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@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@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

Dear Armin Hodaei, You could just hide the other residues, but I’m guess you mean you want them to be partly transparent, rather than hidden. There are two general ways. (1) just specify transparent colors for the lower values in Render by Attribute: click on the square color well for a slider to show the Color Editor, then in the Color Editor make the color transparent by checking the “Opacity” option and adjusting the “A” value. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#colors> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortool.html> (2) select all the lower-value residues and then apply tranparency. You can select all the lower-scoring residues (the ones you want to make transparent) by score value using “Select by Attribute” which is really just the other tab on the “Render by Attribute” dialog you already used for coloring (Chimera menu: Select… by Attribute Value). Choose your attribute and then move the sliders on the histogram to enclose the values for residues you want to select. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select> You didn’t say whether you are trying to make atoms, or residues, or surface (or all of those) transparent… it would help to be more specific in your question, but I’ll try to cover the possibilities. With the residues you want to make transparent already selected, to simply hide them, choose Actions… Atoms/Bonds… hide, Actions… Surfaces… hide, Actions…Ribbon… hide. To make them partly transparent instead: (A) if surface: choose menu Actions… Surface… transparency… [ the amount of transparency you want ] (B) if atoms and/or ribbons, use the “transparency” command with the percent value that you want. For example, 50% transparent atoms and 70% transparent ribbons would be commands: transparency 50,a sel transparency 70,r sel By default you would only see the top transparent layer, so if you had transparent atoms inside of transparent surface, you would only see the surface (the atoms would disappear). If you really want to see multiple transparent layers you could use command ~set singleLayer … but that often looks messy and is sometimes rendered incorrectly. So if you have transparent surface, it may be better to not make other things transparent, or not to show them at all. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 10, 2017, at 4:20 AM, ARMIN HODAEI <ahodaei15@ku.edu.tr> wrote:

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?

Sincerely,