Re: [PyMOL] syntax for lone pair removal

2012-05-29 Thread Thomas Holder
Hi Martin, > when visualising data out of a GOLD docking run, where the software > has added lone pairs to active site residues and ligands is it > possible to remove them post hoc in Pymol? The "atoms" look like: > > 62 45.6415 30.9229 12.1185 LP 1 <1> > 0. the at

[PyMOL] syntax for lone pair removal

2012-05-29 Thread Martin Stoermer
Hi folks, when visualising data out of a GOLD docking run, where the software has added lone pairs to active site residues and ligands is it possible to remove them post hoc in Pymol? The "atoms" look like: 62 45.6415 30.9229 12.1185 LP 1 <1> 0.00

[PyMOL] regarding slerpy

2012-05-29 Thread ccp4 pymol
Hi This is my first post to pymol-users lists. I have a problem regarding usage of slerpy. Firstly i must admit that i have no clue of how to go about using it in the first place. I know the pymol wiki has the list of commands but do not know how to exploit them in a real case. If someone can sugg

Re: [PyMOL] problems with pse file

2012-05-29 Thread Jason Vertrees
Hi Jen, We need more information before we can try to help. When you create a session on computer A and try to load it on computer B the visualization is incorrect, right? Does this also happen when you create the session on computer B and try to load it on computer A? What versions of PyMOL are

Re: [PyMOL] calculate the rotation angle of a certain helix in structures with different ATP analogues

2012-05-29 Thread Thomas Holder
Hi Xinghua, you can install the "psico" module which provides commands for both of your tasks: * angle_between_helices * angle_between_domains PyMOLWiki page: http://pymolwiki.org/index.php/Psico Direct download link: https://github.com/speleo3/pymol-psico/zipball/master After having inst