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 _______________________________________________________ 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 _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?21598> _______________________________________________ Message sent via/by Gna! http://gna.org/ _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel