Dear Pavel,<br>I always use command line, below is the parameters I used for refinement of this structure<br><br>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<br>
<br>Thanks.<br><br><div class="gmail_quote">On Tue, Jan 11, 2011 at 12:32 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
Hi Hasan,<br>
<br>
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.<br>
<br>
Can you send some more details about the refinement you did:<br>
<br>
- did you use command line or GUI<br>
- send a parameter file<br>
etc...<br><font color="#888888">
<br>
Pavel.</font><div><div></div><div class="h5"><br>
<br>
On 1/11/11 8:55 AM, Hasan Demirci wrote:
<blockquote type="cite">Hi,<br>
I am trying to refine a structure with a bound ligand "PAR".<br>
Unfortunately, input b-factor of the ligand and output values are
matching exactly even tough I copied the ligand from a different
structure.<br>
I manually changed the occupancy of the ligand to see if it
changes the b-factor but again B-factor didn't change.<br>
Can someone help me to solve this issue?<br>
Below, I attached the first four lines of the pdb after occupancy
change.<br>
<br>
input<br>
"HETATM51786� C11 PAR V�� 1 ��� 140.982� 67.469� 10.830� 1.00
58.13���������� C� <br>
HETATM51787� O11 PAR V�� 1 ��� 140.549� 68.782� 10.389� 1.00
58.13���������� O� <br>
HETATM51788� C21 PAR V�� 1� �� 139.714� 66.811� 11.362� 1.00
58.13���������� C� <br>
HETATM51789� N21 PAR V�� 1 ��� 138.632� 66.819� 10.352� 1.00
58.13���������� N " <br>
<br>
output<br>
"HETATM51828� C11 PAR V�� 1 ��� 157.285 114.375 -64.249� 0.80
58.13���������� C� <br>
HETATM51829� O11 PAR V�� 1 ��� 157.335 115.251 -65.379� 0.80
58.13���������� O� <br>
HETATM51830� C21 PAR V�� 1 ��� 158.559 113.509 -64.364� 0.80
58.13���������� C� <br>
HETATM51831� N21 PAR V�� 1 ��� 159.738 114.342 -64.677� 0.80
58.13���������� N"� <br>
<br>
<br>
Thanks.<br>
<br>
-- <br>
Hasan DeMirci, Ph.D.<br>
Postdoctoral Fellow<br>
Department of Molecular Biology, Cellular Biology &
Biochemistry<br>
Brown University<br>
185 Meeting Street<br>
Providence, RI� � 02912<br>
<br>
(401) 863-3652 lab (SFH)<br>
(401) 863-6124 lab (ship st)<br>
(401) 226-7852 cell<br>
<br>
<a href="mailto:Hasan_DeMirci@Brown.edu" target="_blank">Hasan_DeMirci@Brown.edu</a><br>
<a href="mailto:demircha99@gmail.com" target="_blank">demircha99@gmail.com</a><br>
</blockquote>
<br>
</div></div></div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Hasan DeMirci, Ph.D.<br>Postdoctoral Fellow<br>Department of Molecular Biology, Cellular Biology & Biochemistry<br>Brown University<br>185 Meeting Street<br>Providence, RI� � 02912<br>
<br>(401) 863-3652 lab (SFH)<br>(401) 863-6124 lab (ship st)<br>(401) 226-7852 cell<br><br>Hasan_DeMirci@Brown.edu<br><a href="mailto:demircha99@gmail.com">demircha99@gmail.com</a><br>