Re: [PyMOL] question on differential coloring of protein chains

2004-02-18 Thread Michael Bovee
On Tuesday, February 17, 2004, at 02:57 PM, ALEX DAJKOVIC wrote: hello- i am new to pymol and am trying to figure out how to differentially color different chains (i.e. different proteins) in the structure i am viewing. the structure i am working with is actually a structure of two proteins

[PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread John Berrisford
I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript

RE: [PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread Warren DeLano
John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01,

FW: [PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread David A. Horita
Warren, Personally, I'd much rather have wild-card selections in atom names and have to deal individually with the ill-conceived PDB files than the other way around. Regards, David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net

[PyMOL] wild card

2004-02-18 Thread Eric Zollars
Anyone who works with nucleic acids will certainly prefer the current situation. From the PDB format guidelines: * The asterisk (*) is used in place of the prime character (') for naming atoms of the sugar group. The prime was avoided historically because of non-uniformity of its external

RE: [PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread Warren DeLano
-Original Message- From: Charlie Sent: Wednesday, February 18, 2004 8:56 AM To: Warren DeLano Subject: Re: [PyMOL] selecting multiple atoms ie oxygen Warren DeLano wrote: John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names

Re: [PyMOL] PyMOL/MacPyMOL Beta Feedback

2004-02-18 Thread Nick Skelton
Hi there Warren, I have been using the v0.94 MacPyMOL that we got from you last december. It has been very stable on my desktop system: dual cpu G4867 MHz power PC (version 2.1) OSX 10.2.8 (6R73) v0.94 However, using the same version on my lap top has not been so reliable G4

[PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-18 Thread Buz Barstow
Hi, I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm having trouble ray tracing graphics. I installed Pymol from the source file pymol-0_93-src.tgz. Each time I start the ray tracer Pymol quits with a segmentation fault error; /usr/local/pymol/pymol.com: line 2: 29720

[PyMOL] molecular surface colored by hydrophobicity

2004-02-18 Thread guanr
Dear all, I am preparing a figure of a molecualr surface, colored by the hydrophobicity of surface residues. Can pymol do this job? How about showing atom C* in a color, and N* and O* in another color? In fact I have tried GRASP but failed in coloring the surface. I used r=hyd, but could not

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-18 Thread Thomas Siegmund
Dear Buz, I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm having trouble ray tracing graphics. Each time I start the ray tracer Pymol quits with a segmentation fault error; I guess you are running into a compiler bug (or a bug in PyMol which gets exposed only by