[phenixbb] geometry weight and rmsd bonds - angles

Pavel Afonine pafonine at lbl.gov
Fri Aug 13 12:20:47 PDT 2010

  Hi Lionel,

> 1-"At 1.32A I would expect phenix.refine resulting in something like 
> 0.022 and 2.2" (Pavel): 0.022 and 2.2 might indeed be correct for my 
> structure at 1.32A.
> However, if I set  bonds_rmsd_max = 0.012 and angles_rmsd_max = 1.5, 
> providing I set the wc weight correctly, I would expect refine to -at 
> least try to- reach this rmsd values.

not necessarily. These values are not the precise targets that are 
expected to achieve in refinement but rather the soft boundaries for 
optimal weight search. However this difference is a bit surprising to me 
- I will check it.
Anyway, actual values achieved in refinement 0.022 and 2.2 look more 
realistic for 1.32A resolution than ad hoc ones, 0.012 and 1.5.

> 2- I did use optimize_wxc=true and optimize_wxu=true without much 
> better results.

What is "better"?

> - I used mostly the default parameters of the gui and just modified 
> strategy (individual_sites all, individual_adp all, occupancy), 10 
> macro_cycles, and target_weights already mentioned.
> So hydrogens were not added (find_and_add_hydrogens = False) and none 
> was in the input pdb, but refined as riding (hydrogens.refine=riding), 
> solvent was not updated (ordered_solvent = False) -there is already 
> 510 waters almost all well defined.
> To my knowledge, parameters were fine (including refining riding 
> hydrogens) except maybe for the anisotropy of waters for which Pavel 
> recommend isotropy at this resolution.

H-atoms should be added to your model before the refinement, so the 
input PDB contains hydrogens. You can do it using ReadySet! tool:

phenix.ready_set model.pdb

The command "find_and_add_hydrogens = False" is used for refinement 
against ultra-high resolution data to add H atoms to water oxygens based 
on residual map. It's not you case, so you shouldn't use this option.

> Do you recommend to automatically update waters, even during late 
> stages of refinement?

Yes. I guess I wrote it to bb yesterday or so. Refinement changes your 
structure, and changing the structure means some map improvement. Since 
solvent is added using the maps (mFo-DFc and 2mFo-DFc) it is a good idea 
to re-check it (solvent) once the maps are updated. The result of such 
re-check may be some more good water added, or removing some wrong 
waters originally added to noise density peaks. So, the solvent update 
is irrelevant to the stage of refinement.

Good luck!

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