[phenixbb] how to exclude a residue in the refinement in command line
PAfonine at lbl.gov
Tue Sep 8 15:52:20 PDT 2009
phenix.refine uses the following criteria for water picking/refinement:
1) peak at mFo-DFc map is higher than ~3sigma, and
2) peak center is within a hydrogen bond to another atom (water or
3) peak has approximately the same shape as a water molecule would have
at this resolution and local environment, and
4) peak at 2mFo-DFc is higher than ~1.0 sigma,
after a round of coordinate and B-factor refinement,
the criteria (2-3-4) are still ok, and
5) refined B-factor of newly placed water is meaningful (didn't jump to
large value), otherwise a water is deleted.
All the relevant parameters are specified under
refinement.ordered_solvent scope of parameters. To see them just type
from the command line:
You can find some information about this in phenix.refine manual:
but I have to update it to reflect recent changes.
Normally you don't change these parameters, simply run something like
this to add and refined water:
phenix.refine model.pdb data.hkl ordered_solvent=true
On 9/8/09 3:43 PM, Raja Dey wrote:
> Hi Ralf,
> Thanks for the right command. It is now working. One more question. Which map is using by the command
> ordered_solvent=true ?
> Is it 2fo-fc and at 1 sigma level?
> How can I specify a map and sigma level(say fo-fc at 3 sigma level) to pick up the waters?
> Thanks for your help.
> ----- Original Message -----
> From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
> Date: Monday, September 7, 2009 4:36 pm
> Subject: Re: [phenixbb] how to exclude a residue in the refinement in command line
> To: phenixbb at phenix-online.org
>> Could you try this?
>> phenix.refine YCd1p3_output.mtz sep71_001.pdb_modified.pdb
>> simulated_annealing=true main.ncs=true
>> refinement.ncs.excessive_distance_limit=6 ncs_groups_3.params
>> ncs.find_automatically=False ordered_solvent=true
>> strategy=rigid_body+individual_sites+group_adp+tls sites.individual="((chain A and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain B and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain C and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain D and not (resid 176 or resid 179 or resid 238 or resid 242)))" output.write_maps=true output.prefix=sep72 --overwrite
>> Changes are:
>> - sites.individual=...
>> - double-quotes in the selection removed
>> - added one at the end of the selection
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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> phenixbb at phenix-online.org
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