[phenixbb] hydrogens in riding model create steric clashes after refinement
amadrona at uci.edu
amadrona at uci.edu
Thu Aug 19 10:16:44 PDT 2010
Hi,
I am having a problem with hydrogens causing steric clashes after refinement.
I added hydrogens to my pdb using: "phenix.ready_set model.pdb".
I was given two sets of coordinates (my model and a pdb for Iron atoms) I
included this new model in the next round of refinement but I did not
include the pdb for the Iron atoms.
I ran refinement with the folowing parmeter file:
refinement.main.ordered_solvent = true
#refinement.main.ordered_solvent.mode=filter_only
refinement.refine.strategy = individual_sites+individual_adp
#refinement.refine.adp.individual.isotropic = "chain W"
refinement.output.prefix = CIN4_refine
refinement.output.serial = 18
refinement.output.write_def_file = True
resolution is 1.37A with close to 400,000 unique observations (obs/param
is still about 4)
Stats:
Rwork Rfree bonds angles
start: .1444 .1723 .016 1.617
end: .1371 .1657 .010 1.301
I also ran wxu and wxc optimization from the command line.
I know that the defualt is "riding-model" so that the hydrogen atoms are
not refined. However, I thought that the program would be able to avoid
steric clashes. Is there an aditional command I need to turn on to
account for this? I am currently fixing every hydrogen that clashes on an
individual basis in coot. There are also a handfull of hydrogens that
exist out in space that I decided to delete.
Thank you very much for your help.
-Yarrow
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