[phenixbb] Can Phenix refine B factors for several residues only?

[zhangh1 at umbc.edu]

Hi Pavel:

I tried the following script to refine B factors for only several residues
on chain J:

*****************
phenix.refine 1KP8.pdb t.mtz strategy=individual_adp
electron_density_maps.map_coefficients.mtz_label_amplitudes=FP \
              adp.individual.iso="chain J and resseq 349:365"  >log
*********************

However, it turned out the all the B factors of the whole molecules has
been changed. Not sure whether there is a problem with my script in order
to do that...

Best Regards, Hailiang

>   Hi Hailiang,
>
> no problems! Let me know if you have any questions or problems with this
> and I will be happy to help.
>
> All the best!
> Pavel.
>
>
>   On 8/26/10 12:50 PM, zhangh1 at umbc.edu wrote:
>> Hi Pavel:
>>
>> That's cool! I should have read phenix.refine doc more carefully. I will
>> give it a try and see how it comes. Thanks a lot!
>>
>> Best Regards, Hailiang
>>
>>>    Hi Hailiang,
>>>
>>> you can easily do it in phenix.refine.
>>>
>>> Example:
>>>
>>> phenix.refine model.pdb data.mtz strategy=individual_adp
>>> adp.individual.iso="chain A and resseq 10:20"
>>>
>>> This will refine isotropic B-factors of atoms in residues from 10 to 20
>>> in chain A. All the other atomic model parameters will not be refined.
>>>
>>> Let me know if you need more examples or need any help with this.
>>>
>>> In general, you can apply any combination of refinement strategies
>>> (coordinates, B-factors, etc..) to any selected part of your model.
>>>
>>> Pavel.
>>>
>>>
>>> On 8/26/10 12:00 PM, zhangh1 at umbc.edu wrote:
>>>> Hi,
>>>>
>>>> I want to refine B factors for several residues only (all the other B
>>>> factors and all coordinates fixed, I know it sounds weird but there is
>>>> a
>>>> reason to try that). Is there anyway Phenix can do this? Thanks for
>>>> any
>>>> suggestions!
>>>>
>>>> Best Regards, Hailiang
>>>>
>>>>
>>>> _______________________________________________
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>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>
>
>
>