Hi Tim and Carsten, I wonder what exactly you have tried so far to change the color of the alignment object. In fact, the "color" command should do the job.
Example: fetch 1oky 1t46, async=0 align 1oky, 1t46, object=aln color blue, aln I don't think that two-color gradients were ever intended, and I don't remember which version of PyMOL created them. That might have been a bug. Cheers, Thomas On 11 Jan 2016, at 09:19, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Hi Tim, > > I ran into the same issue a while back as well. I gets complicated very > quickly when you dive deeper into the subject. Your are right the colors of > the CGO lines seem to be hardcoded. A way to get around this is to extract > the matching residues with cmd.get_raw_alignment(alignment_object). The > result is a tuple of tuples of matching atoms as determined by the alignment > algorithm. You could then take these atoms pairs and draw distance lines > between them. These distance lines can be customized with color, linewidth, > etc. > > It has been a while since I worked on this, but I believe that the assignment > of pairs is a non-trivial issue and sometimes fraught with mismatches. So > manual checking against a sequence alignment is always a good idea especially > for rather unrelated proteins. > > I do have a script which can accomplish this, it is based on > “colorbyrmsd.py”. However it is not ready for primetime, but I can share this > with you if there is interest. Contact me offline to arrange something. > > Cheers, > > Carsten > > From: Timothy Umland [mailto:uml...@gmail.com] > Sent: Sunday, January 10, 2016 9:08 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] OBJECT argument in ALIGN command - color > > > > Hi: > > I am trying to use the Alignment Objects (i.e., lines between the paired > aligned atoms) created by using the OBJECT argument of the ALIGN command to > illustrate domain movement between the superimposed ligand-bound and unbound > forms of an enzyme. > > I successfully made the basic aligned image, and now I want to tweak it. > > Is it possible to change the color of the Alignment Object lines between > paired atoms? For me, they display only in yellow. From what I have read > online these lines are CGO objects with the color hardwired in upon creation, > and so it can’t be changed in PyMol latter on. However, I haven’t been able > to find a way to assign a color upon creation. Is there a way to assign a > specific color? > > Additionally, I have seen this type of image where the lines between the > paired aligned atoms are two colors, with half of the line in one color (say > blue) and the other half another color (say red) to better illustrate which > protein is the origin of each end of the connecting line. I haven’t > discovered a way to make these bi-colored lines in ALIGN. Any ideas? > > I have tried the open source version 1.8.0, plus several earlier versions > from various origins (all on Macs) with similar results. > > > Thanks much for any ideas. > > Tim > > Tim Umland, Ph.D. > Hauptman-Woodward Institute -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
