[PyMOL] Saving each residue to file

2011-08-15 Thread Martin Hediger
Dear List I was wondering if there could be a way of having every residue of a protein structure being saved to a separate file. How could this be done? I believe the 'iterate' method might be useful in combination with the 'byres' identifier, but I havent figured out how to combine them in the

Re: [PyMOL] Saving each residue to file

2011-08-15 Thread Thomas Holder
Hi Martin, there are for sure several ways to achieve this, one might be using the pop command (there is no PyMOLWiki page, but help pop gives a quick example how to use it). fetch 2xwu, async=0 select _justca, byca 2xwu python while cmd.pop(_tmp, _justca): cmd.iterate(_tmp,

[PyMOL] loading gro files

2011-08-15 Thread Michael Daily
Hi all, Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I know it's simple to convert them to pdb using editconf, but I want to load gro files directly (as you can in vmd) because they permit higher max. atom and residue numbers (100K vs. 10K for pdb) and permit longer