Equivalent of surface colour by radius in tools/Volume viewer of Chimera
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, 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 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
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
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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participants (2)
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Elaine Meng
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Shabih Shakeel