[phenixbb] Can Phenix fix rotamers for several residues only?

Edward A. Berry BerryE at upstate.edu
Sat Aug 28 16:33:28 PDT 2010

Pavel Afonine wrote:
> Hi Ed,
> sorry for the trouble. The error you get is a memory problem indeed.
> "fix_rotamers" is not a strategy. If you do:
> phenix.refine --show-defaults=all
> it will print out all phenix.refine parameters and you will see the list
> of "strategy" keywords:
> strategy = *individual_sites individual_sites_real_space rigid_body \
> *individual_adp group_adp tls *occupancies group_anomalous
> where "*" means selected.
> "fix_rotamers" option may consume a lot of memory since it is using 3
> maps: mFo-DFc, 2mFo-DFc and Fc maps. All these maps are computed on the
> grid with the step high_resolution/4. I found that the scale 1./3
> sometimes works worse than 1./4, although of course using 1./3 will
> result in smaller maps.
Thanks, Pavel,
If nothing else works, can I change this factor with:
   real_space_refinement {
     mode = simple *diff_map
     target_map_name = 2mFo-DFc
     model_map_name = Fc
     grid_resolution_factor = 1./4

? Or its hard-wired for all three maps?

> Currently you can't select residues to apply "fix_rotamers".
> phenix.refine automatically decides which residues need a fix. The
> details of "fix_rotamers" protocol you can find here:
> http://cci.lbl.gov/~afonine/rsr.pdf
> My plan is :
> - find a way of using less memory since it seems to be an issue for
> small memory machines/large structures;
> - enable user-defined atom selection so one can apply "fix_rotamers" to
> selected residues only;
> - improve quality assessment criteria to reduce false fixes.
> I was working on this option beginning of this year and then I got some
> sidetracks so I still consider it "under development". For example, it
> doesn't play very well if you use NCS restraints. At low resolution I
> need to experiment with B-factor sharpened maps or/and 3Fo-2Fc or higher
> order, etc. More efficiently use H atoms.
> Anyway, if you try "fix_rotamers" option I would be interested to hear
> you feedback. Thanks!
> All the best!
> Pavel.

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