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

[Lewis James martin]

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)
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