Hi Lorenzo and Blaine, There is a "set_bond" command which can set (some) settings for individual bonds.
To change stick color and radius for the bond between atom 2 and 3: set_bond stick_color, yellow, index 2, index 3 set_bond stick_radius, 0.2, index 2, index 3 Cheers, Thomas > On Dec 11, 2019, at 4:57 PM, Mooers, Blaine H.M. (HSC) > <blaine-moo...@ouhsc.edu> wrote: > > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ 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
