[phenixbb] Clashes problem

Pavel Afonine pafonine at lbl.gov
Mon Feb 11 09:06:27 PST 2008

Hi All,

1) phenix.refine has a standard set of geometry restrains as other 
refinement programs: bond, angle, planarity, chirality, dihedral, 
non-bonded. Clash score is not something that is included into 
refinement as a target and then used directly in refinement. Clash 
scores may be bad at the beginning of structure refinement and should be 
good at the end.

2) Using H atoms as a riding model should normally help in fixing 
clashes, however it's not 100% guaranteed: some clashes may be "locked" 
so the refinement cannot overcome the barriers even with H atoms. In 
this case what's Luca Jovine suggesting (see one of the emails in this 
thread) is an excellent thing to do (to add to his receipt: you may also 
consider using more than default number of macro-cycles). Running 
simulated annealing is also helpful (use "simulated_annealing=true" flag 
for this).

3) Since handling of H atoms in phenix.refine is significantly improved 
in newer versions, I would warmly recommend to use the latest 
phenix.refine available (currently from CCI Apps: 

4) Also, clashes related concerns may be a result of inoptimal weight 
between Xray target and restrains. Although one can play with the weight 
adjusting scales manually by trying different values of "wxc_scale" 
parameter ("wxu_scale" is analog for b-factors refinement) the new 
version of phenix.refine has an automatic procedure for finding the best 
weight (here "the best" means the weight that leads to the lowest Rfree) 
(Carsten's suggestion). To use this option:

% phenix.refine model.pdb data.mtz your_parameters.par optimize_wxc=true

Note this this may take a while to run (depending on resolution and 
structure size) so consider running it overnight.

If none of the above helps, I would be *very* interested to look at the 
data and model myself to 1) help you find the best strategy to overcome 
this problem, and 2) find and fix problem in phenix.refine (if any). As 
always, I promise to keep all data confidential.


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