Hi Lorenzo,
You could make an object out of the elastic bonds with the 'create' command,
show it as sticks, and use the stick_color setting to color the sticks only.
You could make different objects for different subsets of the elastic bonds and
color them differently.
Here is an example of the 'create' command that I used to make an object out of
six coordinate covalent bonds between a sodium, a N7 nitrogen of an adenine,
and five waters.
cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or resi
319 or resi 419 or resi 519 or (resi 3 and name N7)))')
cmd.set('stick_color','magenta','coorCov')
cmd.show('sticks','coorCov')
The color of the atoms, if shown as spheres, will remain the same.
Although the above two commands are in the Python form, you can paste them onto
the top command line in PyMOL.
By specifying the object as your selection in the argument to the set command,
you can also change the thickness of the sticks in only than object so
you can have sticks of different thickness in the same scene.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Lorenzo Gaifas [[email protected]]
Sent: Wednesday, December 11, 2019 8:38 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
representation
Dear pymol users,
I'm trying to properly represent a coarse-grained protein model that has an
elastic network.
I would like to show the bonds that are part of the elastic network with a
different color (and possibly representation) from the normal bonds between
atoms. However, as far as I know, color settings are atom-based, so I wasn't
able to do what I wanted, because all bonds that lead to an atom will always
share the same color.
The only solution I found was to create a copy of the protein with pseudoatoms
and draw the elastic network there. However, I expect this has a negative
effect on the performance, which is relevant since I plan to use this for
molecular dynamics trajectories.
Am I trying to do this the wrong way? Is it just unfeasible?
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