Program output

The basic program output is a series of PDB files containing the final coordinates of your search model(s) from each minimisation. The program will also create a PDB file containing the coordinates of all symmetry equivalent copies of all search models, which can be viewed directly with a molecular graphics program (to check for bad contacts).

QS will create quite a number of files. A directory devoted to the program will look like this after the end of a typical single-model run :

-rw-r--r--    1 glykos   user      200182 Apr  1 19:16 001.ps
-rw-r--r--    1 glykos   user      200182 Apr  1 19:16 010.ps
-rw-r--r--    1 glykos   user      100240 Apr  1 19:16 100.ps
-rw-r--r--    1 glykos   user      532644 Apr  1 23:42 LOG
-rw-r--r--    1 glykos   user       66661 Apr  1 19:16 Qs.pdb
-rw-r--r--    1 glykos   user       66708 Apr  1 19:26 Qs001_mol_1.pdb
-rw-r--r--    1 glykos   user      133306 Apr  1 19:26 Qs001_packing.pdb
-rw-r--r--    1 glykos   user       66708 Apr  1 19:35 Qs002_mol_1.pdb
-rw-r--r--    1 glykos   user      133306 Apr  1 19:35 Qs002_packing.pdb
-rw-r--r--    1 glykos   user       66708 Apr  1 19:44 Qs003_mol_1.pdb
-rw-r--r--    1 glykos   user      133306 Apr  1 19:44 Qs003_packing.pdb
-rw-r--r--    1 glykos   user       66708 Apr  1 19:53 Qs004_mol_1.pdb
-rw-r--r--    1 glykos   user      133306 Apr  1 19:53 Qs004_packing.pdb
-rw-r--r--    1 glykos   user       66708 Apr  1 20:02 Qs005_mol_1.pdb
-rw-r--r--    1 glykos   user      133306 Apr  1 20:02 Qs005_packing.pdb
-rw-r--r--    1 glykos   user         392 Apr  1 09:59 Qs_auto.in
-rw-r--r--    1 glykos   user       44892 Apr  1 09:59 data.hkl
-rw-r--r--    1 glykos   user      196808 Apr  1 19:18 mod_001.ps
-rw-r--r--    1 glykos   user      201390 Apr  1 19:18 mod_010.ps
-rw-r--r--    1 glykos   user      101407 Apr  1 19:18 mod_100.ps
-rw-r--r--    1 glykos   user       80578 Apr  1 09:59 model.pdb

In the case of a multi-model run of the program, you will see something similar to this :

-rw-rw-r--    1 glykos   glykos    2046649 Jul 23 15:28 LOG
-rw-rw-r--    1 glykos   glykos     492202 Jul 19 20:59 Model1_001.ps
-rw-rw-r--    1 glykos   glykos     492202 Jul 19 20:59 Model1_010.ps
-rw-rw-r--    1 glykos   glykos     269308 Jul 19 20:59 Model1_100.ps
-rw-rw-r--    1 glykos   glykos     492202 Jul 19 20:59 Model2_001.ps
-rw-rw-r--    1 glykos   glykos     492202 Jul 19 20:59 Model2_010.ps
-rw-rw-r--    1 glykos   glykos     269308 Jul 19 20:59 Model2_100.ps
-rw-rw-r--    1 glykos   glykos     492202 Jul 19 20:59 Model3_001.ps
-rw-rw-r--    1 glykos   glykos     492202 Jul 19 20:59 Model3_010.ps
-rw-rw-r--    1 glykos   glykos     269308 Jul 19 20:59 Model3_100.ps
-rw-rw-r--    1 glykos   glykos     150202 Jul 22 22:23 Qs001_mol_1.pdb
-rw-rw-r--    1 glykos   glykos      58345 Jul 22 22:23 Qs001_mol_2.pdb
-rw-rw-r--    1 glykos   glykos      54660 Jul 22 22:23 Qs001_mol_3.pdb
-rw-rw-r--    1 glykos   glykos    4205578 Jul 22 22:23 Qs001_packing.pdb
-rw-rw-r--    1 glykos   glykos     150202 Jul 25 03:17 Qs002_mol_1.pdb
-rw-rw-r--    1 glykos   glykos      58345 Jul 25 03:17 Qs002_mol_2.pdb
-rw-rw-r--    1 glykos   glykos      54660 Jul 25 03:17 Qs002_mol_3.pdb
-rw-rw-r--    1 glykos   glykos    4205578 Jul 25 03:17 Qs002_packing.pdb
-rw-rw-r--    1 glykos   glykos     150143 Jul 19 20:59 Qs_1.pdb
-rw-rw-r--    1 glykos   glykos      58286 Jul 19 20:59 Qs_2.pdb
-rw-rw-r--    1 glykos   glykos      54601 Jul 19 20:59 Qs_3.pdb
-rw-rw-r--    1 glykos   glykos       1953 Jul 19 20:59 Qs_auto.in
-rw-rw-r--    1 glykos   glykos     486034 Jul 19 20:59 Transform_Model1_001.ps
-rw-rw-r--    1 glykos   glykos     486034 Jul 19 20:59 Transform_Model1_010.ps
-rw-rw-r--    1 glykos   glykos     266752 Jul 19 20:59 Transform_Model1_100.ps
-rw-rw-r--    1 glykos   glykos     486034 Jul 19 20:59 Transform_Model2_001.ps
-rw-rw-r--    1 glykos   glykos     486034 Jul 19 20:59 Transform_Model2_010.ps
-rw-rw-r--    1 glykos   glykos     266752 Jul 19 20:59 Transform_Model2_100.ps
-rw-rw-r--    1 glykos   glykos     486034 Jul 19 20:59 Transform_Model3_001.ps
-rw-rw-r--    1 glykos   glykos     486034 Jul 19 20:59 Transform_Model3_010.ps
-rw-rw-r--    1 glykos   glykos     266752 Jul 19 20:59 Transform_Model3_100.ps
-rw-r--r--    1 glykos   glykos     927318 Jul 19 18:46 data.hkl
-rw-r--r--    1 glykos   glykos     172542 Jul 19 20:57 model1.pdb
-rw-r--r--    1 glykos   glykos      66975 Jul 19 20:57 model2.pdb
-rw-r--r--    1 glykos   glykos      62740 Jul 19 20:58 model3.pdb

The files data.hkl and model.pdb (or model1.pdb, model2.pdb, ..., in the case of the multi-model mode) is where you started from. File Qs_auto.in is the parameter file generated by QS when you choose the automatic mode (by giving Qs -auto <xxx>). The LOG file is exactly what you think it is. The .ps files are colour postscript files containing projections of the model unit cell and central sections through the molecular transform(s), and are completely useless from the structure determination point of view (they are discussed in more detail under the POSTscript keyword). The file Qs.pdb (or Qs_1.pdb, Qs_2.pdb, ..., in multi-model mode) contain your search model(s) after QS applied a translation and a rotation.

The real results are contained in the files of the form Qs###_mol_#.pdb. These contain the final atomic coordinates of your search model(s) from each of the independent minimisations performed by the program. They are minimal PDB files that should look like this :

REMARK  R-factor  0.0278  Free R-value -1.0000
CRYST1   38.070   33.200   46.120  90.00 110.06  90.00 P 1
ATOM      1  N   LYS     1       8.677  16.604  37.021  1.00 20.00
ATOM      2  CA  LYS     1       7.975  15.873  38.045  1.00 20.00
ATOM      3  C   LYS     1       8.898  14.827  38.643  1.00 20.00
ATOM      4  O   LYS     1       9.843  14.369  37.973  1.00 20.00
..................................................................
ATOM    994  OXT LEU   129       2.565  -5.064  34.429  1.00 20.00
END

(the R_free value was not calculated in this case, which explains the -1.00 value. When the -auto scheme is used, the R_free is calculated). If you had two molecules in the asymmetric unit, then for every Qs###_mol_1.pdb file, you would also be getting a Qs###_mol_2.pdb file as well (containing the coordinates of the second model). To save you some time, for every finished minimisation QS writes out a PDB file (of the form Qs###_packing.pdb) containing the coordinates of all molecules in the asymmetric unit plus their crystallographically related ones (all reseted to lie within a volume of 2x2x2 unit cells). With this file at hand, it is quite easy to check a putative solution for the presence (or otherwise) of bad contacts. ¹⁵

NOTE WELL : If you decided to edit the script file and to define the crystallographic symmetry operators explicitly (through the SYMMetry keyword, QS will know nothing about the lattice type of your space group, and so, all copies of your model(s) that are related by non-primitive symmetry operators will be missing from the Qs###_packing.pdb files. A solution would be to define even the non-primitive symmetry operators with the SYMMetry keyword, but this would at least double the CPU time requirements.

Footnotes

... contacts.¹⁵

If your eyes are trained for side-by-side stereo viewing, then the fastest way to check for bad contacts is via RasMol : just do rasmol Qs003_packing.pdb and then type set unitcell on followed by set stereo on and colour chain. You should now have a coloured side-by-side stereo image of the contents of 2x2x2 unit cells corresponding to the 3rd minimisation.