<div dir="ltr">Dear Daniel,<div><br></div><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">- Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops?<br></blockquote><div>Although it is not currently possible to completely "freeze" some atoms (exclude them from coordinate refinement) in phenix.real_space_refine, you can try reference coordinate restraints described in #14 in documentation here:</div><div><a href="https://www.phenix-online.org/documentation/reference/real_space_refine.html">https://www.phenix-online.org/documentation/reference/real_space_refine.html</a><br></div><div>to restrain certain atoms to their initial position. Depending on sigma you provide these restraints could be more or less strict (use smaller sigma to make them stronger).</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
- In the instructions it says that you can do both NCS constraints and restraints. How you do the latter? I can only do the former by default or by defining ncs_constraints=True and give a NCS definition file.<br></blockquote><div>I'm afraid it is mistake in the instructions. I believe that presently NCS torsion restraints are not available in phenix.real_space_refine.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
- When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm? If I do a run=minimization_global, things work a bit better in this regard, but is not really what I want (at this stage). Am I doing something wrong? Here is the run command and the rigid body definition file:<br></blockquote><div>Hopefully, Pavel will be able to answer this question.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div><div> <br></div></div><br></div></div>