[chimerax-users] Surfaces & color by attribute

[Hernando J Sosa]

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 at sonic.net]
Sent: Tuesday, March 06, 2018 1:01 PM
To: chimerax-users at 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


[cid:image001.png at 01D3B556.66CC3430]


On Mar 6, 2018, at 8:12 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at 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 at einstein.yu.edu<mailto:hernando.sosa at 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


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