IF servers help page for output formats you find explanations for the Molecule, Range, Type, and Set Name columns (albeit that the Set name only holds meaningful information when you run WHAT IF interactively. The last, untitled column, holds a numerical value for each molecule. These values range 1-7 for:

  1. protein
  2. ligand without known topology
  3. nucleic acid
  4. single atomic entity (ion, or C-terminal oxygen)
  5. (group of) water
  6. ligand with known topology
  7. sugar

The additional, redundant text "No topology" is added for us to easily find ligands for which we must produce WHAT IF topology entries for the next update of the whole facilities-suite.

By the way, LRM stands for 

2-AMINO-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-3-{[(S)-HYDROXY{[(2R,3R,4R,5R)-3-HYDROXY-4-METHOXY-5-(3-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHOXY}PHOSPHORYL]OXY}-4-METHOXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}-5-(6-AMINO-9H-PURIN-9-YL)-4-METHOXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}-5-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-4-METHOXYTETRAHYDROFURAN-2-YL}METHOXY)(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-7-METHYL-6-OXO-6,9-DIHYDRO-3H-PURIN-7-IUM

(one word) so don't hold your breath on me solving this one any time soon...

Alternatively, you can send your file to the WHAT IF administration server List a file

Anyway, if WHAT IF has trouble correctly interpreting the file, skip it in your calculations, but please mail us (vriendgert@gmail.com) so we can either fix the bug, or reject the PDB file.

Here Coos will produce a small form that gives access to the .sou file and if applicable to the corresponding .whynot file for a PDB file of user-choice.