<div dir="ltr"><div class="markdown-here-wrapper" style=""><p style="margin:1.2em 0px!important">Hi,<br>for calculation of an omit map, with the atoms in question fully removed from the model, I experimented with the modify_start_model.modify.remove option and got:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline;white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important">====================== Modifying start model if requested =====================

Size before: 505 size after: 491
Traceback (most recent call last):
  File &quot;/home/user1/phenix-1.16-3549/build/../modules/phenix/phenix/command_line/refine.py&quot;, line 11, in 
    command_line.run(command_name=&quot;phenix.refine&quot;, args=sys.argv[1:])
  File &quot;/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/command_line.py&quot;, line 106, in run
    log=log)
  File &quot;/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/driver.py&quot;, line 271, in __init__
    self.model.set_xray_structure(modify_model_obj.xray_structure)
  File &quot;/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py&quot;, line 693, in set_xray_structure
    self.set_sites_cart_from_xrs()
  File &quot;/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py&quot;, line 1722, in set_sites_cart_from_xrs
    self._pdb_hierarchy.adopt_xray_structure(self._xray_structure)
  File &quot;/home/user1/phenix-1.16-3549/modules/cctbx_project/iotbx/pdb/hierarchy.py&quot;, line 688, in adopt_xray_structure
    raise RuntimeError(&quot;Incompatible size of hierarchy and scatterers array.&quot;)
RuntimeError: Incompatible size of hierarchy and scatterers array.</code></pre>

<p style="margin:1.2em 0px!important">I verified that my intended selection indeed comprises 14 atoms. Has anyone used the remove option inside phenix.refine successfully.<br>Thanks.<br>Wolfram Tempel</p>
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