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, [email protected] 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, [email protected] 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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