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 – [cid:image002.jpg@01D31FF0.B3613260] I'm more interested in the first issues - can I color ByResidue (with any color scheme)? ☺ 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 [mailto:meng@cgl.ucsf.edu] Sent: Monday, August 28, 2017 9:59 AM To: Tom Skillman <TSkillman@benaroyaresearch.org> Cc: 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> 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 <TSkillman@benaroyaresearch.org<mailto:TSkillman@benaroyaresearch.org>> 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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I went ahead and added MSE to the protein “amino” coloring script and also made a script for the protein “shapely” coloring. Caveat emptor, but attached here for your convenience. As mentioned before, you would add the target option to each “color” command to restrict it to a particular representation. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#general-options>

On Aug 28, 2017, at 2:16 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Tom, The schemes aren’t built in (predefined) in ChimeraX, but certainly you can color residues whatever colors you want, for example by specifying the color hex codes from the table you showed ( http://jmol.sourceforge.net/jscolors/ ):

color :ala #c8c8c8 color :arg #145aff (etc.)

Putting the commands in a plain text file named something.cxc and then opening it in ChimeraX applies the coloring scheme. You could include the “target” option in each command if you want to limit coloring to only the atoms (or only the cartoons or surfaces).

For your convenience, I’ve made and attached a ChimeraX command file for the “amino” scheme. I doublechecked it, but you should probably verify for yourself that I copied the color codes correctly. I’m sure you can generalize to make a similar file for any other residue-name-based scheme that you wish. These schemes are pretty old; one minor modification you might want to consider is making MSE residues the same color as MET.

Of course the commands could be typed in interactively, but if this is a scheme you want to use over and over, at least for now the command file is the way to go.

Re the VR, it sounds interesting, but I will leave it to others on our team (those who would actually be working on the VR stuff) to respond. As you may have seen, we have ChimeraX working with VR as per this description: <http://rbvi.ucsf.edu/chimerax/docs/user/vr.html>

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

<amino-coloring.cxc>

...

On Aug 28, 2017, at 11:27 AM, Tom Skillman <TSkillman@benaroyaresearch.org> 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 –

<image002.jpg>

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.

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