[Chimera-users] Coloring peptide bonds in Chimera

[Elaine Meng]

A cautionary note: I would recommend using transparency only sparingly, if at all, because it is frequently rendered incorrectly.  Also even if rendered correctly, it makes the depth-cuing harder to understand, i.e. for people to tell what is near and what is far based on color shading.  In other words, transparent items might be interpreted as being far away because they seem dim rather than transparent.

In case you haven't seen it already, there is a "tips on preparing images" page which covers various related topics, including transparency.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>

Elaine

> On Jan 19, 2021, at 12:39 PM, Tynan A. Becker <tabecker at alaska.edu> wrote:
> 
> Hi Elaine,
> 
> I Have made a lot of progress on figuring this out today due to your directions.  Thank you very much for the info as to how to do this in the command line.  I was looking at having to manually find many bonds, highlight them all at the same time, change color, then save.  Turns out if I change color on 1 bond, then click off it, it reverts...  The command line will help with this (I think!).
> 
> But I'm also trying to see if I can set the molecule color at a certain transparency, then color bonds at 100% opacity now.
> 
> Thank you again for all the pointers - this has been a journey (albeit a fun one).
> 
> Cheers,
> Tynan
> 
> On 1/19/21 12:34 PM, Elaine Meng wrote:
>> Hi Tynan,
>> If you need to do it in a command, e.g. if scripting movie contents, then you would need to specify the two atoms on either side of the bond.  Example to color the bond between residue 5 atom C and residue 6 atom N in chain A of model 0:
>> 
>> color purple,b #0:5.a at c:6.a at n
>> 
>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>
>> 
>> I hope this helps,
>> Elaine
>> 
>>> On Jan 19, 2021, at 8:43 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Tynan,
>>> For a real bond (not chain trace):
>>> 
>>> (1) select the bond (Ctrl-click on it, shows green selection outline)
>>> (2) open the Selection Inspector by clicking the green magnifying glass icon near the bottom right of the Chimera window, it will be set to Inspect: Bond
>>> (3) in the Selection Inspector dialog, change halfbond mode to "off" and click the square next to "color" to open the Color Editor to change the color interactively.
>>> 
>>> Screenshot below.  If you are showing chain trace those sticks are pseudobonds, not bonds, and you can do the same steps as above, except that you have to change the Selection Inspector to Inspect: Pseudobond.
>>> 
>>> 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 2021-01-19 at 8.36.57 AM.png>
>>> 
>>>> On Jan 18, 2021, at 5:15 PM, Tynan A. Becker <tabecker at alaska.edu> wrote:
>>>> 
>>>> Good afternoon,
>>>> 
>>>> I have been trying to figure out how to color just a single peptide bond between 2 residues in a protein.
>>>> 
>>>> What I have figured out so far is to show chain trace under actions|atoms/bonds.  Then invert the selection (whole protein). This shows the bonds.
>>>> 
>>>> I can select a residue and color the bond on both sides.  But I want to color the bond between 2 residues.  If I pick the bond by manual selection, the action|color|choice doesn't work.  The manual tantalizingly suggests using the "halfbond" setting or "bondcolor" for the command line.  The problem that I encounter is that I can't figure out how to tell the program which bond I want.  I've read the "atom specifications" page of the manual and tried every logical combination I can figure to tell the program which bond I want to color.  But each time, I get the "mangled atom specifier" error.
>>>> 
>>>> I was told today that there is a way to do this, but I'm stuck. Any input is welcome.
>>>> 
>>>> Thank you,
>>>> Tynan