group_adp default ? and other phenix questions?
Hi I quite new to the phenix environemnt and just ran a phenix refinement with the following command line *phenix.refine myfile.mtz mymodel.pdb simulated_annealing=true model.ncs refinement.main.ncs=true --overwrite refinement.ncs.excessive_distance_limit=None >phenix_06_18_2008_2.log * The model.ncs file is structured as follows refinement.ncs.restraint_group { reference = chain A selection = chain B selection = chain C selection = chain D } My data is good to 3.3 A ( membrane protein) and thus far I have been refining with refmac5. After the phenix run indicated above, I had a dramatic reduction in r/rfree ( post refmac 33/36 AND post phenix 28/31). This is despite relatively small changes to my model by the simulated annealing refinement. I have a few questions about the process and am hoping some phenix veterans can help me out. 1) At my resolution I guess I should at best be refining only one B-factor / ADP per residue is this the default behavior with the command line above 2) I have seen the emails about syntax for forcing group-B refinement at this locationhttp://www.phenix-online.org/pipermail/phenixbb/2007-March/000161.htmland this onehttp://www.phenix-online.org/download/documentation/cci_apps/structure_refin.... Basically they use strategy=group_adp . I am imagining this calculates one ADP per residue or per defined group. In my case if I force the behavior with the syntax , how is group ADP for NCS-mates handled? 3) On a general note , when I say phenix.refine --show-defaults , the section on strategy has a long list, what do the asterisks (*) in the syntax mean .Does that mean those are the defaults . Also how can I infer the syntax from this hierarchy? Sorry for the long list of questions but I am very happy with phenix and just thought I should understand the syntax better. Thanks for your help Hari Jayaram Attachments: phenix.refine --show-defaults returns refine { strategy = *individual_sites rigid_body *individual_adp group_adp tls \ individual_occupancies group_occupancies group_anomalous sites { individual = None rigid_body = None } adp { individual { isotropic = None anisotropic = None } group = None one_adp_group_per_residue = True tls = None }
Hi,
Hi I quite new to the phenix environemnt and just ran a phenix refinement with the following command line
*_phenix.refine myfile.mtz mymodel.pdb simulated_annealing=true model.ncs refinement.main.ncs=true --overwrite refinement.ncs.excessive_distance_limit=None >phenix_06_18_2008_2.log _*
The model.ncs file is structured as follows
refinement.ncs.restraint_group { reference = chain A selection = chain B selection = chain C selection = chain D }
this looks good.
My data is good to 3.3 A ( membrane protein) and thus far I have been refining with refmac5. After the phenix run indicated above, I had a dramatic reduction in r/rfree ( post refmac 33/36 AND post phenix 28/31). This is despite relatively small changes to my model by the simulated annealing refinement.
This sounds great!
1) At my resolution I guess I should at best be refining only one B-factor / ADP per residue is this the default behavior with the command line above
No. By default, phenix.refine does individual ADP and coordinates refinement. The R/Rfree ~ 28/31 does not indicate an overfitting so you are most likely ok refining individual ADP. Of course it costs nothing to try to refine group ADP with one B per residue and the compare the results. At 3.3A it is not given that you must refine group B, refining individual B may be good too (as it looks like in your case). BTW, I would also include refinement of TLS parameters which is good at this resolution.
2) I have seen the emails about syntax for forcing group-B refinement at this location http://www.phenix-online.org/pipermail/phenixbb/2007-March/000161.html and this one http://www.phenix-online.org/download/documentation/cci_apps/structure_refin... . Basically they use strategy=group_adp . I am imagining this calculates one ADP per residue or per defined group. In my case if I force the behavior with the syntax , how is group ADP for NCS-mates handled?
NCS restraints are not applied to B-factors if you refine them as "group_adp".
3) On a general note , when I say phenix.refine --show-defaults , the section on strategy has a long list, what do the asterisks (*) in the syntax mean .Does that mean those are the defaults .
"*" means selected. For example, by default you see: strategy = *individual_sites rigid_body *individual_adp group_adp tls \ *occupancies group_anomalous which means individual sites, ADP and occupancies are refined (see manual for details which occupancies are in fact refined). For example, if you want to include TLS to the list above, then just add a "*" in front of corresponding keyword: strategy = *individual_sites rigid_body *individual_adp group_adp *tls \ *occupancies group_anomalous
Sorry for the long list of questions but I am very happy with phenix and just thought I should understand the syntax better.
No problems! Ask as many questions as you need to keep going. Also, you may also look at the Manual where there are plenty of examples and relevant explanations: http://www.phenix-online.org/documentation/refinement.htm Please let me know if you have any other questions, Pavel.
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hari jayaram -
Pavel Afonine