Re: [PyMOL] pdbml

2015-10-22 Thread Arthur Zalevsky
Hi Thomas, thank you very much for help. Since PDB made pdbml default for large systems (i'm particularly interested in ribosomes) it was a kind of pain. And it seems i have to upgrade my PyMOL and read documentation more often: help for fetch in PyMOL from svn shows '{default: cif (default wa

Re: [PyMOL] pdbml

2015-10-22 Thread Thomas Holder
Hi Arthur, The script I sent you earlier had one Incentive PyMOL specific line and won't work in Open-Source PyMOL unless you delete that line. My apologies. However, if you are compiling the latest code from SVN you don't need the script, I already have incorporated it into the code base! Simp

Re: [PyMOL] pdbml

2015-10-22 Thread Arthur Zalevsky
Hi Thomas! I've tried your parser with pymol 1.4.1 from ubuntu 12.04 repos and freshly compiled 1.7.7.2 from svn with no luck at all. I've tried to load PDB ID 4V50 (full E.coli ribosome). Pymol simply hangs with 100% cpu usage. From 1.4.1 i've got following traceback (after i left it overnig