<div dir="ltr">Hi Tom,<div>Sorry for a late reply. I tried by first extracting one strand of DNA density in Chimera and then I used the phenix.map_to_model my_map.ccp4 seq.dat nproc=8 resolution=4 to build the DNA, but it did not work. Nothing was built. I am wondering if it is because of the phenix.map_box command you were mentioning? Could you give me a bit more advice on how to proceed? Thank you!</div><div>Best,</div><div>Yangqi</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jun 14, 2022 at 12:54 PM Tom Terwilliger <<a href="mailto:tterwilliger@newmexicoconsortium.org">tterwilliger@newmexicoconsortium.org</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 dir="ltr">Hi Yangqi,<div><br></div><div>You can try using</div><div><br></div><div> phenix.map_to_model my_map.ccp4 seq.dat nproc=8 resolution=3</div><div><br></div><div>or something like that. You might first want to cut out the DNA part of the map with phenix.map_box. Your seq.dat can in this case be just the DNA sequence. It will usually know it is DNA from the sequence but you could also say "chain_type=DNA"</div><div><br></div><div>Let us know if that doesn't work!</div><div>All the best,</div><div>Tom T</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jun 14, 2022 at 10:13 AM Yangqi Gu <<a href="mailto:yangqi.gu@yale.edu" target="_blank">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 dir="ltr">Dear PHENIX users and developers,<div>I am currently building a model for a cryo-EM map of a helical complex. I could build the protein easily into the map. However, the map also contains a long chain of DNA density, I am wondering what could be the best way to build this DNA model? I have no previous experience building models with a DNA complex, therefore any suggestion would be helpful!</div><div>Best.</div><div>Yangqi<br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><br></div>Yangqi Gu<div>Ph.D.</div><div>Yale University, West Campus</div></div></div></div></div></div>
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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"><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>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div><br></div>Yangqi Gu<div>Ph.D.</div><div>Yale University, West Campus</div></div></div></div>