[Chimera-users] B-value coloring

ARMIN HODAEI ahodaei15 at ku.edu.tr
Wed Oct 4 03:43:49 PDT 2017

Dear Elaine,

          I really do appreciate your kind attention. I did it, thank you
very much,

Best Wishes,

On Tue, Oct 3, 2017 at 7:05 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Armin Hodaei,
> In Chimera, you do not need to change the B-factor values to do the
> coloring.  Instead you can create your own new “attribute” by making an
> input text file that simply lists the residues (or atoms) and the values
> that you want to assign.  When you read that file into Chimera, your
> attribute values will be shown in a histogram just like B-factor values,
> and you can do the coloring however you like: any colors, etc.
> The input text file format is described here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> defineattrib/defineattrib.html#attrfile>
> See also the example files linked at the bottom of the page.  The first
> one (percentExposed.txt) is an example of assigning values to residues
> based on their residue numbers. Most of the lines are of the form:
> (Tab):residue-number(Tab)value
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> defineattrib/percentExposed.txt>
> After you make that text file:  start Chimera, open the structure, and
> read the text file in with Define Attribute (in menu under Tools… Structure
> Analysis) or the command “defattr”.  When the file is read, by default the
> Render by Attribute dialog will automatically pop up for choosing the
> coloring that you want.
> Define Attribute
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> defineattrib/defineattrib.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html>
> Render by Attribute (how to change coloring etc.)
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/
> render.html#colors>
> You can also do the coloring with the “rangecolor” command instead of the
> Render by Attribute GUI, but unless you are trying to script everything, it
> is probably easier for you to use the GUI because it shows the histogram of
> the values.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> P.S. although you can just make your own new attribute instead of changing
> B-factor, you could also change the B-factor values if you really wanted
> to… however, it would still require making an attribute assignment file.
> In that file you would need to give attribute name as “bfactor” and the
> recipient level of assignment as “atoms” (not residues)
> > On Oct 3, 2017, at 1:51 AM, ARMIN HODAEI <ahodaei15 at ku.edu.tr> wrote:
> >
> > Dear Chimera users,
> >           I would like to change the b-values of a Protein and color the
> residues in the ranking that I want. I have a sequence of residues from the
> most functionally important sites to less functionally important. I wanna
> define them to look red and blue respectively due to the new ranking.
> > Sincerely,
> > Armin Hodaei

Armin Hodaei
Department of Physics,
Faculty of Arts and Sciences
Koc University, Istanbul
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20171004/310efae3/attachment.html>

More information about the Chimera-users mailing list