Re: [PyMOL] Drawing lines between residues

Hi Jorge, I have written a script that will draw lines between arbitrary pairs of atoms using CGO cylinders. The script is called "draw_links.py" and can be found on my script page: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Besides listing the pairs of atoms to connect you can

Re: [PyMOL] Drawing lines between residues

Hi Jorge and Blaine Another was to do this is to take a measurement between the residues and then use the command, “set dash_gap, 0” This will also allow you to control the thickness of the lines using the “set dash_radius” command Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate &

Re: [PyMOL] [EXTERNAL] Drawing lines between residues

Hi Jorge, You can use the "bond" command if the structures to be linked are in the same molecular object. You may have to use the "create" command with both objects in a selection to merge two objects into one. bond [atom1, atom2 [,order]] You can control the bond thickness via the

[PyMOL] Drawing lines between residues

Hi all. I have a list of pairs of residues. I want to draw lines between the residues in each pair. The lines can have different colors. So in the end I would like to achieve a figure like this one: [image: 2019-10-15.png] What commands can I use to get this done in PyMOL? Thanks

Re: [PyMOL] dots with/without ray tracing

Hi Vaheh, Try this: set dot_radius, 0.1 set dot_as_spheres Cheers, Thomas > On Oct 15, 2019, at 9:53 PM, Oganesyan, Vaheh > wrote: > > Hello PyMOLers, > > Figure that contains dots getting unwanted metamorphosis after ray tracing > (figures before ray tracing and after are attached).

Re: [PyMOL] feature request

Hi Jared and Vaheh - We've implemented two modes and pushed the change to the github repository. set internal_gui_name_color_mode, set internal_gui_name_color_mode, 2 Mode 1 is color by first carbon color. We think this is the most relevant use case and what the user typically would expect.