[chimerax-users] Coulombic color combined surface

[Cao, Wenxiang]

Dear Elaine:

Thank you so much! I struggled for days trying to achieve it. Yes, you are right and it is the way to do it. The green line in the attached picture is the line between two chains and color is continuously across the interface.

Thanks again!
WC

From: Elaine Meng<mailto:meng at cgl.ucsf.edu>
Sent: Friday, August 13, 2021 4:27 PM
To: Cao, Wenxiang<mailto:wenxiang.cao at yale.edu>
Cc: ChimeraX Users Help<mailto:ChimeraX-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Coulombic color combined surface

Hi WC,
Actually you can do this already:  after creating the surface with "surface enclose," then you have to use the "surfaces" keyword of the "mlp" or "coulombic" command to actually use that pre-existing surface instead of calculating new surfaces (which would just be one per chain, as you said).

Example:
open 1zik
surface #1 enclose protein

[... then you can look in the model panel and see that the surface is #1.1 ...]

mlp surfaces #1.1
... or ...
coulombic surfaces #1.1

 <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmlp.html&data=04%7C01%7Cwenxiang.cao%40yale.edu%7Cb9eaa60881ba43b79c6f08d95e98a861%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637644832493884419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9fGIOGUNxY%2B%2Bd9Q9FPYPBCPThydtr0q%2FK6Vgj2K0Llw%3D&reserved=0>
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoulombic.html&data=04%7C01%7Cwenxiang.cao%40yale.edu%7Cb9eaa60881ba43b79c6f08d95e98a861%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637644832493884419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=VbzzSEy3%2FAg9nR%2Fpk5GJqviM%2Bm7ZHq4zumuxIRnXjPw%3D&reserved=0>

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

P.S. we put this message on the chimerax-users list since it's really a how-to question, not a bug

> On Aug 13, 2021, at 12:52 PM, W. C. via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I  generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210813/abb7a98b/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: color one continuous surface.PNG
Type: image/png
Size: 689295 bytes
Desc: color one continuous surface.PNG
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210813/abb7a98b/attachment-0001.png>