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Hi,<br>
<br>
in addition, see implementation of <br>
<br>
iotbx.show_distances your.pdb > all_distances<br>
<br>
that will output potentially long file with distances "all with all"
(with some cut-off I think) including symmetry related.<br>
<br>
Also, a method expand_to_p1() of xray.structure
(cctbx/xray/structure.py) may be of help: this will expand model
into P1 (isn't it what you want!).<br>
Actual code that does the calculations:<br>
cctbx_project/cctbx/xray/scatterer_utils.h (expand_to_p1)<br>
<br>
All in all, cctbx offers a variety of tools to do what you want.
Perhaps someone needs to add a command like<br>
<br>
iotbx.expand_to_p1 your_model_in_any_space_group.pdb >
model_p1.pdb<br>
<br>
though it sounds like you want this at your script level, not as
end-user-ready application.<br>
<br>
Let me know if you have more questions or need help with this.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/7/15 2:16 PM, Oleg Sobolev wrote:<br>
</div>
<blockquote
cite="mid:CADd3otH+yxNMCtJ7_1FcW75qCEEXky1uS3=7qJmR60ga00PC9g@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Nicholas,
<div><br>
</div>
<div>Please find the script for searching contacts attached. It
reads in .pdb file (file name is passed through command-line
arg) and prints out symmetry contacts with some additional
info. Hopefully this will help, or feel free to ask more
questions. I believe that you have already read this
description of the machinery you are trying to use:�</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf">http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf</a><br>
</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Apr 7, 2015 at 9:33 AM, <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div link="blue" vlink="purple" lang="EN-GB">
<div>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dear
Nicholas,</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">�</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I
found the CCP4 program ncont to be the easiest way
to identify crystal contacts.<a
moz-do-not-send="true"
name="14c94bb5ae4a3f3b__MailEndCompose"></a></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">�</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">If
you�re interested in a completed unit cell I have a
PDBCUR/PDBSET script somewhere, which might provide
a useful starting point.</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">�</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I
have tried using cctbx a couple of years back to
compute either of these, but got inconsistent
results. (Also at that time I didn�t really know
what I�m doing. Which may still be true.) </span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">�</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">-Markus</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">�</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">�</span></p>
<div>
<div style="border:none;border-top:solid #b5c4df
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif""
lang="EN-US">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif""
lang="EN-US"> <a moz-do-not-send="true"
href="mailto:cctbxbb-bounces@phenix-online.org"
target="_blank">cctbxbb-bounces@phenix-online.org</a>
[mailto:<a moz-do-not-send="true"
href="mailto:cctbxbb-bounces@phenix-online.org"
target="_blank">cctbxbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>Nicholas Pearce<br>
<b>Sent:</b> 07 April 2015 17:26<br>
<b>To:</b> <a moz-do-not-send="true"
href="mailto:cctbxbb@phenix-online.org"
target="_blank">cctbxbb@phenix-online.org</a><br>
<b>Subject:</b> [cctbxbb] Generating crystal
copies</span></p>
</div>
</div>
<div>
<div class="h5">
<p class="MsoNormal">�</p>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Hi
Everyone,<br>
<br>
I'm currently trying to generate crystal
contacts/copies. What I want out at the end is
a list of symmetry operations to generate the
crystallographic copies that form contacts
with my input model.<br>
<br>
I've been using the asu_mappings object, but
I'm not sure I'm using the output correctly or
if it's the right thing to use.<br>
<br>
Code snippet used to calculate the mappings:<br>
<br>
�� # Extract the xray structure from the
reference hierarchy<br>
��� ref_struc =
ref_hierarchy.extract_xray_structure(crystal_symmetry=crystal_symmetry)<br>
��� <br>
��� # Extract the mappings that will tell us
the adjacent symmetry copies<br>
��� asu_mappings =
ref_struc.asu_mappings(buffer_thickness=5)<br>
<br>
��� # Symmetry operations for each atom<br>
��� mappings = asu_mappings.mappings()<br>
<br>
I printed out all of the mappings, as I
presumed the vast majority of the them would
be the identity, meaning that any non-identity
operations would be from atoms in the buffer
area I have defined. These non-identity
operations would presumably be the ones that
would generate the crystal contacts.<br>
<br>
However, a large number of the atoms only had
one mapping, which was not the identity - e.g.
asu_mappings.get_rt_mx(x).as_xyz() might give
'-x+1/2,-y+1/2,z-1/2' for an atom with only
one mapping.<br>
<br>
The effect of this is that the operations
given by this generate symmetry copies that do
not contact my input model in real space.<br>
<br>
I presume this means that asu_mappings is
mapping the atoms in my model to some other
arbitrary asu, as well as the atoms in the
buffer zone around it? Therefore the symmetry
operations given are for these mapped atoms?<br>
<br>
Can anyone help, or suggest an alternative way
to generate the crystal contacts?<br>
<br>
Thanks,<br>
Nick</span></p>
</div>
</div>
</div>
</div>
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