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
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