[chimerax-users] centering the view on an atom or marker

[Megan Mayer]

Hi Elaine, again, thank you very much. The hover tool is incredibly useful.
I am now able to zoom the the sulphur atom.

However, is there a way to slowly zoom from the entire structure, to the
desired model number, in my video? Here is the example of what I use, but
isn't quite right (i attached an example movie):

#zoom into specific area then zoom back out to original

movie record ; view orient ; wait 20 ; zoom 1.2 100; view #3 clip false ;
wait 20; view orient ; movie encode ~/


Thank you very much,
Megan



Megan Mayer, M.S.
Microscopist, Cryo-EM
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
888-675-8261


On Wed, Jul 29, 2020 at 12:37 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Megan,
> If the marker is model #3 (the whole model is just that marker) then
> "spec" is just #3.  The "view" command does not take a "models" keyword,
> and the "#" symbol itself means model number.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
>
> view #3
>
> If model #3 has other markers or atoms in it, maybe you want to also
> specify the residue number of your specific marker, which you can probably
> see by hovering the mouse over it to see a balloon with its information.
> E.g. if its residue number is 4,
>
> view #3:4
>
> However, focusing the view on just a single atom or marker will give you
> an extreme close-up, including narrowing the space between front and back
> clip planes.  You can turn off the clipping with command "clip off"
> (without any other words).  To focus on your marker but not with such an
> extreme closeup, maybe you instead want something like this (assuming the
> marker = model #3):
>
> view #3 clip false; zoom .3
> - or -
> view #3 :< 2.5 clip false
>
> clip false is explained in the view manual page, the zoom command zooms
> back out, and "#3 :< 2.5" means residues within 2.5 angstroms of #3, see
> specification by zone.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones>
>
> 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 29, 2020, at 7:23 AM, Megan Mayer <mmayer at nanoimagingservices.com>
> wrote:
> >
> > 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
> > >
>
>
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