Re: [phenixbb] B-Factor issue - P.S.

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 mailto:[email protected]> 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

[email protected] mailto:[email protected] [email protected] mailto:[email protected]

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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

[email protected] [email protected] mailto:[email protected]

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