<div dir="ltr">Hello Luca,<div><br></div><div>You can refer to this tutorial:</div><div><a href="https://www.youtube.com/watch?v=qB8W_6yuw5k&ab_channel=PhenixTutorials">https://www.youtube.com/watch?v=qB8W_6yuw5k&ab_channel=PhenixTutorials</a><br></div><div>which exemplifies setting custom parameters in phenix.refine, but real-space-refine has exactly the same machinery.</div><div><br></div><div>Also you can prepare a .eff file with parameters you need to set and supply it as input file along with model and data files.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Aug 31, 2022 at 2:55 AM Luca Pellegrini <<a href="mailto:lp212@cam.ac.uk">lp212@cam.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Hello,
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<div>Phenix.real_space_refine keeps pushing a residue out of density so I'd like to restrain it to its current position. Can you please let me know how to implement in the GUI the first example at point 14 at <a href="https://phenix-online.org/documentation/reference/real_space_refine.html#usage-examples?" target="_blank">https://phenix-online.org/documentation/reference/real_space_refine.html#usage-examples?</a></div>
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<pre style="margin-left:2em;margin-right:2em;font-variant-ligatures:normal">phenix.real_space_refine model.pdb map.mtz \
reference_coordinate_restraints.enabled=true \
reference_coordinate_restraints.selection="chain A and resseq 12:21" \
reference_coordinate_restraints.sigma=0.05</pre>
<div>Best wishes,</div>
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<div>Luca</div>
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<div>Luca Pellegrini, PhD<br>
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<div>Department of Biochemistry<br>
University of Cambridge<br>
Cambridge CB2 1GA<br>
UK</div>
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