<div dir="ltr"><div><div><div><div><div><div>Dear luzuok,<br></div>The merging job can easily be done in Pymol. <br>1.Create
symmetry molecules (say at 4A radius) -> Select the symmetry related
molecules of your choice -> save the selected coordinates of the
same <br></div> or<br>2.You can also do the same by saving the
coordinates of two symmetry related molecules separately and merge in a
text file with proper TER records.<br><br></div>regards<br></div>Ashok <br></div>CSIR-CDRI<br></div>Lucknow, INDIA</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 18, 2015 at 9:09 PM, Ashok Nayak <span dir="ltr"><<a href="mailto:ashokgocrackin@gmail.com" target="_blank">ashokgocrackin@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 dir="ltr"><div><div><div><div><div><div>Dear luzuok,<br></div>The merging job can easily be done in Pymol. <br>1.Create symmetry molecules (say at 4A radius) -> Select the symmetry related molecules of your choice -> save the selected coordinates of the same <br></div> or<br>2.You can also do the same by saving the coordinates of two symmetry related molecules separately and merge in a text file with proper TER records.<br><br></div>regards<br></div>Ashok <br></div>CSIR-CDRI<br></div>Lucknow, INDIA<br><div><div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Wed, Nov 18, 2015 at 5:59 PM, luzuok <span dir="ltr"><<a href="mailto:luzuokun@126.com" target="_blank">luzuokun@126.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear Tom,<br>I have the same question too. <br>Another simple question is that how can I merge two symmetry related molecule? Though I can easily expand them by coot.<br><br>Best!<br>Lu<br></div><br><br><div style="zoom:1">--<br><br><div style="color:rgb(51,51,51);font-family:'Microsoft Yahei',verdana;font-size:12px;line-height:19.992000579834px"><br></div><div style="color:rgb(51,51,51);font-family:'Microsoft Yahei',verdana;font-size:12px;line-height:19.992000579834px">Lu Zuokun, Ph.D. Candidate</div><div style="color:rgb(51,51,51);font-family:'Microsoft Yahei',verdana;font-size:12px;line-height:19.992000579834px">College of Life Science, Nankai University</div><div style="clear:both"></div></div><div><div><div></div><br>在 2015-11-18 23:14:48，"Terwilliger, Thomas Charles" <<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>> 写道：<br> <blockquote style="PADDING-LEFT:1ex;MARGIN:0px 0px 0px 0.8ex;BORDER-LEFT:#ccc 1px solid">
<p>Hi Ashok,<br>
</p>
<p>If you have a PDB file with 2 crystallographically-related copies of your molecule, with one called chain A and one called chain B, you can run phenix.simple_ncs_from_pdb on your PDB file to find the matrices and translations. Let me know if that doesn't
do it!<br>
</p>
<p>All the best,<br>
</p>
<p>Tom T<br>
</p>
<p><br>
</p>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>> on behalf of Ashok Nayak <<a href="mailto:ashokgocrackin@gmail.com" target="_blank">ashokgocrackin@gmail.com</a>><br>
<b>Sent:</b> Wednesday, November 18, 2015 7:58 AM<br>
<b>To:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] (no subject)</font>
<div> </div>
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<div dir="ltr">
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<div>Hello Phenix BB,<br>
</div>
Like every amateur crystallographer I could easily generate symmetry mates in a given radius in coot, but I wondered always which is the crystallographic two fold axis axis(my space group being C2) through which the molecule is rotated and translated (if it
is) to get the next molecule. I tried superpose to find the answer, but could only get the Euler angles and transformation matrix and not the axis. Are there any programs where I can get to know this, would be grateful to be enlightened for the same<br>
<br>
</div>
thanks BB in advance<br>
<br>
<div><br>
<br>
<div>regards<br clear="all">
</div>
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<div><br>
-- <br>
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<div dir="ltr"><font face="courier new, monospace"><font size="2">Ashok<u> </u></font>Nayak<br>
PhD student- <br>
Molecular and Structural Biology Division <br>
CSIR-CDRI, Janakipuram Extension<br>
Lucknow-226031<br>
India</font></div>
</div>
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</blockquote></div></div></div><br><br><span title="neteasefooter"><p> </p></span><br></div></div><span class="">_______________________________________________<br>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a><br></span></blockquote></div><br><br clear="all"><br>-- <br><div><div dir="ltr"><font face="courier new, monospace"><font size="2">Ashok<u> </u></font><br>Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008<span class=""><br>Molecular and Structural Biology Division <br></span>Central Drug Research Institute, Janakipuram Extension<br>Lucknow-226031<br>India</font></div></div>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><font face="courier new, monospace"><font size="2">Ashok<u> </u></font><br>Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008<br>Molecular and Structural Biology Division <br>Central Drug Research Institute, Janakipuram Extension<br>Lucknow-226031<br>India</font></div></div>
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