[Chimera-users] Creating discs

[Elaine Meng]

Hi Prathvi,
Both Chimera and ChimeraX have an "Axes/Planes/Centroids" tool and also a "define" command to create planes, etc. from sets of atoms.

However, the "atoms" that are showing the membrane boundary locations are from the Orientations of Proteins in Membranes (OPM) database as described in the link that you sent.  So you have to first get the PDB file from that database with the extra membrane "atoms," then use the tool or command mentioned above to show these sets of atoms as planes (discs).

The link that you sent describes the Chimera process.
<https://www.cgl.ucsf.edu/chimera/ImageGallery/framedD3R.html>

The following and links therein (including an example script that does everything and the example PDB from the OPM database) describe the ChimeraX process:
<https://www.rbvi.ucsf.edu/chimerax/features.html#axesplanes>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 13, 2023, at 4:43 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> Is it possible in chimera or chimeraX to create such planes for membrane proteins which show the plasma membrane boundaries as shown in: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedD3R.html
> If yes, then kindly tell me how to do it.