Multiple redundant dihedral restraint lists from talos+ exported to xplor for refinement

[GoogleCodeExporter]

Talos-predicted dihedral restraints are exported xplor for refinement along 
with other dihedral restraint lists possibly also originating from talos+. As a 
result, the forces on most dihedrals are twice as high.

We have three options
- only use talos+ predictions if no dihedral restraint list (covering most of 
the residues in the molecule) was deposited
- use both, unless we can figure out (how??) if the deposited dihedral 
restraint list was also predicted by talos+
- always use both (now).

What has your preference?

The issue affects all entries with deposited chemical shifts (for which talos+ 
runs in NRG-CING). 

Furthermore, the label 'talos_plus_predicted_dihedrals' is lost upon export to 
xplor and is stored as 'ACL_00n.tbl' where n is 1+(the number of the last 
deposited dihedral restraint list): e.g. (2lt9)

-- doSetup --
----------- Project: 2lt9 -----------
created:    Fri Aug  3 01:55:53 2012
molecules:  [<Molecule "2lt9" (C:1,R:157,A:2860,M:20)>]
peaks:      []
distances:  [<DistanceRestraintList "distance_constraint_list" (keep,2901)>]
dihedrals:  [<DihedralRestraintList "dihedral_constraint_list" (keep,186)>, 
<DihedralRestraintList "talos_plus_predicted_dihedrals" (keep,223)>]
rdcs:       []
coplanars:  []
----------------------------------------------
==> validateRestraints, output to 2lt9.cing/2lt9/Cing/restraints.txt
==> Superposing: fitted <Molecule "2lt9" (C:1,R:157,A:2860,M:20)> on 402 atoms 
(residues=cv, backboneOnly=True, includeProtons=False)
==> Calculating rmsd's (ranges: 528-604,612-668, models: 0-19)
==> Exporting <Project 2lt9> to 2lt9.cing/Refine/2lt9_redo for refinement
==> Exported <DistanceRestraintList "DRL_001" (keep,2901)> to 
"2lt9.cing/Refine/2lt9_redo/Tables/DRL_001.tbl"
==> Exported <DihedralRestraintList "ACL_001" (keep,186)> to 
"2lt9.cing/Refine/2lt9_redo/Tables/ACL_001.tbl"
==> Exported <DihedralRestraintList "ACL_002" (keep,223)> to 
"2lt9.cing/Refine/2lt9_redo/Tables/ACL_002.tbl"

At the end of a redo run, the talos+ prediction is run again, and another 
talos+ restraint list is stored, now as talos_plus_predicted_dihedrals, so that 
talos_plus_predicted_dihedrals and ACL_00n.tbl are identical: 

==> Running talos+ ... Done!
==> Created <DihedralRestraintList "talos_plus_predicted_dihedrals" (keep,223)>
==> Saved talos+ results to "2lt9.cing/2lt9_redo/talosPlus/talosPlus.sml"
...
==> Analyzing <DistanceRestraintList "DRL_001" (keep,2901)>, output to 
2lt9.cing/2lt9_redo/Cing/DRL_001.txt
==> Analyzing <DihedralRestraintList "ACL_001" (keep,186)>, output to 
2lt9.cing/2lt9_redo/Cing/ACL_001.txt
==> Analyzing <DihedralRestraintList "ACL_002" (keep,223)>, output to 
2lt9.cing/2lt9_redo/Cing/ACL_002.txt
==> Analyzing <DihedralRestraintList "talos_plus_predicted_dihedrals" 
(keep,223)>, output to 
2lt9.cing/2lt9_redo/Cing/talos_plus_predicted_dihedrals.txt
...
==> Saving <DistanceRestraintList "DRL_001" (keep,2901)> to 
2lt9.cing/Data/Restraints/DRL_001.distances
==> Saving <DihedralRestraintList "ACL_001" (keep,186)> to 
2lt9.cing/Data/Restraints/ACL_001.dihedrals
==> Saving <DihedralRestraintList "ACL_002" (keep,223)> to 
2lt9.cing/Data/Restraints/ACL_002.dihedrals
==> Saving <DihedralRestraintList "talos_plus_predicted_dihedrals" (keep,223)> 
to 2lt9.cing/Data/Restraints/talos_plus_predicted_dihedrals.dihedrals
==> Saved talos+ results to "2lt9.cing/2lt9_redo/talosPlus/talosPlus.sml"

Original issue reported on code.google.com by WGTouw on 20 Dec 2012 at 11:21

[GoogleCodeExporter]

Sounds like an executive decision needs to be made.
Technically, it might not be that hard to update CING to give the talos derived 
ones an id that is clearly indicating it's nature. I've added that in several 
places already.
You can find the places here:
http://code.google.com/p/cing/source/search?q=TALOSPLUS_CLASS_STR

Original comment by jurge...@gmail.com on 20 Dec 2012 at 2:47

[GoogleCodeExporter]

This issue was closed by revision r1201.

Original comment by WGTouw on 21 Dec 2012 at 10:52

• Changed state: Fixed