Re: [PyMOL] Memory not released after load and delete of structure

2013-01-21 Thread Gianluigi Caltabiano
The suspension of undo  doesn't have any effect on my accumulation of GB when working with Hybrid PyMol... Gianluigi Da: Thomas Holder A: pymol-users@lists.sourceforge.net Inviato: Venerdì 21 Dicembre 2012 17:31 Oggetto: Re: [PyMOL] Memory not released after

[PyMOL] Renumber Script problem

2013-01-21 Thread Alex Truong
Hi All, I've been having a bit of trouble recently with the renumber script. I have a pdb file that I'm trying to renumber, but unlike the other times I've used it, it is renumbering incorrectly. The numbers are usually spaced out 5 residues apart, but I have one number right near the beginning th

Re: [PyMOL] Renumber Script problem

2013-01-21 Thread Jordan Willis
Does it have to be a pymol script. Renumbering pdbs is the bread and butter of biopython pdb module: #!/blue/meilerlab/apps/Linux2/x86_64/bin/python2.5 import sys from Bio.PDB import * from optparse import OptionParser import warnings def main(): usage = "%prog input.pdb output.pdb" parse

Re: [PyMOL] Renumber Script problem

2013-01-21 Thread Thomas Holder
Hi Alex, the renumber script only sets the residue number, it does not reorder atoms internally. Just type PyMOL> sort to sort internally based on the new residue numbers. See also: http://pymolwiki.org/index.php/Sort Cheers, Thomas Alex Truong wrote, On 01/21/13 19:21: > Hi All, > > I've

Re: [PyMOL] Renumber Script problem

2013-01-21 Thread Thomas Holder
Hi Jordan, nice script, but it does not do the same like the renumber script from the PyMOLWiki (http://pymolwiki.org/index.php/Renumber). Try this: set all residue numbers to 1, the renumber script will not care because it walks along the bonds and increases the count whenever it passes a peptide