[PyMOL] writing out coordinates
Hey Warren, I've done a structural alignment of 2 domains using your align command. How do I write out the new coordinates? Craig
[PyMOL] two_sided_lighting
Hello everybody, For two_sided_lighting, is there a way to change the relative brightness of the two lights? Thanks, Meitian Wang
RE: [PyMOL] two_sided_lighting
Meitian, Sorry, this is not possible. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of M Wang Sent: Monday, September 22, 2003 9:49 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] two_sided_lighting Hello everybody, For two_sided_lighting, is there a way to change the relative brightness of the two lights? Thanks, Meitian Wang --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] HELP Load biological unit
Dear All, Help, I don't know what I am doing wrong. I want to load a dimer into pymol, 3GRS, the standard PDF file from the PDB bank only gives co-ordinates for a monomer but if I download the PDB file for the biological unit http://www.rcsb.org/pdb/cgi/explore.cgi?job=downloadpdbId=3GRSpage=0pid=1521064246710 ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/gr/3grs.pdb1.gz If I load 3grs.pdb1 into pymol it still only shows a monomer. If I edit out ENDMDL after the co-ordinates for the first monomer , pymol will then show a dimer with sidechains or sticks but if I try to draw a cartoon it messes up and draws the ribbons ect all wrong. I tried to also change all the A's in the second set of co-ordinates to B's indicating subunit B but still it does not work. Is there a program I can use that will fix my pdb files downloaded from pdb bank into correct format for pymol? Also, once I get the dimer loaded properly I want to colour each of the four domains. How will I do that? Mac OS X 10.2.6 / x11 0.3 / pymol-0_90-bin-osx.dmg Well I managed to make it work after editiing out all the ENDMDL comments and making the second subunit with B's and duplicating the comments for Helix and Sheets then replacing A'S with B . Are these errors in the original biological unit file or a bug in pymol? Also still tring to work out how to label eg residues 1-124 red 125-250 blue ect, how do I do this? Asam
[PyMOL] RE:
One quick question... how do I tell PyMOL to draw a cylinder (or bond) of a given radius between two positions X,Y,Z and X', Y',Z'? (From Python...) from pymol.cgo import * from pymol import cmd obj = [] obj.extend( [ CUSTOM_CYLINDER, 1.0, 2.0, 3.0, # XYZ 1 4.0, 5.0, 6.0, # XYZ 2 2.0,# Radius 1.0, 1.0, 1.0, # RGB Color 1 1.0, 1.0, 1.0, # RGB Color 2 1, 1, # End caps (0=none, 1=flat, 2=round) ] ) cmd.load_cgo(obj,'my_cgo') Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
