[phenixbb] B-Factor issue - P.S.
Pavel Afonine
pafonine at lbl.gov
Tue Jan 11 12:25:52 PST 2011
P.S.: If you decide to send me the file please do so to my email
address and not to the whole bulletin board.
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.
>>
>> --
>> 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 <mailto:Hasan_DeMirci at Brown.edu>
>> demircha99 at gmail.com <mailto: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 <mailto:demircha99 at gmail.com>
>
>
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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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