Hi Hernando, Although we don’t have the general color by attribute capability in ChimeraX yet, there is hydrophobicity surface coloring using the ChimeraX “mlp” command (molecular lipophilicity potential). For example, open 1bxw mlp Documentation https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> The PDB uses ChimeraX mlp for hydrophobicity images on their structure web pages, for example 1BXW image from the PDB web site below. http://www.rcsb.org/structure/1BXW Tom

On Mar 6, 2018, at 8:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Hernando, As mentioned in a recent post and also in the “Missing Features” on the download page, ChimeraX does not yet have coloring by attribute value, sorry.

<http://www.rbvi.ucsf.edu/chimerax/download.html> <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-February/000212.html>

In Chimera you could try making a molmap surface, coloring the atoms under that surface by attribute, and then using Color Zone to color the surface to match the nearby atoms. See #3 in the surface workarounds page:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

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 6, 2018, at 6:10 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:

Dear ChimeraX Is it possible to color a surface by atom/residue attribute (hydrohobicity, charge)? I know it is possible to do it in ucsf-chimera but unfortunately surface calculation does not work in chimera for the files I am working on. Thanks Hernando

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

I’m glad you found a solution! Ah yes, for completeness I should have mentioned that ChimeraX does have coloring by map value (volume data, values on a 3D grid). For example, you could color a surface by electrostatic potential (ESP) if you created an ESP map file using another program and then opened it in ChimeraX. The “mlp” command mentioned by Tom automatically calculates a “lipophilic potential” map and then uses it for coloring. Coloring by map value: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> Elaine

On Mar 6, 2018, at 11:27 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:

Thanks this would work. I also tried the chimera workarounds to display surfaces of problematic molecules and found that changing the vdw radii vdwdefine +.01 as suggested solved the problem. The graphics and lighting of chimeraX are nicer though.

Thanks

Hernando

From: Tom Goddard [mailto:goddard@sonic.net] Sent: Tuesday, March 06, 2018 1:01 PM To: chimerax-users@cgl.ucsf.edu Cc: Hernando J Sosa Subject: Re: [chimerax-users] Surfaces & color by attribute

Hi Hernando,

Although we don’t have the general color by attribute capability in ChimeraX yet, there is hydrophobicity surface coloring using the ChimeraX “mlp” command (molecular lipophilicity potential). For example,

open 1bxw mlp

Documentation

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html

The PDB uses ChimeraX mlp for hydrophobicity images on their structure web pages, for example 1BXW image from the PDB web site below.

http://www.rcsb.org/structure/1BXW

Tom

On Mar 6, 2018, at 8:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Hernando, As mentioned in a recent post and also in the “Missing Features” on the download page, ChimeraX does not yet have coloring by attribute value, sorry.

<http://www.rbvi.ucsf.edu/chimerax/download.html> <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-February/000212.html>

In Chimera you could try making a molmap surface, coloring the atoms under that surface by attribute, and then using Color Zone to color the surface to match the nearby atoms. See #3 in the surface workarounds page:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

I hope this helps, Elaine

On Mar 6, 2018, at 6:10 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:

Dear ChimeraX Is it possible to color a surface by atom/residue attribute (hydrohobicity, charge)? I know it is possible to do it in ucsf-chimera but unfortunately surface calculation does not work in chimera for the files I am working on. Thanks Hernando