<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Nick,
<div class=""><br class="">
</div>
<div class="">Explicitly inputting my intended occupancy groups into phenix seems to have done the trick, thanks very much!</div>
<div class=""><br class="">
</div>
<div class="">Cheers</div>
<div class=""><br class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
Andrew Thompson<br class="">
PhD Candidate<br class="">
Molecular and Cellular Biology<br class="">
School of Biological Sciences<br class="">
The University of Adelaide</div>
</div>
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 31 Jan 2019, at 2:57 pm, Schnicker, Nicholas J <<a href="mailto:nicholas-schnicker@uiowa.edu" class="">nicholas-schnicker@uiowa.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Hi Andrew,<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
You should use group constrained refinement to link the occupancies of each isomer. You can see the documentation for how to implement it.<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<a href="https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement" style="color: purple; text-decoration: underline;" class="">https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Cheers,<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Nick<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class=""><<a href="mailto:phenixbb-bounces@phenix-online.org" style="color: purple; text-decoration: underline;" class="">phenixbb-bounces@phenix-online.org</a>>
on behalf of Andrew Philip Thompson <<a href="mailto:andrew.thompson@adelaide.edu.au" style="color: purple; text-decoration: underline;" class="">andrew.thompson@adelaide.edu.au</a>><br class="">
<b class="">Date:<span class="Apple-converted-space"> </span></b>Wednesday, January 30, 2019 at 10:18 PM<br class="">
<b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:phenixbb@phenix-online.org" style="color: purple; text-decoration: underline;" class="">phenixbb@phenix-online.org</a>" <<a href="mailto:phenixbb@phenix-online.org" style="color: purple; text-decoration: underline;" class="">phenixbb@phenix-online.org</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>[phenixbb] Occupancy larger than 1<o:p class=""></o:p></span></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Hi Phenix BB,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
We discovered that a fragment had degraded in our crystallography condition and the product was observed bound in the resulting crystal structure. Unfortunately we have been unable to separate certain stereoisomers of this compound or its analogues, and so
are looking to simultaneously model two of the isomers into the crystal structure. I have made a .cif file corresponding to each isomer and modelled them into my crystal structures with altloc tags A & B, however after refinement, the occupancy of the two
adds up to more than 1 in some instances (ie. 0.51 and 0.53). I’ve never had this before when trying to model dual conformations of the stereoisomers. I tried to make the ligands the same residue number as discussed in a previous thread (<a href="http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html" style="color: purple; text-decoration: underline;" class="">http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html</a>),
however neither coot or pymol will open the pdb file after refinement if I do this. Unfortunately I am unable to share the pdb file as we do not want to disclose the compound structure. <o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Does anyone have any suggestions as to how to proceed?<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Thanks in advance,<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Andrew<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 9pt; font-family: Helvetica;" class="">Andrew Thompson<br class="">
PhD Candidate<br class="">
Molecular and Cellular Biology<br class="">
School of Biological Sciences<br class="">
The University of Adelaide, Australia</span></div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>