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Hi,<br>
<br>
in a nutshell, the problem with CIF files created by PRODRG is that
sometimes PRODRG assigns too small sigmas (esds), which in turn
means that the corresponding terms in restraint targets become much
larger than the others (since they are proportional to 1/sigma**2),
and this results in distorting overall geometry during refinement.<br>
<br>
So, if you do refinement using phenix.refine it is the best to use
phenix.ready_set to obtain cif files for your ligands, or if you get
them from elsewhere then make sure they are correct.<br>
<br>
You can use phenix.reel to check your cif files - my recollection is
that it will highlight bad esds.<br>
<br>
Pavel. <br>
<br>
On 5/25/11 12:09 AM, ChenTiantian wrote:
<blockquote
cite="mid:BANLkTi=iE5dv31V4BG481A8GgmykL6OrWA@mail.gmail.com"
type="cite">Hi,there<br>
I found that the cif file of ligand from ProDRG server is not good
for phenix.refine.<br>
I always got my ligand pdb file using ProDRG, and use the refmac
file as the restraint file of the ligand, but I found that after
running the phenix.refine, the rmsANGLE is very high.<br>
the I followed someone's advice, using phenix.elbow to produce the
ligand's cif file, that really make sense, now I can easily get
the refinement value of the complex structure in a <br>
reasonable level.<br>
Hope it works with your structure too.<br>
<br>
Tiantian<br>
<br>
<div class="gmail_quote">On Tue, May 24, 2011 at 3:34 PM, Priit
Eek <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:priit.eek@gmail.com">priit.eek@gmail.com</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;">
Thanks Nigel and Yuri! elbow.where_is_that_cif_file gave me
the right cif to use in coot. Off to fix that sucrose now...<br>
<font color="#888888"><br>
Priit<br>
</font>
<div>
<div class="h5"><br>
<br>
On 23.05.2011, at 17:55, Yuri wrote:<br>
<br>
> All coot needs to run its real-space refinement is a
.cif file as Nigel pointed out.<br>
> You can also get this file from other ligand library
websites (proDrg, hic-cup, etc...). The only catch here
is. The name of your sucrose atoms must match, exactly,
those in the file.<br>
> Once you have such file go to the the file drop-down
menu and click on Import CIF dictionary in coot. That
should enable to rotate the rotatable bonds of your ligand<br>
><br>
> --<br>
> Yuri Pompeu<br>
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<br>
-- <br>
Drug Discovery and Design Center,<br>
Shanghai Institute of Materia Medica, Chinese Academy of Sciences<br>
Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,<br>
Pudong New Area, Shanghai, 201203, P.R. China<br>
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