[chimerax-users] Assistance: ChimeraX save scene

[Elaine Meng]

Hi Priyanka,
I agree with all that Guillame said, including that you should send ChimeraX questions to chimerax-users at cgl.ucsf.edu instead of any one person.

A few additional comments:

(1) if you want to color the whole chain /A, why not skip selecting and just use command:

color /A royal blue

This works fine for me on any structure that has a chain A.

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>

Or, if you wanted only the protein part of chain A  (not waters, ligand, etc.):

color /A & protein royal blue

Also, if you want select the whole chain A (for any purpose), there is no need to show the sequence, you could just select it with command:

select /A

(2) yes, use "volume zone" like Guillame suggested.  You can see the help with command "help volume zone" or view it at our website here:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone>

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 19, 2020, at 1:51 AM, Guillaume Gaullier <guillaume at gaullier.org> wrote:
>> 
>> On 16 Oct 2020, at 03:31, Priyanka Abeyrathne <pabeyrat at gmail.com> wrote:
>> 
>> 1. I used the following commands to color the pdb
>> seq chain /A 
>> Then I highlighted the chain A
>> color sel blue
>> 
>> I can see the chain A color is blue. Now ChimeraX has really nice color scheme. I tried to color chain A to royal blue (#4169E1 26,41,88). When I use the above commands
>> seq chain /A
>> highlighted the chain A
>> color sel royal blue
>> Didn't change the color blue to royal blue. Cod you please assist me how to fix theis?
>> 
>> 2. pdb of the protein has three chains (A, B and C). I have a cryo-EM structure of the same protein. How can I extract only chain A density from cryo-EM structure. I think I have to use a segment map command. Could you please assist me how to do this in ChimeraX.
> 
> Hi Priyanka,
> 
> Sorry for this late reply. I am copying the chimerax-users list (if you had sent your last email to the list, somebody else would maybe have answered you earlier; also a good idea to communicate through the list because all emails are archived and that sometimes enables people to find answers to their questions directly by searching the archives).
> 
> Regarding you question about colors: in ChimeraX, the command "color list" will print in the log a list of colors with their names. Color names made of more than one word are listed twice: spelled with and without a space. I just checked that if you spell color names as they are listed by this command, it works. So, in your case, try spelling it "royalblue" with no space.
> 
> Regarding your second question, I think this should work, but I am not quite sure what you are trying to do:
> 
> volume zone #1 nearAtoms sel range 2 newMap true minimalBounds false
> 
> in which #1 is your main map (so not necessarily #1 in your session, use the correct model number for your map as seen in the model panel) and sel is a selection of the atoms of interest (in your case "/A" for chain A), "range 2" is how many angstroms away from the model atoms you want to perform the map cut-out (I put 2 arbitrarily; try different values and use what you think is best for what you are trying to do), "newMap true" tells it to generate a new object for this map cut-out (it should show up in the model panel after you run the command) and "minimalBounds false" tells it to keep the same box size as your original map (if set to true instead, it will choose the minimal box size that encloses your map cut-out; not sure which one you need, but keeping the same box size should be safe).
> 
> Once you have this, you can write this map cut-out to a file with the following command:
> 
> save /path/to/your/new/map.mrc models #2
> 
> (replace #2 by the correct object identifier for your new map, as reported in the model panel).
> 
> I hope this helps,
> 
> Guillaume
>