Hi Shabih, Sorry, not yet. There is coloring by map value and by zone (to match nearby atoms or markers), but coloring by distance (radial, topographic height) is not yet implemented in ChimeraX. http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html

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

On Apr 17, 2018, at 4:35 AM, Shabih Shakeel sshakeel@mrc-lmb.cam.ac.uk wrote:

Hi, In ChimeraX, is there an equivalent of surface colour by radius in tools/Volume viewer of Chimera? I would like to colour an EM density map of a virus from its centre to the outside of the capsid with direct colour range in ChimeraX. Thanks. Regards, Shabih

Hi Shabih, There is no ESP calculation tool or interface in ChimeraX, but you can open a pre-existing .phi file (from DelPhi academic or GRASP), .grd file (from UHBD), or .dx file (from APBS) e.g. to use it to color a molecular surface by map values.

ChimeraX input map formats: http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume

Regards, Elaine

On Apr 17, 2018, at 11:47 AM, Shabih Shakeel sshakeel@mrc-lmb.cam.ac.uk wrote:

Hi Elaine,

Thanks a lot for the information. Is it possible to calculate electrostatic potential within ChimeraX or load Delhpi files?

Thanks.

Regards, Shabih

...

On 17 Apr 2018, at 16:22, Elaine Meng meng@cgl.ucsf.edu wrote:

Hi Shabih, Sorry, not yet. There is coloring by map value and by zone (to match nearby atoms or markers), but coloring by distance (radial, topographic height) is not yet implemented in ChimeraX. http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html

Regards, Elaine

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

...

On Apr 17, 2018, at 4:35 AM, Shabih Shakeel sshakeel@mrc-lmb.cam.ac.uk wrote:

Hi, In ChimeraX, is there an equivalent of surface colour by radius in tools/Volume viewer of Chimera? I would like to colour an EM density map of a virus from its centre to the outside of the capsid with direct colour range in ChimeraX. Thanks. Regards, Shabih

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