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P.S.: If you decide to send me the file please do so to my email
address and not to the whole bulletin board.<br>
Pavel.<br>
<br>
<br>
On 1/11/11 10:46 AM, Hasan Demirci wrote:
<blockquote
cite="mid:AANLkTinC-kEMrWLHhUuREEWcAZXAY-CKKJ8Q4_TM+4+0@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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 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 moz-do-not-send="true"
href="mailto:Hasan_DeMirci@Brown.edu"
target="_blank">Hasan_DeMirci@Brown.edu</a><br>
<a moz-do-not-send="true"
href="mailto:demircha99@gmail.com" target="_blank">demircha99@gmail.com</a><br>
</blockquote>
<br>
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<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>
<a class="moz-txt-link-abbreviated" href="mailto:Hasan_DeMirci@Brown.edu">Hasan_DeMirci@Brown.edu</a><br>
<a moz-do-not-send="true" href="mailto:demircha99@gmail.com">demircha99@gmail.com</a><br>
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