[phenixbb] how to exclude a residue in the refinement in command line

Pavel Afonine PAfonine at lbl.gov
Tue Sep 8 15:52:20 PDT 2009


Hi Raja,

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 
macromolecule), and
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:

phenix.refine --show-defaults=all

You can find some information about this in phenix.refine manual:

http://www.phenix-online.org/documentation/nightlies/1.4-159/refinement.htm#anch26

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

Pavel.


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.
>
> Raja
>
>
>
> ----- 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
>>
>> Ralf
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>     
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090908/d483349c/attachment-0003.htm>


More information about the phenixbb mailing list