Hi Krish, I added the "measure contactArea" command to ChimeraX needed to make the image you asked about. It will be in ChimeraX daily builds dated April 4, 2024 or newer. The commands to make the image are slightly different in ChimeraX and I've attached the modified command script needed to make the image in ChimeraX. Tom

On Apr 1, 2024, at 8:33 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

...

On Mar 31, 2024, at 7:59 PM, Krishnan Raman <RKrishnan@BIOCRYST.com> wrote:

https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.htm... Hi Elaine, How can I mimic this image with chimerax? Thanks Krish

Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals

Hi Krish, That Chimera example includes a Chimera command script that uses a "measure contactArea" command with a "slab" option to draw a surface. <https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.htm...>

However, I can't think of a way to do it in ChimeraX, since as far as I know there is no analogous command in ChimeraX currently. ChimeraX has "measure buriedArea" but it does not have an option to create a surface model of just the contact region.

Maybe others have ideas?

Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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