<div dir="ltr"><div dir="ltr">Hi Yangqi,</div><div dir="ltr">Oh I'm sorry, I didn't read carefully enough. For a map-model FSC, these normally do not go to 1. A value of 0.8 is fine at low -res. Half-map FSC values should go to 1.<div>All the best,</div><div>Tom T</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Dec 11, 2019 at 2:28 PM BuddySphinx <<a href="mailto:yangqi.gu@yale.edu">yangqi.gu@yale.edu</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 lang="EN-US"><div class="gmail-m_-5805853892625350647WordSection1"><p class="MsoNormal">Hi Tom,</p><p class="MsoNormal">Thanks for your reply. I am wondering to get FSC starting from 1, does it require the model and map to be perfectly matching? I mean, my model is not built to every density (extra density for extra copy of the protomer, but I did not build the model on these density, since they are not complete). Which means there is more density than model, does it matter or do you think this is more likely to be the bug of the phenix version.</p><p class="MsoNormal">Best,</p><p class="MsoNormal">Yangqi</p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p class="MsoNormal"><u></u> <u></u></p><div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0in 0in"><p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Tom Terwilliger</a><br><b>Sent: </b>Wednesday, December 11, 2019 4:12 PM<br><b>To: </b><a href="mailto:yangqi.gu@yale.edu" target="_blank">Yangqi Gu</a>; <a href="mailto:phenixbb@phenix-online.org" target="_blank">PHENIX user mailing list</a>; <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">Thomas Charles Terwilliger</a><br><b>Subject: </b>Re: [phenixbb] map to model fsc did not start from 1</p></div><p class="MsoNormal"><u></u> <u></u></p><div><p class="MsoNormal">Hi Yangqi,</p><div><p class="MsoNormal">There was a bug in mtriage in a few versions that did lead to this behavior of the FSC not being 1 at low-res. You could try a nightly build and see if this is the cause (or perhaps it really should be lower but that is not likely).</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">In principle at least you should be able to use the helical symmetry for creation of a complete model from a protomer (if that is what you are asking) You can try phenix.map_symmetry and see if that finds the NCS. Otherwise, you can input your NCS with helical symmetry to phenix.map_symmetry and it should check that ncs. The most likely problem is if the helical axis is not along (0,0,1).</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Let me know if that doesn't work,</p></div><div><p class="MsoNormal">All the best,</p></div><div><p class="MsoNormal">Tom T</p></div><div><p class="MsoNormal"><u></u> <u></u></p></div></div><p class="MsoNormal"><u></u> <u></u></p><div><div><p class="MsoNormal">On Wed, Dec 11, 2019 at 2:04 PM Yangqi Gu <<a href="mailto:yangqi.gu@yale.edu" target="_blank">yangqi.gu@yale.edu</a>> wrote:</p></div><blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in"><div><p class="MsoNormal">Dear Phenix developer, </p><div><p class="MsoNormal">I have a question regarding the map to model fsc. I have a filament map and a model with arbitrary copy of the protomer ( I built them in Chimera), then I used the filament model to refine against my map. But I encountered an issue is that the reported FSC (map to model) did not start from 1 but rather 0.8. I am wondering if there is anyway to fix it. Also, in the case of a filament, how do I use NCS operator to refine rather than manual building the filament model? I tried specifying NCS with helical symmetry, but it did not work. </p></div><div><p class="MsoNormal">Best,</p></div><div><p class="MsoNormal">Yangqi<br clear="all"></p><div><p class="MsoNormal"><u></u> <u></u></p></div><p class="MsoNormal"><u></u> <u></u></p></div></div><p class="MsoNormal">_______________________________________________<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" 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></p></blockquote></div><p class="MsoNormal"><br clear="all"></p><div><p class="MsoNormal"><u></u> <u></u></p></div><p class="MsoNormal">-- </p><div><div><div><div><div><div><div><div><div><p class="MsoNormal">Thomas C Terwilliger</p><div><p class="MsoNormal">Laboratory Fellow, Los Alamos National Laboratory</p></div><div><p class="MsoNormal">Senior Scientist, New Mexico Consortium</p></div><div><p class="MsoNormal">100 Entrada Dr, Los Alamos, NM 87544</p></div><div><p class="MsoNormal">Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></p></div><div><p class="MsoNormal">Tel: 505-431-0010</p></div></div></div></div></div></div></div></div></div></div><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p></div></div>
</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>