Hi I quite new to the phenix environemnt and just ran a phenix refinement with the following command line<br><br><b><u>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 </u></b> <br><br>The model.ncs file is structured as follows<br><br>refinement.ncs.restraint_group {<br> reference = chain A <br> selection = chain B<br> selection = chain C<br> selection = chain D<br>
}<br><br>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. <br>
<br>I have a few questions about the process and am hoping some phenix veterans can help me out.<br><br>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<br>
<br>2) I have seen the emails about syntax for forcing group-B refinement at <a href="http://www.phenix-online.org/pipermail/phenixbb/2007-March/000161.html">this location</a> and <a href="http://www.phenix-online.org/download/documentation/cci_apps/structure_refinement.html">this one</a> . <br>
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?<br><br>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 .<br>
Also how can I infer the syntax from this hierarchy?<br><br>Sorry for the long list of questions but I am very happy with phenix and just thought I should understand the syntax better.<br>Thanks for your help <br>Hari Jayaram<br>
<br><br><br>Attachments:<br>phenix.refine --show-defaults returns<br><br>refine {<br> strategy = *individual_sites rigid_body *individual_adp group_adp tls \<br> individual_occupancies group_occupancies group_anomalous<br>
sites {<br> individual = None<br> rigid_body = None<br> }<br> adp {<br> individual {<br> isotropic = None<br> anisotropic = None<br> }<br> group = None<br> one_adp_group_per_residue = True<br>
tls = None<br> }<br><br><br>