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
[cid:image001.png@01D3B556.66CC3430]
On Mar 6, 2018, at 8:12 AM, Elaine Meng <meng@cgl.ucsf.edumailto: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.edumailto: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
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