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

On 16 Oct 2020, at 03:31, Priyanka Abeyrathne pabeyrat@gmail.com wrote:

Hi Guillaume,

Thank you so much for your assistance. I am going to use it soon and if I happened to have questions I will let you know.

I have two other questions to clarify with you.

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.

Thank you so much. Kind regards, Priyanka

On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <guillaume@gaullier.org mailto:guillaume@gaullier.org> wrote: Hi Priyanka,

If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful:

1. set the scene the way you want it
2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings)
3. rotate or translate, move around, etc.
4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above

I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file.

You will find more details in the documentation, with command "help view". Also here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name

I hope this helps,

Guillaume

...

On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <pabeyrat@gmail.com mailto:pabeyrat@gmail.com> wrote:

Hi All,

Is there a save scene command in ChimeraX?

Thanks, Priyanka _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users