[phenixbb] group_adp default ? and other phenix questions?
Pavel Afonine
pafonine at lbl.gov
Tue Jun 24 20:22:56 PDT 2008
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_refinement.html>
> .
> 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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