<div dir="ltr"><div dir="ltr">Hi Christian,<div><br></div><div>You can use your helical twist and rise to create the operators representing your helical array with phenix.find_ncs and these parameters:</div><div><br></div><div><ul style="list-style:none;color:rgb(0,0,0);font-family:monospace;font-size:11.7px"><li class="gmail-phil-param" style="clear:both;padding:5px"><span class="gmail-phil-name">helix_extend_range</span><span class="gmail-phil-words" style="color:red"> = None</span><span class="gmail-phil-help" style="color:blue;float:right;width:500px">Range in z to extend helical operators (A)</span></li><li class="gmail-phil-param" style="clear:both;padding:5px"><span class="gmail-phil-name">helix_trans_along_z</span><span class="gmail-phil-words" style="color:red"> = None</span><span class="gmail-phil-help" style="color:blue;float:right;width:500px">Along with helix_theta, defines helical parameters. Note: matrices are for mapping position k on to identity, this may be the opposite of what you would expect.</span></li><li class="gmail-phil-param" style="clear:both;padding:5px"><span class="gmail-phil-name">helix_theta</span><span class="gmail-phil-words" style="color:red"> = None</span><span class="gmail-phil-help" style="color:blue;float:right;width:500px">Along with helix_trans_along_z, defines helical parameters. Note: matrices are for mapping position k on to identity, this may be the opposite of what you would expect.</span></li></ul><div><font color="#0000ff" face="monospace"><span style="font-size:11.7px"><br></span></font></div></div><div><br></div></div>Then you can say something like:<div><br></div><div>phenix.find_ncs map_in=mymap.mrc ncs_in=my_ncs.ncs_spec resolution=3</div><div><br></div><div>and it will try to use those ncs operators and update them to make a new ncs_spec file.</div><div><br></div><div>Once you have the operators, you can use map_box as you have in the past, adding</div><div><br></div><div> symmetry_file=my_ncs.ncs_spec</div><div><br></div><div>but it may not work as well as for non-helical symmetry. It will also give you the asymmetric unit</div><div>of helical symmetry, not of your monomer. You can take the box you get, then find the symmetry in </div><div>the box with find_ncs (using find_ncs_from_density) and then apply map_box again if you need to.</div><div><br></div><div>Let me know if that doesn't work!</div><div>All the best,</div><div>Tom T</div><div><br></div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 9, 2022 at 3:31 AM Christian Tüting <<a href="mailto:christian.tueting@biochemtech.uni-halle.de">christian.tueting@biochemtech.uni-halle.de</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">Dear PHENIX mailing list,<br>
<br>
I have a question regarding a helical reconstruction, done in cryoSPARC.<br>
<br>
<br>
Usually, I work with "normal" symmetric particles, and there I can<br>
simply run phenix.map_box to isolate the asymmetric unit. This is<br>
somehow not possible with a helical map.<br>
<br>
As we also don't have an atomic model yet, we cannot just crop it with<br>
map_box.<br>
<br>
<br>
In our helical reconstruction, we have helical twist (in degree) and the<br>
helical rise (in Å) and a additional point group symmetry. We would like<br>
to isolate a single protofilament for further model building. Is this in<br>
principle possible in PHENIX?<br>
<br>
<br>
Additionally, is there a way to rebuild the helical structure, analogous<br>
to apply_ncs?<br>
<br>
Thanks<br>
<br>
Christian<br>
<br>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <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></div></div>