<div dir="ltr">Hi Manoj,<div>I forgot to mention...if you cut out just a small piece of a map with map_box and run map_to_model, be sure to specify:</div><div> segment=False</div><div> asymmetric_map=True</div><div>so that it knows what to do with this piece of the map.</div><div>All the best, </div><div>Tom T</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 4, 2020 at 5:53 AM 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"><div dir="ltr">Hi Manoj,<div><br></div><div>At a resolution of 3.3 A map_to_model is supposed to be able to build regular DNA structures reasonably well, so it is worth trying a few things to see if it can work better.</div><div><br></div><div>If you want only the DNA to be built by map_to_model then you do need to tell map_to_model the solvent_content:</div><div>Usually it figures this out from the sequence file, but yours will only represent a part of the model so you should specify it directly. This could have an effect but perhaps not huge.</div><div><br></div><div>Another thing to try is to cut out the density for a part of your DNA chains and just work with that. Map_to_model can work with a part of a map just fine. So try this: find your best double-stranded DNA regular helix and cut it out with map_box to make a small map. Now try to build with that map. If it doesn't work, you can send me this small map and I'll have a look. If it does work, you can make a few overlapping boxes and build up overlapping parts of the molecule. Then you can combine them all with phenix.combine_models and a map that covers all of them.</div><div><br></div><div>Let me know if these things don't help!</div><div><br></div><div>All the best,</div><div>Tom T </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 4, 2020 at 3:19 AM Manoj saxena <<a href="mailto:mks131@gmail.com" target="_blank">mks131@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 dir="ltr"> Hello,<div> I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A) using the<br> map to model<br> in Phenix 1.18.2.3874, with a DNA sequence input in fasta format and the<br> map as a .ccp4 file.<br> However the output model fitted in the map I am getting is many fragmented<br> PDB files and only one chain of DNA.<br> What is the best way to get a higher fraction of the DNA model fitted into<br> the map, can I switch off the segmentation of map and get both strands<br> fitted into the map. Or the only option is to manually build?<br> Thanks for your help<br> Regards<br> Manoj Saxena<br></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></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>