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

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