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Alejandro<br>
<br>
Currently you have to have LINK records in your model.pdb that contain
the symmetry details and use<br>
<br>
phenix.link_edits<br>
<br>
to generate the correct "edits". I'll have to look into putting the
smarts into the metal_coordinate code.<br>
<br>
Nigel<br>
<br>
On 2/3/09 9:26 AM, Alejandro Buschiazzo wrote:
<blockquote cite="mid:49887E56.7040105@pasteur.edu.uy" type="cite">
<pre wrap="">Thank you Nigel!
I'll try this immediately.
...in the meantime, I still have a question for you : will this handle
as well the coordination with atoms on symmetry-related protein
neighbors? (don't see those in the elbow.edits that
phenix.metal_coordination generates...or am I missing something silly here?)
ale
Nigel W Moriarty wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Alejandro
There are a number of options. The most direct is to use
phenix.metal_coordination --use-default-bondlengths=1 model.pdb
to get an "edits" file which contains a number of bond and angle
directives for phenix.refine. Without the --use-default-bondlengths
option, the bonds in the model.pdb are used as ideal distances. With
the option, the ideal values are quantum chemical calculated distances.
Always look in the edits file to make sure it contains the restraints
you want. You can remove some (angles are the most likely candidates)
and add if desired.
You can also run
phenix.ready_set model.pdb
which will generate the "edits" file and add hydrogens to your model.
Nigel
On 2/3/09 3:10 AM, Alejandro Buschiazzo wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear PHENIX users,
I wonder what is the 'correct' way of (re)defining geometric restraints
among atoms.
Here's what I need to do : I have several cations that are chelated by
protein residues; some of them involve residues from the same monomer,
yet others involve atoms from both the ASU monomer as well as crystal
neighbors (i.e. symmetry mates).
I see that in the .geo file, these parameters are taken into account as
nonbonded simple and nonbonded asu respectively ... how can I change the
ideal distances to get proper Zn+2 coordination bonds for both kind of
partners?
Thank you in advance for your help!
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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