bugrelax - Bugs: bug #21598, Considering molecule numbers when...

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bug #21598: Considering molecule numbers when writing pyMol (or Molmol) macros

Submitted by:  Martin Ballaschk <mab>
Submitted on:  Wed Feb 5 10:16:04 2014  
Category: relax's source codeSpecific analysis category: Model-free analysis
Priority: 5 - NormalSeverity: 1 - Wish
Status: PostponedAssigned to: None
Originator Name: Open/Closed: Open
Release: 3.1.5Operating System: All systems

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Tue Nov 11 16:36:09 2014, comment #2:

This is being postponed as no reasonable solution can currently be found.

Edward d Auvergne <bugman>
Project Administrator
Mon Feb 17 17:05:43 2014, comment #1:

This issue is discussed here:

Troels E. Linnet <tlinnet>
Project Member
Wed Feb 5 10:16:04 2014, original submission:

Hi Edward.

Relax automatically creates mappings of the various model-free parameters onto the loaded structure by generatiing .pml (or Molmol .mac) scripts/macros. To use them, the PDB structure has to be opened in PyMol, and then the mapping script has to be run.

The problem: when loading the mapping script, all chains of the current molecule are treated the same, i.e. the values are not only mapped to chain A of my multimer, but also onto chain B, C, etc.

The reason is that these mappings are based on residue numbers only. To make one's life easier, all present molecules should be treated individually.

E.g., Instead of:
select pept_bond, (name ca,n AND resi 2) or (name ca,c AND resi 1)

it should read:
select pept_bond, (name ca,n AND resi 2 AND chain A) or (name ca,c AND resi 1 AND chain A)

in the pymol script.

To fix this, one just would have take into account the molecule number that is read by relax:

structure.read_pdb(file='XYZ.pdb', read_mol=1)

"Molecule 1" would translate into "chain A", "molecule 2" to "chain B" , etc in the PyMol script, by looping over the molecules present, assuming all present molecules have been loaded from the same pdb. If the different molecules are loaded from different files, the molecule-chain mapping would make little sense. One way to circumvent this problem could be something like a "multimer" flag to tell relax to specify molecule/chain numbers.

I don't know what the scripts would look like if there are several molecules loaded into relax at the same time. If there is no seperate treatment for them, a fix like this would probably help.


Martin Ballaschk <mab>


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    Follows 1 latest change.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue Nov 11 16:36:09 2014bugmanStatusNone=>Postponed
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