Dear ChimeraX Team, I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities). Thank you for your help and attention! Andrea
Hi Andrea, The way that the "clashes" tool and command do it are to draw straight lines between the pairs of atoms that clash. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> There is no way I can think of in ChimeraX to draw arbitrary squiggly lines. The only related approaches that I can think of are to - use a 2D Labels symbol like a circle (you can use any size/color and drag it to wherever you want) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html> - use a 2D Labels arrow (you can use any size/color and control where the endpoints are) - select some item (you can change the selectionoutline color from the default green to some other color) but then the outline will go all the way around that item <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> However, there is no option to just draw a line freehand on top of the image. However, most image-editing programs have a simple drawing tool to do it. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 21, 2022, at 1:38 PM, Andrea Dallapè via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team,
I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities).
Thank you for your help and attention!
Andrea
<image.png>
Andrea, I've made a script that does approximately what is in your picture. You give it two atom selections, and it will display the VDW radii of atoms in one group that intersect with the other group. A red line (it's really a bunch of small red spheres, but I think it looks fine) is added at the intersection. Opening the script will add the "displayClash" command. To make the attached image, I defined a selector called "BINAP" and another called "EDA" for the two ligands on this structure. Then, I ran "displayClash EDA with BINAP". The command also has a 'scale' option to scale the VDW radii, and a 'color' option to change the intersection color (e.g. "displayClash EDA with BINAP scale 1.2 color purple"). If you don't want to see the red intersection through the VDW radii, you can make it slightly transparent. ChimeraX doesn't display transparent things that are behind other transparent things. I've attached the Python script as a .txt file because Outlook doesn't like Python files. You'll have to change the extension to .py before trying to open it in ChimeraX. Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Andrea Dallapè via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Saturday, May 21, 2022 4:38 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] (no subject) [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Dear ChimeraX Team, I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities). Thank you for your help and attention! Andrea
Hi Tony, thank you so much! This is what I was looking for! Andrea Il giorno dom 22 mag 2022 alle ore 23:06 Anthony James Schaefer < tony.schaefer@uga.edu> ha scritto:
Andrea,
I've made a script that does approximately what is in your picture. You give it two atom selections, and it will display the VDW radii of atoms in one group that intersect with the other group. A red line (it's really a bunch of small red spheres, but I think it looks fine) is added at the intersection.
Opening the script will add the "displayClash" command. To make the attached image, I defined a selector called "BINAP" and another called "EDA" for the two ligands on this structure. Then, I ran "displayClash EDA with BINAP". The command also has a 'scale' option to scale the VDW radii, and a 'color' option to change the intersection color (e.g. "displayClash EDA with BINAP scale 1.2 color purple").
If you don't want to see the red intersection through the VDW radii, you can make it slightly transparent. ChimeraX doesn't display transparent things that are behind other transparent things.
I've attached the Python script as a .txt file because Outlook doesn't like Python files. You'll have to change the extension to .py before trying to open it in ChimeraX.
Best,
Tony ------------------------------ *From:* ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Andrea Dallapè via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Sent:* Saturday, May 21, 2022 4:38 PM *To:* ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> *Subject:* [chimerax-users] (no subject)
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Dear ChimeraX Team,
I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities).
Thank you for your help and attention!
Andrea
participants (3)
-
Andrea Dallapè -
Anthony James Schaefer -
Elaine Meng