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Maia<br>
<br>
Yes, please do download the latest PHENIX version and run ReadySet!
again. To ensure that the ASG-GCU complex is handled correctly, you
should put in the CONECT records into the PDB file that link the two
"residues" in your ligand complex together. This is a rather complex
example and I'd be interested in seeing your PDB file.<br>
<br>
Nigel<br>
<br>
On 3/17/09 3:10 PM, Maia Cherney wrote:
<blockquote cite="mid:49C01FCC.3010805@ualberta.ca" type="cite">
<pre wrap="">Thank you Nigel,
However, your cif file did not help with the problem (carboxylate is not
planar) when using the PHENIX 1.4-3 version that we have now. You
mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to get
them both? By the way, phenix.ready_set (in our current version) screwed
up all hydrogens in my other ligand (trimer of ASG-GCU). I think that
the ready.set needs to know that the monomers are linked. With this
particular ligand that is a hexamer, ASG is in the library, but GCU is
not. Should I give a cif_link file for the ready.set, too? After I get a
newer version of phenix, I 'll try it again.
Maia
Nigel W Moriarty wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar
groups including the carboxyl group missing from the earlier PHENIX
version I believe you used. I have attached it. There are a few
other things I should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the
model using the data from the Chemical Components database from the
PDB. I would recommend that you use ReadySet! for preparing a PDB
file for refinement. It also adds hydrogens to your model which is
usually a good thing.
Your example does have some nuances. You mention that it is
covalently bound to the CYS. I have attached the two additional files
needed to inform phenix.refine of the covalent bond. I used eLBOW
directly for this but will ensure that ReadySet! will do the same
function in the next release.
An additional function that I have been working on recently is the
removal of the hydrogen in a carboxyl group when the ligand is in the
model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the
carboxyl group remained planar.
If you have any problems with any of the files, feel free to contact
me directly.
Nigel
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<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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