<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Irina,<br>
<br>
meaningfulness of what you are trying to do mostly depends on data
resolution. If data resolution is better than 3A then it is all good
to refine individual isotropic B factors of all atoms. Since Os is
electron-rich compared to the rest it may be good to refine
anisotropic B for Os only (isotropic for the rest). I don't think
you need to refine group B. Yes, you need to refine all -
coordinates, B and likely occupancies of Os. Error in one of these
parameters will go into other parameters. R-factors 25/34 is not
good so I guess you are using incorrect refinement strategy and/or
model parametrization.<br>
<br>
If you send me model and data and ligand cif files (if any) off-list
I might be able to suggest something that may work better.<br>
<br>
A good approach is to run with all defaults first, and then if not
satisfied with results try to find a better way.<br>
<br>
Good luck,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 10/11/15 09:18, Irina PROKHOROVA
wrote:<br>
</div>
<blockquote cite="mid:1444580325958.61374@igbmc.fr" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<style type="text/css" style="display:none"><!--P{margin-top:0;margin-bottom:0;} --></style>
<p>Hello,</p>
<p><br>
</p>
<p>I have many Osmium ions in my structure. They have 6
coordinated ammonium groups and I would like to refine the
B-factors for them: one B-factor for Os�in each residue�and�one
B-factor�for�all 6 ammonium groups in each residue.
</p>
<p>For this I have chosen *group_adp with following syntax</p>
<p><br>
</p>
<p>��� adp {<br>
���� group_adp_refinement_mode = one_adp_group_per_residue \<br>
��������������������������������� two_adp_groups_per_residue
*group_selection<br>
����� group = chain O and element Os<br>
����� group = chain O and element N<br>
��� }<br>
</p>
<p><br>
</p>
<p>I wanted to refine only B-factor for Osmiums in this
refinement. To avoid the bias from previously refined values of
B-factor I presetted B-factors for all Osmiums to 50.<br>
</p>
<p><br>
</p>
<p>As a result I got the change of B-factors for all residues in
the model to the same value (which probably means that all model
was refined as one group) and R-free increased from 0.25 to
0.34.</p>
<p><br>
</p>
<p>What should be the correct syntax for this refinement?</p>
<p>Should I also refine ions coordinates for a�good�refinement of
B-factors?</p>
<p><br>
</p>
<p>Irina<br>
</p>
</blockquote>
<br>
</body>
</html>