Re: [PyMOL] problem with pymol on FC6

2008-08-21 Thread DeLano Scientific
Jhon, This sounds like a typo in your bashrc file, wherein code is being accidentally run instead of being used to define a path or alias, etc. Another possibility could be that the Terminal application has somehow stored some kind of state that is being restored on launch (this used to happen

[PyMOL] how to outline as in ray_trace_mode=2

2008-08-21 Thread O. J. Ganesh
Hey once again everyone, This is along the lines as my previous questions... When I do: set ray_trace_mode, 2; It produces a 'black and white image', however this really is of the outlines of the objects in the model. Is there a way I can manually make certain objects into this outline

[PyMOL] hydrogen naming

2008-08-21 Thread David A. Horita
Hi, How do I get proper (HN,HA, HE1, etc) hydrogen naming when using h_add (instead of H01, H02, ...)? Worst case I can build them in Xplor/CNS; second worst would be if there is a uniform rule per residue that I could write a script to convert on a residue type basis. Thanks, Dave

[PyMOL] Selecting Negative Residues

2008-08-21 Thread Buz Barstow
Dear All, Does anyone know how to select residues with negative sequence numbers in Pymol? I have a protein molecule with two residues with negative sequence numbers (-2 and -1). When I issue the command: cmd.select('temp', 'resi -2 and name CA') Pymol selects the alpha carbons of

Re: [PyMOL] hydrogen naming

2008-08-21 Thread Schubert, Carsten [PRDUS]
phenix.reduce is an option -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of David A. Horita Sent: Thursday, August 21, 2008 3:32 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] hydrogen naming

Re: [PyMOL] Selecting Negative Residues

2008-08-21 Thread Buz Barstow
Hi Warren, Thanks! That did the trick. All the best, --Buz On Aug 21, 2008, at 4:25 PM, DeLano Scientific wrote: Buz, This is something PyMOL didn't handle well until recently, but I think you can now prefix the minus sign with a backslash in order to force PyMOL to interpret the