[phenixbb] Real Space Refinement with marginal data

Pavel Afonine PAfonine at lbl.gov
Wed Apr 14 23:29:15 PDT 2010

Hi Rongjin,

> can you show me how to select some residues that are excluded from 
> refinement?
> You suggested this earlier but I did not know how to do it. I looked 
> through the
> manual and I can see how to select a chain, but do not know how to 
> select some residues.

see phenix.refine Documentation web page:


then click on "Atom selection examples". For example:

phenix.refine model.pdb data.mtz refine.sites.individual="chain A and 
resseq 23:36"

will refine coordinates of atoms in chain A belonging to residues from 
23 to 36. The coordinates of all other atoms will be unchanged. You can 
be more specific and specify atoms names, chemical element types, 
alternative conformation identifiers and so on.

The above page contains many other examples of atom selection syntax.

If you still having trouble with this, please tell me in plain English 
(or Russian -;) ) what you want to select and I will return you the 
corresponding atom selection string.

All the best!
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