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

[Pavel Afonine]

  Hi Hailiang,

the B-factor can change by +/- a constant. This is because the trace of 
overall anisotropic scale matrix is subtracted from it and added to all 
atoms and to Bsol (similarly to what CNS does).

I will add an option to turn this feature off, although I hope it's not  
problem in your case anyway.

Pavel.


On 8/26/10 3:33 PM, zhangh1 at umbc.edu wrote:
> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>
>>
>