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Hi Scott,<br>
<br>
another alternative: phenix.map_box can cut out a box around
selected atoms.<br>
<br>
Inputs:<br>
- map in xplor or ccp4 format, or MTZ wih Fourier map coefficients;<br>
- PDB model;<br>
- atom selection string;<br>
<br>
Output:<br>
- PDB with selected atoms in a box;<br>
- three map files (ccp4, xplor and MTZ) with map in a box.<br>
<br>
Examples:<br>
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and
resseq 1:10"<br>
<br>
Pavel<br>
<br>
�<br>
<br>
<div class="moz-cite-prefix">On 2/3/15 8:16 AM, Terwilliger, Thomas
Charles wrote:<br>
</div>
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Hi Scott,
<div>Yes, I think that phenix.cut_out_density should do
something close to what you need, if you specify the same box
and padding for each case. �The output of cut_out_density is a
set of map coefficients in a P1 cell; you then would need to
just create a map of the whole "unit cell" from those
coefficients.</div>
<div>All the best,</div>
<div>Tom T<br>
<div style="font-family: Times New Roman; color: #000000;
font-size: 16px">
<hr tabindex="-1">
<div id="divRpF505685" style="direction: ltr;"><font
color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>] on behalf of Scott
Horowitz [<a class="moz-txt-link-abbreviated" href="mailto:horowsah@umich.edu">horowsah@umich.edu</a>]<br>
<b>Sent:</b> Tuesday, February 03, 2015 8:09 AM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] generating xplor map of
specific size<br>
</font><br>
</div>
<div>
<div dir="ltr">This may be answering my own question:
should cut_out_density do this if I make the original
map bigger than necessary and then pare it down?
<div><br>
</div>
<div>Scott</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Feb 3, 2015 at 9:48 AM,
Scott Horowitz <span dir="ltr">
<<a moz-do-not-send="true"
href="mailto:horowsah@umich.edu" target="_blank">horowsah@umich.edu</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 all,
<div><br>
</div>
<div>Sorry for yet another map question: what I'd
like to do is be able to generate xplor maps
with an explicitly defined size and shape from
the command line using phenix. Just choosing a
buffer around a selection will result in
slightly different sizes for different PDB
files, which I'd like to avoid. In my
comparisons, having exactly the same dimensions
and centering for maps I'm calculating from
multiple slightly different variants would be
very helpful. Is there a way to do this?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Scott</div>
<span class="HOEnZb"><font color="#888888">
<div>
<div><br>
</div>
-- <br>
<div>
<div dir="ltr"><span><font color="#888888">
<div dir="ltr">
<div style="font-family:Helvetica;
word-wrap:break-word"><font>Scott
Horowitz, Ph.D.<br>
</font></div>
<div style="font-family:Helvetica;
word-wrap:break-word"><font>Research
Associate</font></div>
<div style="font-family:Helvetica;
word-wrap:break-word"><font>Howard
Hughes Medical Institute</font></div>
<div style="font-family:Helvetica;
word-wrap:break-word"><font><br>
University of Michigan<br>
Department of Molecular,
Cellular, and�Developmental
Biology<br>
Bardwell lab<br>
830 N. University Ave, Room
4007<br>
Ann Arbor, MI 48109<br>
phone:�<a
moz-do-not-send="true"
value="+17346476683"
style="color:rgb(17,85,204)">734-647-6683</a><br>
fax:�<a moz-do-not-send="true"
value="+17346154226"
style="color:rgb(17,85,204)">734-615-4226</a></font></div>
</div>
</font></span></div>
</div>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature">
<div dir="ltr"><span><font color="#888888">
<div dir="ltr">
<div style="font-family:Helvetica;
word-wrap:break-word"><font>Scott Horowitz,
Ph.D.<br>
</font></div>
<div style="font-family:Helvetica;
word-wrap:break-word"><font>Research
Associate</font></div>
<div style="font-family:Helvetica;
word-wrap:break-word"><font>Howard Hughes
Medical Institute</font></div>
<div style="font-family:Helvetica;
word-wrap:break-word"><font><br>
University of Michigan<br>
Department of Molecular, Cellular,
and�Developmental Biology<br>
Bardwell lab<br>
830 N. University Ave, Room 4007<br>
Ann Arbor, MI 48109<br>
phone:�<a moz-do-not-send="true"
value="+17346476683"
style="color:rgb(17,85,204)">734-647-6683</a><br>
fax:�<a moz-do-not-send="true"
value="+17346154226"
style="color:rgb(17,85,204)">734-615-4226</a></font></div>
</div>
</font></span></div>
</div>
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<br>
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<br>
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