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For the record: the answer is in the documentation, see<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/version_docs/1.11rc3-2553/reference/real_space_refine.html">https://www.phenix-online.org/version_docs/1.11rc3-2553/reference/real_space_refine.html</a><br>
<br>
-> Usage examples, #4.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 10/5/16 14:27, Billy Poon wrote:<br>
</div>
<blockquote
cite="mid:CAHmYUcb6GjikQ5UjUzWGN4rWWyaUJHv=7uhZnbBfcX+UzquMQA@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Oliver,
<div><br>
</div>
<div>Actually, I think it's just "label"</div>
</div>
<div class="gmail_extra"><br clear="all">
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<div class="gmail_signature" data-smartmail="gmail_signature">
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<div>--</div>
<div><span
style="font-size:12.8000001907349px">Billy
K. Poon</span><br>
</div>
</div>
<div>Research Scientist, Molecular
Biophysics and Integrated Bioimaging</div>
<div>Lawrence Berkeley National
Laboratory</div>
<div>1 Cyclotron Road, M/S 33R0345</div>
<div>Berkeley, CA 94720</div>
<div>Tel: (510) 486-5709</div>
<div>Fax: (510) 486-5909</div>
<div>Web:�<a moz-do-not-send="true"
href="https://phenix-online.org"
target="_blank">https://phenix-online.org</a></div>
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<br>
<div class="gmail_quote">On Wed, Oct 5, 2016 at 2:21 PM, Billy
Poon <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:bkpoon@lbl.gov" target="_blank">bkpoon@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 dir="ltr">Hi Oliver,
<div><br>
</div>
<div>Oops, the keyword for the command-line would be
"map_coefficients_label". I think you have to wrap the
label in quotes. Let us know if that doesn't work.</div>
</div>
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data-smartmail="gmail_signature">
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<div dir="ltr">
<div dir="ltr">
<div>
<div>--</div>
<div><span
style="font-size:12.8000001907349px">Billy
K. Poon</span><br>
</div>
</div>
<div>Research Scientist,
Molecular Biophysics and
Integrated Bioimaging</div>
<div>Lawrence Berkeley
National Laboratory</div>
<div>1 Cyclotron Road, M/S
33R0345</div>
<div>Berkeley, CA 94720</div>
<div>Tel: <a
moz-do-not-send="true"
href="tel:%28510%29%20486-5709"
value="+15104865709"
target="_blank">(510)
486-5709</a></div>
<div>Fax: <a
moz-do-not-send="true"
href="tel:%28510%29%20486-5909"
value="+15104865909"
target="_blank">(510)
486-5909</a></div>
<div>Web:�<a
moz-do-not-send="true"
href="https://phenix-online.org"
target="_blank">https://phenix-online.org</a></div>
</div>
</div>
</div>
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</span>
<div>
<div class="h5">
<div class="gmail_quote">On Wed, Oct 5, 2016 at 2:16
PM, Oliver Clarke <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:olibclarke@gmail.com"
target="_blank">olibclarke@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Billy, I
should clarify that I typically use
real_space_refine on the command line - I have
not checked it in the GUI.�
<div><br>
</div>
<div>On the command line, it provides a list of
the available arrays, but no way to input a
selected array (and the output of
phenix.real_space_refine --help doesn�t
provide any promising looking options).
<div><br>
</div>
<div>Cheers</div>
<div>Oli
<div>
<div class="m_-3422254048928163458h5"><br>
<div>
<div>
<blockquote type="cite">
<div>On Oct 5, 2016, at 5:12 PM,
Billy Poon <<a
moz-do-not-send="true"
href="mailto:bkpoon@lbl.gov"
target="_blank">bkpoon@lbl.gov</a>>
wrote:</div>
<br
class="m_-3422254048928163458m_7206865451393818348Apple-interchange-newline">
<div>
<div dir="ltr">Hi Oliver,
<div><br>
</div>
<div>When you provide a MTZ
file with map coefficients
to the
phenix.real_space_refine
GUI, the widget labeled "Map
coefficients label" should
refresh and provide a list
of available arrays. It
should behave the same way
as the "Data labels" and
"Phase labels" widgets in
the phenix.refine GUI. If
the "Map coefficients label"
widget is not displaying the
arrays in your MTZ file, can
you provide your file so
that I can take a closer
look? Thanks!</div>
</div>
<div class="gmail_extra"><br
clear="all">
<div>
<div
class="m_-3422254048928163458m_7206865451393818348gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
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<div dir="ltr">
<div>
<div dir="ltr">
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<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div>
<div>--</div>
<div><span
style="font-size:12.8000001907349px">Billy
K. Poon</span><br>
</div>
</div>
<div>Research
Scientist,
Molecular
Biophysics and
Integrated
Bioimaging</div>
<div>Lawrence
Berkeley
National
Laboratory</div>
<div>1
Cyclotron
Road, M/S
33R0345</div>
<div>Berkeley,
CA 94720</div>
<div>Tel: <a
moz-do-not-send="true" href="tel:%28510%29%20486-5709"
value="+15104865709"
target="_blank">(510) 486-5709</a></div>
<div>Fax: <a
moz-do-not-send="true" href="tel:%28510%29%20486-5909"
value="+15104865909"
target="_blank">(510) 486-5909</a></div>
<div>Web:�<a
moz-do-not-send="true"
href="https://phenix-online.org/" target="_blank">https://phenix-online.org</a></div>
</div>
</div>
</div>
</div>
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<br>
<div class="gmail_quote">On
Wed, Oct 5, 2016 at 2:02 PM,
Oliver Clarke <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:olibclarke@gmail.com"
target="_blank">olibclarke@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">Hi,<br>
<br>
I find phenix.real_space
refine very effective for
initial refinement of a
model against a density
modified map after
molecular replacement
(with morphing and
reference restraints etc
enabled).<br>
<br>
However, when I do this it
seems like if there is
more than one array of map
coefficients in the file
there is no way to select
which columns to use,
unlike for phenix.refine -
would it be possible to
add such an option?
Currently I just use cad
in ccp4 to make a file
with the desired columns,
but it would be a smoother
process if the desired
column labels could be
specified directly at run
time.<br>
<br>
Cheers<br>
Oli<br>
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