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

[Sergio Garay]

Thank you very much, Eric. Unhappily I am not familiar with Python
scripting, so I will have to wait that someone with that skill adds this
useful tool into Chimera code!
But for now I will take Elaine's hints!

Thank you again
Sergio

On Tue, Jul 31, 2018 at 3:38 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
>
> 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
> >
>
> 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>
> 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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-- 








*Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs.
BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 -
Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54
(342) 4575-221 *
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