Hi Tom, We use Vive and Oculus Rift with ChimeraX to display structures and microscopy data (the “vr” command). I am interested in how you have used VR to look at PDB models. Can you tell me more? Tom
On Aug 28, 2017, at 11:27 AM, Tom Skillman wrote:
Hi Elaine,
I guess I was asking both questions: 1) Is it possible to color a PDB protein by residue, i.e. each of the 23 residues as a different, but consistent, color across the whole protein, and 2) Do you support any of the standard color schemes like this one that I've used in the past –
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I'm more interested in the first issues - can I color ByResidue (with any color scheme)? J
Thanks for your assistance.
Best, Tom
Thomas Skillman Director Research Technology Benaroya Research Institute for Autoimmune Disease Seattle, WA
PS – If you are interested, I created an VR based immersive space for collaborating on PDB models. It adds another dimension to looking at and discussing protein structure. Let me know if you’re interested and we can set up a time to give you a demo.
-----Original Message----- From: Elaine Meng Sent: Monday, August 28, 2017 9:59 AM To: Tom Skillman Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Color protein by residue
Hi Tom, I don’t know what you mean by standard colors. There is “color byelement” for using element color-coding of atoms, “color byhet” for leaving carbons unchanged and element color-coding the other atoms. The element colors are shown here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#element <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#element>>
There is no set of standard colors indicating the amino acid types, if that’s what you meant, at least not in ChimeraX. That may be the reason you couldn’t figure it out. :-)
I hope this clarifies, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 27, 2017, at 8:30 PM, Tom Skillman wrote:
I can’t figure out the command for coloring the proteins of a protein with standard colors.. Can you help? Thx.
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