[phenixbb] B-Factor issue

Pavel Afonine pafonine at lbl.gov
Tue Jan 11 09:32:57 PST 2011


  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 <mailto:demircha99 at gmail.com>

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