<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt"><div>Hi<br>Follow up the shaking the coordinates, I was end up using different R-free set. <br><br>I do have a data is at very low resolution, so only possible to do rigid body refinement. <br><br>How can I avoid over fitting or model bias due to the different R-free set using phenix.<br><br>Thanks<br>ram<br><br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Pavel Afonine <PAfonine@lbl.gov><br><b><span style="font-weight: bold;">To:</span></b> PHENIX user mailing list <phenixbb@phenix-online.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sun, March 28, 2010 10:13:08 PM<br><b><span
style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] shaking a PDB without introducing clashes<br></font><br>
Hi Francois,<br><br>to add to Nat's reply:<br><br>- you can also apply a systematic shift to the model by rotating+translating it:<br><br>phenix.pdbtools model.pdb rotate="10 20 30" translate="1 2 3"<br><br>- you can run SA "refinement" w/o X-ray term:<br><br>phenix.refine model.pdb fake_data.mtz simulated_annealing=true main.bulk_solvent=false main.number_of_macro_cycles=10 output.prefix=distorted_model strategy=individual_sites<br><br>My plan is to add a command line tool called phenix.fake_model_and_data that will create a model and corresponding fake data that will look like a real data and no-one could say that it is a fake data -:) To be available soon!<br><br>All the best!<br>Pavel.<br><br><br>On 3/28/10 5:17 PM, Francois Berenger wrote:<br>> Hello,<br>> <br>> I recently used "phenix.pdbtools modify.sites.shake=..."<br>> in order to have some data from 0.1 to 5A. away from<br>> the true structure in order to test some
scripts.<br>> <br>> I think this introduced clashes in the "shaken" PDBs<br>> I got.<br>> Is there a tool/way to avoid this?<br>> <br>> Best regards,<br>> Francois.<br>> _______________________________________________<br>> phenixbb mailing list<br>> <a ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><span>> <a target="_blank" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br>_______________________________________________<br>phenixbb mailing list<br><a ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></div></div>
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