<div dir="ltr">Hi Michael,<div><br></div><div>The SS bond should be established automatically if S atoms are closer then 3A to each other. If this is not the case for you, I am interested in getting your .pdb file (or just the part with 2 residues in question) to investigate this case.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 25, 2015 at 8:37 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">
<div bgcolor="#FFFFFF" text="#000000">
Hi Michael,<br>
<br>
phenix.refine ignores PDB file header records (or most of them)
except CRYST1, so adding SSBOND is not going to help.<br>
<br>
If this bond is not defined automatically (it should, normally) (you
can check this by looking it up in .geo file that lists all
restraints) then you can always define it manually using "Custom
bonds" mechanism:<br>
<br>
<a href="http://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles" target="_blank">http://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles</a><br>
<br>
Pavel<div><div class="h5"><br>
<br>
<div>On 2/25/15 2:03 AM, Michael Hothorn
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
Dear all, <br>
<br>
I am trying to refine an intermolecular disulfide bond in
phenix.refine. The disulfide involves Cys 188 in chain A and Cys
188 of chain B of a symmetry related molecule, with symop -X,
Y+1/2, Z+1/2. There are two molecules in the AU, SG is P212121. I
generated the following SSBOND entry in the pdb header:<br>
<br>
SSBOND 2 CYS A 188 CYS B 188 1555 3555
2.04<br>
<br>
Based on this: <a href="http://www.wwpdb.org/documentation/file-format/format33/sect6.html" target="_blank">http://www.wwpdb.org/documentation/file-format/format33/sect6.html</a>
the format seems fine, but the disulfide is not being recognized
during refinement. <br>
<br>
Could someone point out to me how to correctly define this for
phenix.refine.<br>
<br>
Thanks!<br>
Michael<br>
<div>
</div>
<br>
<fieldset></fieldset>
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