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Hi Chris,<br>
<br>
it's a bit difficult for me to follow your description without
actually looking at the structure...<br>
Could you send me the PDB file and tell occupancies of which atoms
should be refined and how, then I will try to suggest how to
instruct phenix.refine to do what you want. <br>
<br>
Pavel<br>
<br>
On 3/22/12 7:33 PM, Christopher Wanty wrote:
<blockquote cite="mid:CB920215.50B9%25Christopher.Wanty@uwa.edu.au"
type="cite">
<title>Partially reduced disulfides</title>
<font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size:11pt">Hi,<br>
<br>
I have a structure that appears to have a combination of
reduced and oxidised disulfides.<br>
<br>
From previous reading on the board I’ve taken the strategy of
dropping the disulfide detection cutoff to 0.1 then added back
the disulfides as appropriate using restraints. The problem I
now have is that for some of these cysteine pairs there are
clearly oxidised and reduced positions in the density.
Modelling altloc’s for each of these works, but the
occupancies do not refine as I expected; the altloc’s involved
in the disulfide I expected to have the same occupancy as
their counterpart in the disulfide.<br>
<br>
To try to get these to match, I introduced occupancy
constraint that look like:<br>
constrained_group {<br>
selection = (chain A and resseq 276 and altloc B) or
(chain A and resseq 286 and altloc B)<br>
}<br>
<br>
But with that the sum of occupancies for altloc 276 (for
example) is not adding to 1.00. My thought is that I need to
change the occupancy constraints but I’m not sure how to make
them do what I want.<br>
<br>
Any help/advice is appreciated.<br>
<br>
Regards,<br>
Chris<br>
</span></font><font face="Helvetica, Verdana, Arial"><span
style="font-size:12pt">-------------------------------------------------------<br>
Dr. Christopher Wanty<br>
<a moz-do-not-send="true" href="christopher.wanty@uwa.edu.au">christopher.wanty@uwa.edu.au</a><br>
<br>
Research Associate<br>
Biomolecular, Biomedical and Chemical Sciences,<br>
Building M310<br>
University of Western Australia<br>
35 Stirling Highway<br>
Crawley 6009<br>
Western Australia<br>
Australia<br>
<br>
<br>
<br>
</span></font><font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size:11pt"><br>
</span></font>
<br>
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<br>
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