<div dir="ltr">Pavel,<div><br></div><div>Thanks a lot! I found my situation in the letter you wrote:</div><div><font color="#ff0000">4. Overlapping chains: It may happen that stretches of two or more chains overlap in space such that when one is present the other one isn’t . This situation is not recognized automatically by phenix.refine but can be dealt with successfully. This requires two actions. Firstly, overlapping atoms of both chains need to be assigned different altloc ; this will ensure that these atoms will not be pushed apart by non-‐bonded repulsion. Secondly, one needs to compose a parameter file telling phenix.refine what occupancies need to be coupled; this will override any default behavior applicable to these groups of atoms.</font><br></div><div><font color="#ff0000"><br></font></div><div><font color="#000000">But I feel I do not need to compose a parameter file telling phenix.refine what occupancies need to be couples as in your letter. I just edit it by Phenix PDB Editor set two chains with different ID and set Atloc for each chain, then set 0.5 occupancy for each chain and run Phenix.Refine, it seems Phenix.Refine can handle it well and not asking me to provide a parameter file about occupancies.</font></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Apr 29, 2016 at 6:53 PM, 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"><span class="">
<br>
<blockquote type="cite"><span style="font-size:12.8px">Is there any difference
between using the same chain ID (Chain I, atloc P and Q, half
occupancy) or using the different chain ID (Chain I, atloc P,
half occupancy and then Chain K, atloc Q, half occupancy)?</span></blockquote>
<br></span>
This is addressed in the documentation:<br>
<br>
<a href="http://phenix-online.org/documentation/reference/refinement.html#occupancy-refinement" target="_blank">http://phenix-online.org/documentation/reference/refinement.html#occupancy-refinement</a><br>
<br>
as well as here:<br>
<br>
"13 typical occupancy refinement scenarios and available options in
phenix.refine"<br>
<a href="http://phenix-online.org/newsletter/" target="_blank">http://phenix-online.org/newsletter/</a><span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel<br>
<br>
</font></span></div>
</blockquote></div><br></div>