[Chimera-users] Is there any tool to write some calculated attribute into a header format?

Eric Pettersen pett at cgl.ucsf.edu
Tue Jul 31 11:38:20 PDT 2018

Hi Sergio,
	If you are comfortable writing Python code, there is a provision for adding custom header types to Multalign Viewer.  Look at the MAVHeader module in your Chimera distribution (<your Chimera>/share/MAVHeader), particularly the file ChimeraExtension.py which defines headers for charge variation and CA/backbone/full RMSDs and registers those headers with Multalign Viewer.  I imagine you will have questions (LOL!) so I have directed responses to the chimera-dev mailing list, which would seem more appropriate in this case.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jul 31, 2018, at 11:22 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Sergio,
> Sorry, there isn’t a way to automatically make residue attributes into a header.  We had imagined that people would be calculating properties outside of Chimera, and then using a script or even manually creating a file in the header format to load them as a header.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/defineheader.html#headerformat>>
> However, you can change the sequence lettering colors to match the ribbon, so if you first colored ribbon by some residue attribute (with Render by Attribute or command “rangecolor”), it could be reflected back into the sequence window in that way.  To do that, use sequence window menu Preferences… Appearance, and then for residue letter coloring (near the bottom), choose “coloring scheme: ribbon”. I realize this might not be optimal if some of the coloring makes the letters hard to read.  
> I attached an example image with my protein colored by residue average bfactor (blue -> red -> yellow) and using “ribbon” coloring of the associated sequence in the alignment.
> With a header you could only have one value per column, but with ribbon coloring you could have different values (colors) in the same column if there are multiple structures associated.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> <Screen Shot 2018-07-31 at 11.18.18 AM.png>
>> On Jul 31, 2018, at 6:05 AM, Sergio Garay <sergio.alberto.garay at gmail.com <mailto:sergio.alberto.garay at gmail.com>> wrote:
>> Hi All!
>> I would like to know:
>> Is there any way or tool to write some calculated attribute into a header format?
>> I want to see the same color values obtained for some a calculated attribute projected onto a sequence.
>> I have read in the chimera list the inverse process: exporting a header from a sequence window to be read as an attribute. 
>> Thank you in advance.
>> -- 
>> Sergio Garay
>> Dr. en Ciencias Biológicas
>> Facultad de Bioquimica y Cs. Biológicas
>> Universidad Nacional del Litoral
>> Santa Fe - Argentina
>> C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
>> Argentina
>> Ph. +54 (342) 4575-213
>> Fax. +54 (342) 4575-221
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