<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Thanks Tom! This is very helpful and informative. One more question: if my data resolution is worse than 3Å, should I modify the following parameters to replace the default values of 3 for the mr_rosetta run?<div class=""><br class=""></div><div class="">mr_rosetta.rosetta_modeling.map_resolution=</div><div class="">mr_rosetta.crystal_info.resolution=</div><div class="">mr_rosetta.place_model.mr_resolution=</div><div class=""><div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Wei</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On Jul 17, 2020, at 10:18 PM, Tom Terwilliger <<a href="mailto:tterwilliger@newmexicoconsortium.org" class="">tterwilliger@newmexicoconsortium.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class="">Hi Wei,</div><div dir="ltr" class=""><br class=""><div class="">Your sequence file should be 1 copy of the unique sequence.</div><div class=""><br class=""></div><div class="">Your search model should be either your original search model, or probably better, any one copy of a placed and already refined model (just take your A chain from your existing solution and call it a search model).</div><div class=""><br class=""></div><div class="">Your fixed_model consists of the 5 placed copies you already have.</div><div class=""><br class=""></div><div class="">Your value of ncs_copies is 1 if you are using a fixed_model to hold the 5 existing copies.</div><div class=""><br class=""></div><div class="">This approach assumes that the 6th copy is not that similar to the other 5 and NCS averaging will not be useful. Note that there is an alternative approach to do all this that involves specifying the translations and Euler angles of the 5 placed copies. This alternative method will apply NCS to all 6 copies and will work much better than the way described above if all copies actually are very similar. Probably the way described here is better for your case because you get the advantage of using the refined positions of the first 5 copies to get an accurate description of most of the cell contents and as mentioned below the 6th copy ma not be similar.</div><div class=""><br class=""></div><div class="">Note also that the chances of success are low because you already tried to find the 6th copy with Phaser and it didn't work. MR-rosetta could possibly work if the 6th copy is just in a different conformation. If it is disordered or otherwise not visible...it is not likely to work.</div><div class=""><br class=""></div><div class="">You might also just look very carefully in your 2mFo-DFc map for any indication of where the 6th molecule may be located. If you can see a hint of it, a real-space search may be worth trying instead of further molecular replacement. Also extensive auto-building could possibly show you where the 6th copy is located.</div><div class=""><br class=""></div><div class="">If you want to try the alternative approach, see here:</div><div class=""><a href="https://www.phenix-online.org/documentation/reference/mr_rosetta.html" target="_blank" class="">https://www.phenix-online.org/documentation/reference/mr_rosetta.html</a><br class=""></div><div class=""><br class=""></div><div class="">under this description:</div><div class=""><br class=""></div><div class=""><span style="font-weight: bold; font-family: monospace; font-size: 11.7px;" class="">fixed_ensembles</span><span style="color:blue;float:right;font-weight:bold;font-family:monospace;font-size:11.7px;width:500px" class="">If you already know the placement of one or more molecules you can specify them as fixed ensembles. NOTE 1: you are specifying location and orientation of one or more copies of the search model NOTE 2: you cannot specify use_all_plausible_sg if you have fixed ensembles</span></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><span style="font-family: monospace; font-size: 11.7px;" class="">fixed_ensembleID_list</span><span style="color:red;font-family:monospace;font-size:11.7px" class=""> = None</span><span style="color:blue;float:right;font-family:monospace;font-size:11.7px;width:500px" class="">Enter the word 'ensemble_1' to indicate that you want to specify a copy of your search model that is to be fixed. To specify more than one placement just say 'ensemble_1' more than once. For example if you</span></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">....</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Let me know if that doesn't do it or if I gave you any of the parameters incorrectly.</div><div class=""><br class=""></div><div class="">All the best,</div><div class="">Tom T</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 17, 2020 at 7:07 PM Wei Wang <<a href="mailto:ww2283@columbia.edu" target="_blank" class="">ww2283@columbia.edu</a>> wrote:<br class=""></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="">Dear all,<div class=""><br class=""></div><div class="">I would like to get help on a mr_rosetta run. I have a case that 5 copies of searching model was found by Phaser, and I would like to find the sixth one. In addition I would like to improve the building of the MR solution. </div><div class=""><br class=""></div><div class="">In such case I’m considering a mr_rosetta run, with some parameters like this: phenix.mr_rosetta seq_file=seq.dat search_models=placed_5_copies.pdb already_placed=true ncs_copies=1 …</div><div class=""><br class=""></div><div class="">My question is, should I use the already placed 5 copies model as search_models, with ncs_copies=1, or should I use the original searching model with ncs_copies=6 (in this case I guess I should get rid of the other four copies from the result of Phaser)? For seq.dat, should I use the sequence from one copy of searching model, or paste 5 copies into the seq.dat?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class=""><div class="">
<div class=""><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Wei</div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><br class=""></div><br class=""></div><br class="">
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank" class="">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class="">Thomas C Terwilliger<div class="">Laboratory Fellow, Los Alamos National Laboratory</div><div class="">Senior Scientist, New Mexico Consortium</div><div class="">100 Entrada Dr, Los Alamos, NM 87544</div><div class="">Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank" class="">tterwilliger@newmexicoconsortium.org</a></div><div class="">Tel: 505-431-0010</div><div class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div>
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