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If PDB formatting for alternative conformations or/and values of
occupancies obey some documented rules then as you say you may not
need to cast any parameters or compose any parameter files, this is
correct!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/29/16 19:57, Xiao Lei wrote:<br>
</div>
<blockquote
cite="mid:CABaNifzWVH5aVELTYrsz-Y3gYABEzwOOYx_r8nm0mEUauCCVzA@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
</blockquote>
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