[phenixbb] B-Factor issue

[Hasan Demirci]

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> 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.
>
> --
> Hasan DeMirci, Ph.D.
> Postdoctoral Fellow
> Department of Molecular Biology, Cellular Biology & Biochemistry
> Brown University
> 185 Meeting Street
> Providence, RI    02912
>
> (401) 863-3652 lab (SFH)
> (401) 863-6124 lab (ship st)
> (401) 226-7852 cell
>
> Hasan_DeMirci at Brown.edu
> demircha99 at gmail.com
>
>
>
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>
>


-- 
Hasan DeMirci, Ph.D.
Postdoctoral Fellow
Department of Molecular Biology, Cellular Biology & Biochemistry
Brown University
185 Meeting Street
Providence, RI    02912

(401) 863-3652 lab (SFH)
(401) 863-6124 lab (ship st)
(401) 226-7852 cell

Hasan_DeMirci at Brown.edu
demircha99 at gmail.com
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