[Chimera-users] making residues transparent

[Elaine Meng]

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 at 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,