<div dir="ltr">Hi Dmitry,<div><br><div>Normally you can just supply a symmetry file with N operators produced by Phenix (ends in .ncs_spec) and a model with one chain to ApplyNCS and it should create a new model with N copies of your chain.</div><div><br></div><div>The output model may indeed be missing the header information. You can copy that from your original model if you like.</div><div><br></div><div>As this did not work for you, can you possibly try this example which I have just tested:</div><div><br></div><div>in the Phenix GUI, go to "New Project", and select "Set up Tutorial Data". Then scroll down and choose "Docking and Refinement" of GroEL and hit ok to set up tutorial data.</div><div><br></div><div>1.Superpose 1ss8_A.pdb on chain A of 5w0s.pdb</div><div>Under "Models: superpose, search...", select sequence-based superposition.<br></div><div>Enter a title like "Superpose 1ss8_A.pdb on chain A of 5w0s.pdb"</div><div>Load the 5w0s.pdb as your fixed model</div><div>Load the 1ss8_A.pdb model as your moving model</div><div>Enter 1ss8_A_superposed.pdb as your output model</div><div>Add "ChainA" under selection for fixed model</div><div>Hit Run to superpose 1ss8_A.pdb on chain A of 5w0s.pdb</div><div><br></div><div>2. Get NCS operators from 5w0s.pdb</div><div>Under Models: superpose, search...", select "Find NCS operators"</div><div>Enter at title like "Get NCS operators from 5w0s.pdb"</div><div>For PDB file, select 5w0s.pdb</div><div>Hit run to get your NCS operators.</div><div><br></div><div>3. Apply the NCS operators from 5w0s.pdb to 1ss8_A_superposed.pdb</div><div>The FindNCS GUI will put up a button called "Apply NCS operators". Hit that button and a FindNCS window appears with the symmetry file filled in. You can also open FindNCS directly and select your "groel_dock_refine/FindNCS_2/find_ncs_2.ncs_spec" or similar file.</div><div>Enter 1ss8_A_superposed.pdb as your input pdb file and hit Run.</div><div>Hit Open in Coot to show your expanded PDB file. You can also load in 5w0s.pdb and see that they are similar.</div><div><br></div><div>If that does not work, please let us know! If it does, then you can follow the same steps for your case. If your case does not work, it would be great if you can send in a bug report and attach your files so that we can reproduce the result, and we will fix it!</div><div><br></div><div>I hope that helps!</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br></div><div><br></div><div><div><br></div><div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jun 28, 2023 at 4:10 AM Dmitry Semchonok <<a href="mailto:semchonok@gmail.com">semchonok@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg-5231895070225824384">
<div dir="ltr">
<div style="font-size:12pt;color:rgb(0,0,0)">
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">Dear colleagues,<u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">I use the
</span><span lang="EN-US">«</span><span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">Apply
NFC operators</span><span lang="EN-US">»</span><span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">
tool and would like to use the option described under the "Configuration" sign. <u></u>
<u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">But when I follow these instructions, the outcome model is still
a single subunit. <u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">Initially, I want to get 14mer (with D7 symmetry) with identical
14 monomers.<u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">Could you please prompt how to get it with the
</span><span lang="EN-US">«</span><span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">Apply
NF operators</span><span lang="EN-US">»</span><span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">?<u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u><br>
<u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u>Additionally, the resulting model doesn't
contain description information in the newly created PDB file. <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u>Would you happen to know how to get
the correct PDB file? <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u> <u></u></span></p>
<p style="margin:0in;font-size:11pt"><font face="Segoe UI Emoji, sans-serif">Thanks in advance.</font></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif"><u></u><br>
<u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">Kind regards,<u></u> <u></u></span></p>
<p style="font-family:Calibri,sans-serif;margin:0in 0in 8pt;font-size:11pt">
<span lang="EN-US" style="font-family:"Segoe UI Emoji",sans-serif">Dmitry<u></u> <u></u></span></p>
<br>
</div>
</div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Thomas C Terwilliger<div>Laboratory Fellow, Los Alamos National Laboratory</div><div>Senior Scientist, New Mexico Consortium</div><div>100 Entrada Dr, Los Alamos, NM 87544</div><div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div><div>Tel: 505-431-0010</div><div><br></div></div></div></div></div></div></div></div></div></div>