[phenixbb] B-Factor issue

[Pavel Afonine]

  Hi Hasan,

are you refining at too low resolution so you do not want to refine 
individual B-factors? Although, if the resolution is "too low" then you 
probably shouldn't refine occupancy, which you do. I would just try 
refining individual ADPs.

In this particular case I don't know why the B-factors do not change - 
may be this is what the data suggests. It may be a bug too (although 
unlikely - this code is very well tested).

If you like, you can send me the data and model, and all parameter files 
and I will have a look. In this case you will get THE answer.

Pavel.


On 1/11/11 10:46 AM, Hasan Demirci wrote:
> Dear Pavel,
> I always use command line, below is the parameters I used for 
> refinement of this structure
>
> phenix.refine output.mtz Par.pdb 
> strategy=individual_sites+group_adp+occupancies+tls tls.params 
> modifications.cif Antibiotics.cif zn_link.params 
> restraints_edits.params 
> group_adp_refinement_mode=two_adp_groups_per_residue 
> secondary_structure_restraints=true write_eff_file=false 
> write_geo_file=false wxc_scale=0.15 main.number_of_macro_cycles=2 
> ramachandran_restraints=True
>
> Thanks.
>
> On Tue, Jan 11, 2011 at 12:32 PM, Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> wrote:
>
>     Hi Hasan,
>
>     it sounds like you set up the refinement parameters such that you
>     do not refine B-factors at all. This is the only explanation I can
>     come up.
>
>     Can you send some more details about the refinement you did:
>
>     - did you use command line or GUI
>     - send a parameter file
>     etc...
>
>     Pavel.
>
>
>     On 1/11/11 8:55 AM, Hasan Demirci wrote:
>>     Hi,
>>     I am trying to refine a structure with a bound ligand "PAR".
>>     Unfortunately, input b-factor of the ligand and output values are
>>     matching exactly even tough I copied the ligand from a different
>>     structure.
>>     I manually changed the occupancy of the ligand to see if it
>>     changes the b-factor but again B-factor didn't change.
>>     Can someone help me to solve this issue?
>>     Below, I attached the first four lines of the pdb after occupancy
>>     change.
>>
>>     input
>>     "HETATM51786  C11 PAR V   1     140.982  67.469  10.830  1.00
>>     58.13           C
>>     HETATM51787  O11 PAR V   1     140.549  68.782  10.389  1.00
>>     58.13           O
>>     HETATM51788  C21 PAR V   1     139.714  66.811  11.362  1.00
>>     58.13           C
>>     HETATM51789  N21 PAR V   1     138.632  66.819  10.352  1.00
>>     58.13           N "
>>
>>     output
>>     "HETATM51828  C11 PAR V   1     157.285 114.375 -64.249  0.80
>>     58.13           C
>>     HETATM51829  O11 PAR V   1     157.335 115.251 -65.379  0.80
>>     58.13           O
>>     HETATM51830  C21 PAR V   1     158.559 113.509 -64.364  0.80
>>     58.13           C
>>     HETATM51831  N21 PAR V   1     159.738 114.342 -64.677  0.80
>>     58.13           N"
>>
>>
>>     Thanks.
>

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