[phenixbb] Whic mtz file to use and parameters for phenix.refine (GUI) to set?
pafonine at lbl.gov
Mon Jul 19 17:27:34 PDT 2010
> I thought you initially do not add waters until you have a reasonable
> density fit with the protein molecules. Is it ok to update waters
> right from the begining starting from an MR solution?
yes and no.
Yes, it is bad to add waters into poor map and very partial model IF you
and the software you use are careless (for example, treat once placed
water is God given and never critically re-think it at all subsequent
steps). This is because you will have to deal with model bias later on.
No, it is good to add waters, because by adding waters (even temporarily
into some residue side chain or ligand density), you in turn improve the
map and the map improvement leads to a chance to build some more model
and/or improve existing one in a next cycle, and building some model
improves the map some more, and so on. The important thing is that you
and the software you use should treat waters simply as density peaks
(and not actual atoms) and do not hesitate to remove waters as necessary
and build macromolecular into the density they are taking.
I guess AutoBuild does exactly this. phenix.refine option "fix_rotamers"
does this too. I'm not sure if all tools follow this yet, but I hope it
will be the case sooner or later.
Anyway, you can turn water recycling ON and remove all waters after the
map is computed and before you go into manual model building in Coot or
whatever program you use.
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