[phenixbb] fixing geometry for deposition

Pavel Afonine PAfonine at lbl.gov
Tue Nov 17 12:20:39 PST 2009

Hi Raja,

>               I used the following commands at the last stage of refinement:
> phenix.refine 1205A-p21212.mtz nov138_001.pdb simulated_annealing=false ncs_groups.params main.ncs=true ncs.find_automatically=false refinement.ncs.excessive_distance_limit=None main.bulk_solvent_and_scale=false strategy=rigid_body+individual_sites xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=1 output.write_maps=true output.prefix=nov139 --overwrite

The above command seems extremely weird to me for the following reasons:

1) Bulk-solvent correction and anisotropic scaling always has to be done 
(unless you are experimenting with fake data or these corrections have 
been already applied to Fobs, which is bad ideas anyway). By using 
"main.bulk_solvent_and_scale=false" you turn bulk-solvent correction and 
anisotropic scaling off.

2) By default, phenix.refine does 3 refinement macro-cycles, but often 
(depending how far you are from the final model) this is not enough for 
refinement to converge, so increasing it to 5 or so is a good idea. 
Doing just one macro-cycle (refinement.main.number_of_macro_cycles=1) 
does not make much sense to me. By the way, you can use shortcuts like 

3) You can drop this off the list since it is the default setting 
anyway: "simulated_annealing=false".

4) The refinement strategy: "strategy=rigid_body+individual_sites". 
Normally, you do the rigid body refinement at initial stages of 
refinement when your model is poor, and not at the final run. This is 
because the rigid-body refinement can be very rude on your model: bonds 
can be broken between rigid groups since no restraints is used, for 
example. Also, it's strange that the ADP refinement is turned off - it's 
always good to do, and at 2.8A you can still refined individual ADPs. 
Well, I'm not mention using TLS...

So, I would modify the above command as following:

phenix.refine 1205A-p21212.mtz nov138_001.pdb ncs_groups.params 
main.ncs=true ncs.find_automatically=false 
xray_data.high_resolution=2.9 output.write_maps=true output.prefix=test 

and try running it as is, and with adding keywords "optimize_wxc=true 
optimize_wxu=true", using a model with or w/o H riding H atoms, etc... 
what I wrote in my previous email.

> Regarding amino acids phy, psy..... I tried real space refinement/regularization in coot, 

This is not the same as what I suggested to try in my previous email. 
Anyway, I would first try the modified command above and only then try 
other suggested things.

Good luck,

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