[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


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.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)
          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.


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