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> 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]
> 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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