[chimerax-users] VOP cover command?

[Megan Mayer]

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 at 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 at 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
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200729/d4479450/attachment.html>