wxu_scale during TLS + INDIVIDUAL_ADP refinement
Dear colleagues, I am refining a structure with phenix.refine (cci_apps 2007_08_18_1856). The strategy includes refinement of tls, individual_adp, and individual_sites (during the same run.) In order to test different restraints for ADP´s refinement, I have changed the value of the wxu_scale from the default. Yet, the value of the wxu_scale parameter is always automatically reset to the same value as indicated in the log file under the section "Automatic adjustment due to TLS refinement". That is, phenix.refine uses in all cases the same wxu_scale independently of the value I set in the definitions file. Of course, when TLS refinement is not done, the wxu_scale value remains as specified. I would appreciate if someone could indicate me how to modify the ADPs restraints when doing TLS refinement. Cheers Jose -- -------------------------------------------------- Jose M de Pereda, PhD Centro de Investigación del Cáncer Spanish National Research Council - U. Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294819 Fax: +34-923-294795 http://xtal.cicancer.org/ -------------------------------------------------
Hi Jose,
I am refining a structure with phenix.refine (cci_apps 2007_08_18_1856). The strategy includes refinement of tls, individual_adp, and individual_sites (during the same run.)
OK, this is usually good thing to do.
In order to test different restraints for ADP´s refinement, I have changed the value of the wxu_scale from the default.
Yes, this is the way how you change the strength of ADP restraints in all cases except when you do combined "TLS+individual ADP" refinement. In order to make the refinement very robust and efficient we re-refined ~350 TLS containing structures from PDB performing the grid search for wxu_scale parameter and we found some optimal values for wxu_scale as a function of resolution. We use these values in automatic adjustment that you are mentioning. So currently there is no way you can turn off this adjustment; however I realize that users may want to play with wxu_scale themselves and skip the adjustments so I will provide this option in future. Just out of curiosity, do you have any particular reason to change wxu_scale in TLS+ADP refinement? Let me know if you have any questions. Pavel.
participants (2)
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Jose M de Pereda -
Pavel Afonine