[chimerax-users] Loading MTZ data - volume is restricted to a small sphere within the protein model

[Lewis James martin]

Wonderful, thanks Tristan - it works well! Resolved. 
Lewis

On February 16, 2023, Tristan Croll <tcroll at altoslabs.com> wrote:
> Hi Lewis,
> This default map mode in the Clipper plugin is (like Coot) designed
> that way for two main reasons:
> (a) for a crystallographic dataset there is no one definition of what
> constitutes the “full map” - it just goes on forever in all
> directions.
> (b) the main use case is for investigating the details of the model in
> the context of the map - when zoomed in to the scale of individual
> residues, keeping the whole map drawn just adds lots of unnecessary
> overhead.
> Anyway, here’s the basic overview of what you can do:
> - pan around with middle-click-and-drag - the sphere of density will
> follow where you go;
> - increase/decrease the size of the sphere witb the command “clipper
> spotlight radius {value}”;
> - expand the map and mask it to cover any arbitrary selection within
> your model with “clipper isolate {sel}” (return to the sphere mode
> with “clipper spotlight”);
> - save the currently displayed map region to mrc format using the save
> command in exactly the same way you’d save a standard ChimeraX
> Volume. 
> Hope this helps!
> — Tristan 
> On Wed, 15 Feb 2023 at 01:26, Lewis James martin via ChimeraX-users
> <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> wrote:
> > Hi folks,
> > I recently installed Clipper, and on loading some example PDB and
> > MTZ data, I'm seeing just a sphere of density data that does not
> > cover the full protein model. This behaviour is not restricted to a
> > single example. Is it expected?
> >
> > The example files I used are in 6DIL
> > <https://www.rcsb.org/structure/6DIL>. I downloaded "PDB Format" and
> > "Map Coefficients (MTZ Format)" from the drop-down menu. Loading the
> > PDB by drag-and-drop into ChimeraX works as expected (coordinates do
> > show). On loading the MTZ by drag-and-drop, and selecting the PDB
> > model to import data into, I see the below representation. The
> > density does not cover the full set of protein coordinates - it's
> > limited to a sphere within the protein.
> >
> > Curiously, I saw this on coot too - so maybe I'm just getting the
> > options incorrect? I did try shifting the cutoffs in the "Volume
> > Viewer" Tool, and the mesh does change but it's still limited to
> > this sphere. Changing from a mesh surface to "Maximum" shows that
> > the available data is limited to a cube that does not cover the
> > protein. Is there a way to view the full density? 
> >
> > Out of interest, I also tried generating the mesh myself, but only
> > got halfway. This at least shows that the data does cover the whole
> > protein:
> >
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