[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

[PyMOL] drawing hydrogen bonds or dashes

2004-02-19 Thread John Berrisford
I have searched the manual and forum and cannot find how to draw a hydrogen bond between two specific atoms. I wish to do the equivalent to the following molscript command line position res-atom A97 OE1 to position res-atom M200 MN; which draws a line between two atoms A97 OE1 and Mn200. So not

RE: [PyMOL] drawing hydrogen bonds or dashes

2004-02-20 Thread John Berrisford
for me... Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Berrisford Sent: Thursday, February 19, 2004 10:09 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL

[PyMOL] sphere sizes

2004-02-26 Thread John Berrisford
in the script and effectively ignore any previous sphere_scale command. Am I doing something wrong and there is another, better way of doing this, for example linking the size command to an object? I have been so far unable to work out how to do this. Thanks John -- John Berrisford Department

[PyMOL] shadows on floors

2004-03-24 Thread John Berrisford
, what are the rgb codes that pymol uses, are they standard 0 to 1 (the same as molscript) or 0 to 255? Using some of the rgb codes from molscript only seems to produce a grey background. Thank you John -- John Berrisford Department of Molecular Biology and Biotechnology University of Sheffield

Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread John Berrisford
suggestions on ensuring that there are some polygons in frame would also be appreciated. Say, if there was a way to detect that cartoon would fail so that I can switch to a lines or nonbonded representation (I wish that was the default fallback for cartoon). Thanks, Spencer -- John Berrisford PDBe

Re: [PyMOL] Selection of chains based on PDB header

2017-06-15 Thread John Berrisford
ts.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton