[Chimera-users] Creating discs

[Prathvi Singh]

Thank you once again!

On Mon, 13 Mar, 2023, 21:16 Elaine Meng, <meng at cgl.ucsf.edu> wrote:

> 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.
>
>
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