[bug #21598] Considering molecule numbers when writing pyMol (or Molmol) macros -- February 05, 2014 - 11:16

URL:
  <http://gna.org/bugs/?21598>

                 Summary: Considering molecule numbers when writing pyMol (or
Molmol) macros
                 Project: relax
            Submitted by: mab
            Submitted on: Wed 05 Feb 2014 10:16:04 AM GMT
                Category: relax's source code
Specific analysis category: Model-free analysis
                Priority: 5 - Normal
                Severity: 1 - Wish
                  Status: None
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: 3.1.5
         Discussion Lock: Any
        Operating System: All systems

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Details:

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.

Cheers,
Martin





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