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This is one of many things that has a preliminary implementation in ISOLDE, but is not yet exposed to the main interface. You can get to it via the Python shell, though (Tools/General/Shell). To reimpose strict symmetry: assuming you have your model initialised
in ISOLDE, save your session in case of trouble ("save session.cxs"), prune your model down to one asymmetric unit (e.g. "sel /A,B; del ~sel"), then in the shell:</div>
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<span style="font-family: "Courier New", monospace;">m = session.isolde.selected_model</span></div>
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<span style="font-family: "Courier New", monospace;">from chimerax.isolde.phenix.map_symmetry import parse_map_symmetry_file</span></div>
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<span style="font-family: "Courier New", monospace;">symmetry_map = parse_map_symmetry_file('symmetry_from_map.ncs_spec')</span></div>
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<span style="font-family: "Courier New", monospace;">from chimerax.isolde.atomic.building.ncs import create_all_ncs_copies</span></div>
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<span style="font-family: "Courier New", monospace;">create_all_ncs_copies(m, symmetry_map[0])</span></div>
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One known bug is that any bonds between different chains will be lost - if present, you'll need to re-add them manually.<br>
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That extreme approach should only be necessary if you make really big changes, though (e.g. shifting a segment in register, major movement of bulky sidechains). For smaller changes it may be easier to just use your "working" ASU as a template for torsion restraints
on the remaining chains. A bit repetitive doing it via the command line, e.g.:</div>
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isolde restrain torsions #1/C template #1/A angleRange 180</div>
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... and repeat for each matching NCS copy, one chain at a time. This will restrain the NCS copies to the
<b>current </b>geometry of your template ASU - you'll need to repeat the command later if you make further changes. If you have many chains, you could save yourself some time by setting up a simple loop in the shell, e.g.:</div>
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def reimpose_symmetry(session):<br>
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<span style="font-family: "Courier New", monospace;"> ncs_map = {</span></div>
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<span style="font-family: "Courier New", monospace;"> "A": ["C","E","G"],</span></div>
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<span style="font-family: "Courier New", monospace;"> "B": ["D","F","H"]</span></div>
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<span style="font-family: "Courier New", monospace;"> }</span></div>
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<span style="font-family: "Courier New", monospace;"> from chimerax.core.commands import run</span></div>
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<span style="font-family: "Courier New", monospace;"> for template, ncs_list in ncs_map.items():</span></div>
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<span style="font-family: "Courier New", monospace;"> for ncs_chain in ncs_list:</span><br>
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<span style="font-family: "Courier New", monospace;"> run(session, "isolde restrain torsions #1/{} template #1/{} angleRange 180".format(ncs_chain, template))</span></div>
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<span style="font-family: "Courier New", monospace;">reimpose_symmetry(session)</span></div>
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... and then re-run <span style="font-family: "Courier New", monospace;">reimpose_symmetry(session)</span> every time you want to update the restraints. Of course, you'll need to actually run a simulation encompassing the whole model for these restraints to
take effect. <br>
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Hope this helps! I do hope to flesh out this tool as time permits.</div>
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-- Tristan<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Sean Connell <sean.connell@gmail.com><br>
<b>Sent:</b> 06 April 2021 08:44<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [chimerax-users] Use symmetry information in Isolde</font>
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<div class="PlainText">Hello I have a naive question about using Isolde to build a model into a cryoEM map generated with symmetry (ie. D4). Basically I don't understand how to rebuild a chain and have the changes reflected in the symmetry related chains when
using a cryoEM map. Is it possible to use, for example, a NCS file (like symmetry_from_map.ncs_spec) generated by phenix in order to get Isolde to build simultaneously the NCS related chains? Or is there another way build symmetry related chains into a symmetrical
cryoEM map? <br>
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Thanks for any tips you have.<br>
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