[chimerax-users] Color by Conservation in ChimeraX

[Sean Moore]

Thanks Eric.  I will install and try Chimera, if that doesn’t work out, I can manually edit an attributes file.

Best,

Sean


On Feb 10, 2020, at 5:28 PM, Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>> wrote:

Hi Sean,
Unfortunately, conservation coloring is still not yet available in ChimeraX, so the easiest way to color your structure is in Chimera, yes.  If you really need to use ChimeraX for it (image generation?), there are a couple of less-easy routes available.  For one, you could use Render By Attribute’s File→Save Attribute… menu entry to generate a file giving the conservation value for each residue.  You could then use a text editor to massage that into a series of ChimeraX “setattr” commands that you could run to get the attribute into ChimeraX.  Then you could use the “color byattribute” command to do the coloring.
The other route is that there is a Chimera→ChimeraX scene exporter that I have been working on but isn’t finished.  But it is pretty close to finished for molecular data only (no volumes, molecular surfaces, 2D labels, etc.).  I could put the exporter into the daily build despite it not being really completely ready for anything, since in this case it might be good enough.  I’ve attached an image of a structure with a chain colored by conservation in Chimera, and the same system as exported into ChimeraX.

—Eric

Eric Pettersen
UCSF Computer Graphics Lab

<c1.png><cx.png>

On Feb 10, 2020, at 11:13 AM, Sean Moore <Sean.Moore at ucf.edu<mailto:Sean.Moore at ucf.edu>> wrote:

Hello,

I read an older post that color by conservation is pending for ChimerX.  Is it available now?  When I open a sequence alignment that I generated elsewhere, it shows the alignment and conservation, it identified the correct protein chain, but there is no menu in that window to assign the colors to the protein. (no option to "Again from the Multalign Viewer menu, choose: Structure... Render by Conservation. This will call Render by Attribute, in which…”)

Should I use Chimera for this instead of ChimeraX?

Sean


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