[chimerax-users] Surfaces & color by attribute

[Tom Goddard]

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 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> 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 at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20180306/4a648f1e/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1bxw.0__chimera_tm_surface_ligand_lipophilicity_350_350.png
Type: image/png
Size: 86298 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20180306/4a648f1e/attachment.png>