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Hi Joey,<br>
<br>
your question can accommodate multiple interpretations and thus
multiple answers as result. Dorothee's was one. Here is another one.<br>
<br>
First off, what's the goal? Do you want to get a better model of
your crystal structure or lowest possible R- factors?<br>
<br>
Besides, depending on the data quality (resolution, completeness,
etc) you'd need to choose a good parameterization of ADPs
(individual anisotropic for all but H if resolution is sub-angstrom,
isotropic plus TLS at medium to low, etc). Then also depending on
data quality, you might be able to observe and model static (space)
disorder using alternative locations. If that's the case you will
want to refine occupancy factors of such partially occupied sites.<br>
<br>
If the resolution is not low, are you sure you placed all convincing
water? If not, you may want to let phenix.refine to do this for you
automatically. And then towards the end make sure to check them in
Coot.<br>
<br>
There is a lot of choices and possibilities in-between, as one can
imagine. <br>
<br>
If you have more questions or need more help, we can possibly do it
more efficiently by chatting over Zoom, let me know and I will set
up a call.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/7/20 19:22, Dorothee Liebschner
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAAA+ObkL9FtG8vQrKcNHya0WYwGze5Fb2wFEdu0mMr+91rZKvg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi,
<div><br>
</div>
<div>The strategy depends also on the resolution of the data, so
if you could tell us that, we can give suggestions. Also the
type of data, I guess X-ray diffraction?</div>
<div><br>
</div>
<div>Out of curiosity, how do model quality metrics look like
(clashscore, ramachandran, etc) at this point? If you keep
coordinates fixed, they won't improve in refinement. </div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Dorothee</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Aug 7, 2020 at 2:52 PM
Joey Farrell <<a href="mailto:jpfarrell@uchicago.edu"
moz-do-not-send="true">jpfarrell@uchicago.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-US">
<div class="gmail-m_851941004520673753WordSection1">
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">Hello,</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">I am trying to design a set of input
parameters that I will be passing through the
phenix.refine function. The structures</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">that I am working with have already had
their X,Y, and Z orthogonal Å coordinates optimised
via separate protocol.</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">I am looking for advice on which
strategies and parameter values to use with
phenix.refine to improve the crystallographic
R-factors</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">of such structures while preserving their
earlier optimisation in real space.</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">I have been having some success using
“strategy = tls+individual_adp+occupancies” (where
tls = “chain A”, tls = “chain B”, etc.) as
</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">well as adjusting the wxu_scale value
until R-work and R-free are minimised. Are there other
strategies or phenix.refine functionalities
</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">that may also prove helpful with this end
in mind? I believe there may be ways to further
improve R-work and R-free with this software</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">that I am not yet aware of.</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">Thank you for your help!</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">Best,</span></p>
<p class="MsoNormal"><span style="font-size:11pt"
lang="EN-GB">Joey</span></p>
</div>
</div>
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<div>Project Scientist, Molecular Biophysics and Integrated
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