[Chimera-users] B-value coloring

ARMIN HODAEI ahodaei15 at ku.edu.tr
Tue Oct 10 04:20:23 PDT 2017

Dear Chimera Users,

           Let's say this time I want to display only 20 residues(based on
ranking, the top 20 residues) on the protein and make the other residues
transparent. How can I do that?


On Wed, Oct 4, 2017 at 1:43 PM, ARMIN HODAEI <ahodaei15 at ku.edu.tr> wrote:

> 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/d
>> efineattrib/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/d
>> efineattrib/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/d
>> efineattrib/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

Armin Hodaei
Department of Physics,
Faculty of Arts and Sciences
Koc University, Istanbul
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