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Hi Mark,<br>
<br>
you can have TLS selections in parameter file, however unless you
ask refinement to use TLS they won't be used.<br>
<br>
This allows you to keep selections in your file and gives you
freedom to use them when you decide to.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/4/19 17:37, Mark Saper wrote:<br>
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<blockquote type="cite"
cite="mid:8BF7DA78-BC8F-459C-8EAE-D4ECC0591D82@umich.edu">
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Pavel,
<div class=""><br class="">
</div>
<div class="">Even when I turn off TLS refinement, the definition
for TLS parameters is still there in the .eff effective
parameter file. So I think it's still being applied. It’s
confusing.</div>
<div class="">-Mark</div>
<div class="">
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style="color: rgb(136, 136,
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sans-serif;" class=""> A.
Saper, Ph.D.</font></span>
<div style="color: rgb(136, 136,
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class="">Associate Professor of
Biological Chemistry, U-M
Medical School</div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 4, 2019, at 5:33 PM, Pavel Afonine <<a
href="mailto:pafonine@lbl.gov" class=""
moz-do-not-send="true">pafonine@lbl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-color: rgb(0, 0, 0);
font-family: Helvetica; font-size: 14px; 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;
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text-decoration: none; float: none; display: inline
!important;" class="">Hi Mark,</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; font-style: normal;
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<br style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
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<blockquote type="cite" style="font-family: Helvetica;
font-size: 14px; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
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class="">I have a structure where at one stage TLS
parameters were determined and then refined. It caused
the R-free to increase so I stopped refining the TLS
parameters. Are the TLS parameters still applied to the
structure on subsequent refinement runs even when the
TLS refinement is off?<br class="">
</blockquote>
<br style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; 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;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; 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; float: none; display: inline
!important;" class="">phenix.refine does not use TLS
parameters from PDB file header. So if you disable TLS
atoms are likely to loose TLS component in total ADP.
Optionally, it can use ANISOU (which includes TLS
contribution). At 1.35A is probably what it just does by
default. At lower resolution it would convert
anisotropic ADPs to isotropic.</span><br
style="caret-color: rgb(0, 0, 0); font-family:
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0px; text-transform: none; white-space: normal;
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text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; 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;" class="">
<blockquote type="cite" style="font-family: Helvetica;
font-size: 14px; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
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class="">Is it appropriate to refine anisotropic B’s for
a high resolution (1.35 Å) structure AND apply TLS
parameters?<br class="">
</blockquote>
<br style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; 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;
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text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
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0px; text-transform: none; white-space: normal;
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text-decoration: none; float: none; display: inline
!important;" class="">At this resolution you are best to
use individual anisotropic ADPs for non-H atoms of
macro-molecule, and isotropic ADPs for other atoms.</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 14px; font-style: normal;
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<span style="caret-color: rgb(0, 0, 0); font-family:
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!important;" class="">Pavel</span><br
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