[chimerax-users] Color by Conservation in ChimeraX

Tue Feb 11 13:14:01 PST 2020

thank you Elaine. I tried the newest build of chimera, but it failed to open the structures I am working with, so I used the last stable release and got them opened.  I will work through this using your links.

Sean

> On Feb 11, 2020, at 11:54 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Sean,
> You may know how to do it in Chimera already, but just in case, these Chimera tutorials include coloring by conservation:
> 
> Basic intro to coloring by conservation
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsuper.html&data=02%7C01%7CSean.Moore%40ucf.edu%7C6f040e9f2d1041d24c5408d7af131dcd%7Cbb932f15ef3842ba91fcf3c59d5dd1f1%7C0%7C0%7C637170368956340131&sdata=dCd%2BbH3VjhB3XW%2B%2FXAKClY9QmSWfM0JJ7bulE1swon4%3D&reserved=0>
> More details and different situations
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdata%2Ftutorials%2Fsystems%2Foutline.html&data=02%7C01%7CSean.Moore%40ucf.edu%7C6f040e9f2d1041d24c5408d7af131dcd%7Cbb932f15ef3842ba91fcf3c59d5dd1f1%7C0%7C0%7C637170368956350121&sdata=nB6VKxMFuKghj3tjzoq%2BKQ670pmbbex92AkeaWdjJDs%3D&reserved=0>
> 
> You can save an attribute file in Chimera by choosing File... Save Attributes from the menu of Render/Select by Attribute.
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fdefineattrib%2Fdefineattrib.html%23attrfile&data=02%7C01%7CSean.Moore%40ucf.edu%7C6f040e9f2d1041d24c5408d7af131dcd%7Cbb932f15ef3842ba91fcf3c59d5dd1f1%7C0%7C0%7C637170368956350121&sdata=9bl7F98j9u7%2BamWaMFtW3cJu1sVO%2B6Cnm1zfv%2Bl6RiQ%3D&reserved=0>
> 
> To make a ChimeraX command file (.cxc) from the attribute values in that file, you would need to write “setattr” commands that assign each value to its respective residue.
> 
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsetattr.html&data=02%7C01%7CSean.Moore%40ucf.edu%7C6f040e9f2d1041d24c5408d7af131dcd%7Cbb932f15ef3842ba91fcf3c59d5dd1f1%7C0%7C0%7C637170368956350121&sdata=S%2FqfxKavrr6OWUrf6qdnjTfVi8eLz2Xd5ZgaV9PApNQ%3D&reserved=0>
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fusageconventions.html%23cxc-files&data=02%7C01%7CSean.Moore%40ucf.edu%7C6f040e9f2d1041d24c5408d7af131dcd%7Cbb932f15ef3842ba91fcf3c59d5dd1f1%7C0%7C0%7C637170368956350121&sdata=Io30SJi4rytOlADXccH6o1Qz5eMvxE8R9T6om4rl%2BII%3D&reserved=0>
> 
> This example .cxc file includes several “setattr” commands to assign a hydrophobicity attribute to residues by their names (e.g. :ala):  
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fkyte-doolittle_hydrophobicity.cxc&data=02%7C01%7CSean.Moore%40ucf.edu%7C6f040e9f2d1041d24c5408d7af131dcd%7Cbb932f15ef3842ba91fcf3c59d5dd1f1%7C0%7C0%7C637170368956350121&sdata=adCOK3HyJxv1GIaBSnHZb8IPQQ2yB%2FR%2Bco%2FT9fA2JSc%3D&reserved=0>
> 
> Yours would be similar except you would use residue numbers and maybe also chain IDs (e.g. :128 or /A:128).
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fatomspec.html%23hierarchy&data=02%7C01%7CSean.Moore%40ucf.edu%7C6f040e9f2d1041d24c5408d7af131dcd%7Cbb932f15ef3842ba91fcf3c59d5dd1f1%7C0%7C0%7C637170368956350121&sdata=r7IHjrjQ9meg6UcpJc4NOPNYauVcDqJHBxP8VYnWCyc%3D&reserved=0>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> 
>> On Feb 11, 2020, at 6:18 AM, Sean Moore <Sean.Moore at ucf.edu> wrote:
>> 
>> 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> 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> 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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>>>> 
>>> 
>> 
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