<div dir="auto">Hi Lewis,</div><div dir="auto"><br></div><div dir="auto">This default map mode in the Clipper plugin is (like Coot) designed that way for two main reasons:</div><div dir="auto"><br></div><div dir="auto">(a) for a crystallographic dataset there is no one definition of what constitutes the “full map” - it just goes on forever in all directions.</div><div dir="auto"><br></div><div dir="auto">(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.</div><div dir="auto"><br></div><div dir="auto">Anyway, here’s the basic overview of what you can do:</div><div dir="auto"><br></div><div dir="auto">- pan around with middle-click-and-drag - the sphere of density will follow where you go;</div><div dir="auto"><br></div><div dir="auto">- increase/decrease the size of the sphere witb the command “clipper spotlight radius {value}”;</div><div dir="auto"><br></div><div dir="auto">- 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”);</div><div dir="auto"><br></div><div dir="auto">- 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. </div><div dir="auto"><br></div><div dir="auto">Hope this helps!</div><div dir="auto"><br></div><div dir="auto">— Tristan </div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 15 Feb 2023 at 01:26, Lewis James martin via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
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<div>Hi folks, <br>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? <br><br>The example files I used are in <a href="https://www.rcsb.org/structure/6DIL" target="_blank">6DIL</a>. 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.<br><br>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 <em>cube </em>that does not cover the protein. Is there a way to view the full density? <br><br>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:<br><br></div><pre>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)</pre><div><br>
<img src="cid:1865537822d28b0c6561" alt="Screenshot 2023-02-15 at 11.53.56 am.png" style="width:667px;max-width:100%">
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