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Hi Lionel,<br>
<br>
something I forgot to mention/ask: if you are using a CIF file for
your ligand that was created by ProDRG then I would strongly
recommend using phenix.ready_set or eLBOW to get a new CIF file and
use it from now on with phenix.refine. We had a lot of problems with
nonsensical ProDRG created CIF files in the past and still runinng
into them from time to time.<br>
<br>
The command <br>
<br>
phenix.ready_set model.pdb <br>
<br>
will create a CIF file for use in refinement.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 8/12/10 8:11 AM, Lionel Costenaro wrote:
<blockquote
cite="mid:AANLkTi=poZW8_J1xL0-7xhCVJPWey1309kGWtZBaZNz8@mail.gmail.com"
type="cite">Hi Ralf, <br>
<br>
Indeed some bond length or angle restraint outliers are from the
ligand when refining with phenix.<br>
However I don't think this is the problem, I give to refmac and
phenix the same ligand dictionary (cif file from ProDRG with link
definition added with JLigand). Refmac / phenix give me the
following outliers >4 sigma : bond length 0 / 6, bond angle 0 /
23, dihedral 23 / 13, chiral 0 / 0, plan 3 /13. Clearly phenix is
not doing a good job (R decrease, but not Rfree). <br>
For refmac I'm using an x-ray weighting term (matrix) of 0.8,
which is more or less expected for 1.3A resolution. <br>
I don't really know how to fix the weights in phenix as I never
used it before and did not find any hint in the manual or bb.<br>
<br>
Lionel<br>
<br>
<br>
<br>
<div class="gmail_quote">2010/8/12 Ralf W. Grosse-Kunstleve <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:rwgk@cci.lbl.gov">rwgk@cci.lbl.gov</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
Hi Lionel,<br>
<div class="im"><br>
> wxc_scale (from default 0.5 downto 0.015), wxu_scale
(from default 1 down<br>
> to 0.03), wc (from default 1 up to 8), with and without
optimising wxc wxu.<br>
> Whatever the parameters, phenix never reached final
rmsd better than 0.022<br>
> and 2.2.<br>
<br>
</div>
The first thing I'd check is the phenix.refine log with the
list<br>
of worst restraints. Look for "Sorted by residual". Without<br>
having seen your structure, my first suspect would be problems<br>
with the ligand restraints or the covalent link to the
protein.<br>
<br>
Ralf<br>
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</blockquote>
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