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

[Tristan Croll]

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> 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:
>
> import gemmi
> import numpy as np
> import meshplot as mp
> from skimage.measure import marching_cubes
>
> #run 'gemmi mtz2cif 6dil_phases.mtz 6dil_phases.cif' first
>
> doc = gemmi.cif.read('/Users/ljmartin/Desktop/6dil_phases.cif')
> rblocks = gemmi.as_refln_blocks(doc)
> rblock = rblocks[0]
>
> size = rblock.get_size_for_hkl(sample_rate=2.6)
> full = rblock.get_f_phi_on_grid('pdbx_FWT', 'pdbx_PHWT', size)
> array = np.array(full, copy=False)
> complex_map = np.fft.ifftn(array.conj())
> scale_factor = complex_map.size / full.unit_cell.volume
> real_map = np.real(complex_map) * scale_factor
>
> v,f,n,_ = marching_cubes(real_map, 0.05)
>
> mp.plot(v, f)
>
>
> [image: Screenshot 2023-02-15 at 11.53.56 am.png]
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