<div dir="ltr">Hi Pavel,<div><br></div><div>What's the latest state of this default function to form an unusual covalent bond? I think it would be great useful.</div><div><br></div><div>Tiantian</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Jun 9, 2012 at 6:58 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Nigel,<br>
<br>
can we do it as part of a default phenix.refine, as well as phenix.metal_coordination? I see a growing pressure to do this... I think there is more harm not doing this at all then doing this always but not very optimally.<br>
<br>
Let's keep this in mind and discuss once we have a chance.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On 6/8/12 12:50 PM, Nigel Moriarty wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Charles<br>
<br>
If you have a recent version, you can use the command-line program<br>
<br>
phenix.ligand_linking<br>
Usage:<br>
phenix.ligand_linking pdb_file_name<br>
<br>
<br>
Options:<br>
--version show program's version number and exit<br>
-h, --help show this help message and exit<br>
--show-defaults Display defaults<br>
<br>
to get the files needed for phenix.refine. Don't make a "super<br>
residue" as I believe that will make life difficult when you try to<br>
deposit to the PDB.<br>
<br>
Cheers<br>
<br>
Nigel<br>
<br>
PS. Happy to help you directly if you have issues.<br>
<br>
<br>
On Fri, Jun 8, 2012 at 9:40 AM, Charles Stewart Jr., PhD<br>
<<a href="mailto:cstewart@salk.edu" target="_blank">cstewart@salk.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello all,<br>
<br>
I saw a couple of posts on this from a year ago but didn't find a<br>
conclusive answer to how to tell phenix to insert a covalent bond between<br>
a cysteine residue and a bound inhibitor. I have the inhibitor (a small<br>
molecule) modeled in but haven't figured out how to insert the covalent<br>
bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a<br>
cif file. The distance between the sulfur on the cysteine and the first<br>
carbon atom in the inhibitor is 1.8A.<br>
<br>
Do I need to run eLBOW using the protein-inhibitor pdb to generate an<br>
appropriate cif file?<br>
<br>
I see in phenix.refine under the PDB interpretation tab their is a box for<br>
"add link to CIF"....is this where I need to tell phenix to insert the<br>
covalent bond?<br>
<br>
I guess I could just draw the inhibitor-cysteine complex as a modified<br>
amino acid and try inserting it that way.....<br>
<br>
charles<br>
--<br>
Charles Stewart Jr., PhD<br>
Research Associate<br>
Chemical Biology and Proteomics Laboratory-Noel<br>
Salk Institute for Biological Studies<br>
10010 North Torrey Pines Road<br>
La Jolla, CA 92037<br>
<br>
Phone: <a href="tel:%28858%29%20453-4100%20x1946" value="+18584534100" target="_blank">(858) 453-4100 x1946</a><br>
Fax: <a href="tel:%28858%29%20597-0855" value="+18585970855" target="_blank">(858) 597-0855</a><br>
Email: <a href="mailto:cstewart@salk.edu" target="_blank">cstewart@salk.edu</a><br>
<br>
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</blockquote>
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