Dear Elaine, Thank you very much! I was able to use this vop command for my movie effectively.

Another question if you have a moment: After showing the field of view of my entire model, I am trying to zoom/pan/focus into a specific point on my model (a sulphur atom, which has a marker #3). I see in the chimera instructions for "view" (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#initial) that I should be able to focus onto a specific point, but I am not sure how to specify the sulphur atom marker. Also, is there a way to define the field of view?

"view spec" --> "view #3 models" returns me an error "expected an integer >= 1 or a keyword

Any help or point in the right direction greatly appreciated !!

Best,

Megan

On Tue, Jul 28, 2020 at 11:07 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Megan,
The "vop cover" command (actually "volume cover" in ChimeraX, but both will work) needs both the map model number and the atomic model number. So if your map model is #1 and the atomic model is #2, maybe something like:

volume cover #1 atomBox #2

You can see the help for "volume cover" by using the command "help volume cover" ... or the same thing on our website here:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover>

That manual page shows the command syntax and explains the options. The "volume-spec" in the usage is the map model number.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 28, 2020, at 7:42 AM, Megan Mayer <mmayer@nanoimagingservices.com> wrote:
>
> Hi chimeraX forum,
>
> I am trying to get an electron density map (.mrc) to overlap with atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule.
>
> I am thinking to use the "vop cover" command to get the density to expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response.
>
> Thanks in advance for any help!!
>
> Megan
>