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

[Elaine Meng]

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
> >