Hi Lorenzo, The use the lines instead of sticks may reduce the anticipated hit on performance. There is a line_color setting that use you can.
Best regards, Blaine ________________________________________ From: Lorenzo Gaifas [bris...@gmail.com] Sent: Wednesday, December 11, 2019 9:48 AM To: Mooers, Blaine H.M. (HSC) Cc: pymol-users Subject: Re: [EXTERNAL] [PyMOL] Differentiate between bond types by color and representation Hi Blaine, Yes, that's essentially what I'm doing. My worry is that since this doubles the amount of coordinates to keep track of, it will be detrimental to how long a trajectory I can load. Is there any other way to do this? On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu<mailto:blaine-moo...@ouhsc.edu>> wrote: 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 [bris...@gmail.com<mailto:bris...@gmail.com>] 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? _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
