Re: [PyMOL] Color change of different domain

mment ? Thanks Mohammad On Thu, Aug 16, 2018 at 1:24 AM John Berrisford mailto:j...@ebi.ac.uk> > wrote: Dear Mohammad Please see the PDB plugin which colours each sequence or structural domain differently. https://pymolwiki.org/index.php/PDB_plugin This is used to produce th

Re: [PyMOL] Color change of different domain

Dear Mohammad Please see the PDB plugin which colours each sequence or structural domain differently. https://pymolwiki.org/index.php/PDB_plugin This is used to produce the images on the PDBe web pages. For example see a titin with multiple copies of a CATH domain. https://www.ebi.ac

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

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 Cam

Re: [PyMOL] status of Uppsala EDS server?

nt URL for getting electron density maps and > difference maps? (Which I think is at EBI, right?) > > Bob > -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Te

Re: [PyMOL] pdbml

On 23 Sep 2015, at 03:27, Arthur Zalevsky > >>> > >>> wrote: > >>>> Sorry for bumping old thread, but is support for pdbml still > >>>> unimplemented? In such case i think it's a good project for our > >>>> students. > >>>> > >>>> Regards, > >>>> Arthur > >>>> > >>>&

Re: [PyMOL] Pymol crash when raytracing empty graphics

gt; 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 European Bioi

[PyMOL] shadows on floors

Also as a side note, 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 Uni

[PyMOL] sphere sizes

1" 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 Dep

RE: [PyMOL] drawing hydrogen bonds or dashes

elp with MN.) > > If you don't want dashes, then > >set dash_length, 3 >set dash_gap, 0 > > Seems to work for me... > > Cheers, > Warren > > > > -Original Message- > > From: pymol-users-ad...@lists.sourcefor

[PyMOL] drawing hydrogen bonds or dashes

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 no

[PyMOL] selecting multiple atoms ie oxygen

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 i