<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Hasan,<br>
<br>
are you refining at too low resolution so you do not want to refine
individual B-factors? Although, if the resolution is "too low" then
you probably shouldn't refine occupancy, which you do. I would just
try refining individual ADPs.<br>
<br>
In this particular case I don't know why the B-factors do not change
- may be this is what the data suggests. It may be a bug too
(although unlikely - this code is very well tested).<br>
<br>
If you like, you can send me the data and model, and all parameter
files and I will have a look. In this case you will get THE answer.<br>
<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>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
<br>
</body>
</html>