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</style></head><body style='font-family: Helvetica, Arial, sans-serif; font-size: 13px; '><div>Hi Dmitry,</div><div><br></div><div>just for the records of the mailing list (as somebody have the same issue):</div><div><br></div><div>Load map and model.</div><div><br></div><div>Test your selection (this step is not needed, but helps if the selection includes multiple parts)</div><div># hide all atoms</div><div>hide atoms</div><div># show your selection. The model is #2, you want to only select chlorophyll from chain A<br></div><div>show #2/A:BCL</div><div><br></div><div>This should display just your molecule/residue/ligand of interest.</div><div>For the selection syntax:<br></div><div><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html</a></div><div><br></div><div>Now create a new map, just from your molecule</div><div>volume zone #1 nearAtoms #2/A:BCL newMap true</div><div><br></div><div>One can include also the range parameter (default 3.0), e.g. if the molecule placement is a bit unsure and you want to refine it in there.</div><div><br></div><div>Now, just save the new map by</div><div>save mapZone.mrc #3<br></div><div><br></div><div>If you try multiple volume zones, you might need to correct the id.</div><div><br></div><div>Best</div><div>Christian<br></div><br><div>>>> "Dmitry A. Semchonok via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> 02/08/22 12:42 PM >>></div><div><div class="WordSection1"><p class="MsoNormal"><span>Dear colleagues,</span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span>I have a cryo-em map and a model.</span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span>I would like to extract some the cryo-em density around certain fitted model.</span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span>For example I have Chl molecule fitted into the correspondent cryo-em density. </span></p><p class="MsoNormal"><span>And I want to extract this certain Chl only out of the whole structure.</span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span>How can I do that?</span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span> </span></p><p class="MsoNormal"><span>Kind regards,</span></p><p class="MsoNormal"><span>Dmitry</span></p><p class="MsoNormal"> </p><p class="MsoNormal">Sent from <a target="_blank" href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows</p><p class="MsoNormal"> </p></div></div>_______________________________________________<br>ChimeraX-users mailing list<br>ChimeraX-users@cgl.ucsf.edu<br>Manage subscription:<br>https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br></body></html>