<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Mark!<div>Anybody for the 24th trip to Alba?</div><div>I'll be away from the 1st - 16th of September but I can still arrange the trip before leaving.</div><div>César.<br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div>------------------------------------------------------------------</div><div>Cesar Santiago, Ph. D.</div><div>Dept. of Macromolecules Structure at CNB, CSIC.</div><div>X-ray Crystallography Facility.</div><div>Campus Universidad Autónoma.</div><div>Madrid, 28049</div><div><br></div><div><a href="mailto:csantiag@cnb.csic.es">csantiag@cnb.csic.es</a></div><div><br></div></span><br class="Apple-interchange-newline">
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<br><div><div>On Aug 27, 2015, at 6:42 AM, <a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Send phenixbb mailing list submissions to<br><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span class="Apple-tab-span" style="white-space:pre"> </span>http://phenix-online.org/mailman/listinfo/phenixbb<br>or, via email, send a message with subject or body 'help' to<br><span class="Apple-tab-span" style="white-space:pre"> </span>phenixbb-request@phenix-online.org<br><br>You can reach the person managing the list at<br><span class="Apple-tab-span" style="white-space:pre"> </span>phenixbb-owner@phenix-online.org<br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of phenixbb digest..."<br><br><br>Today's Topics:<br><br> 1. Re: phenix.refine automatic linking options (Engin ?zkan)<br> 2. external passive 3D monitor with macbook pro or imac for coot<br> and pymol stereo view (Xiao Lei)<br> 3. Rank-scaled map (Jianghai Zhu)<br> 4. Re: Rank-scaled map (Pavel Afonine)<br> 5. Re: on the starting mtz file for phenix refine (Pavel Afonine)<br> 6. Ligand addition in COOT for later refinement in<span class="Apple-tab-span" style="white-space:pre"> </span>Phenix.refine<br> (Manoj saxena)<br> 7. Re: Ligand addition in COOT for later refinement in<br> Phenix.refine (Oleg Sobolev)<br> 8. Computational Crystallography Newsletter - Volume 6,<span class="Apple-tab-span" style="white-space:pre"> </span>Number 2<br> (Nigel Moriarty)<br> 9. Starting structure as reference model - crashing in<span class="Apple-tab-span" style="white-space:pre"> </span>1.10-2142<br> (Tristan Croll)<br> 10. Re: Starting structure as reference model - crashing in<br> 1.10-2142 (Pavel Afonine)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Thu, 20 Aug 2015 15:41:31 -0500<br>From: Engin ?zkan <eozkan@uchicago.edu><br>To: Billy Poon <bkpoon@lbl.gov><br>Cc: PHENIX user mailing list <phenixbb@phenix-online.org><br>Subject: Re: [phenixbb] phenix.refine automatic linking options<br>Message-ID: <55D63B7B.6000707@uchicago.edu><br>Content-Type: text/plain; charset="utf-8"; Format="flowed"<br><br>Dear Billy and Nigel,<br><br>Thank you. Phenix.refine GUI in the latest nightly/release candidate no <br>longer has the master enable/disable button, and so the problem is resolved.<br><br>Engin<br><br>On 8/13/15 11:28 AM, Billy Poon wrote:<br><blockquote type="cite">Hi Engin,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks! We updated that part of the GUI so that it should be more <br></blockquote><blockquote type="cite">intuitive. There is now a button that lets you apply automatic linking <br></blockquote><blockquote type="cite">to all the components and a button that disables all automatic <br></blockquote><blockquote type="cite">linking. You can, of course, still pick which components to enable by <br></blockquote><blockquote type="cite">checking the specific boxes.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Tue, Aug 11, 2015 at 7:40 AM, Engin ?zkan <eozkan@uchicago.edu <br></blockquote><blockquote type="cite"><mailto:eozkan@uchicago.edu>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Dear Developers,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Using the latest phenix nightly, I observed something odd in the<br></blockquote><blockquote type="cite"> phenix.refine UI, and I thought I should report it. If one<br></blockquote><blockquote type="cite"> unchecks Automatic ligand linking, this seems to not override its<br></blockquote><blockquote type="cite"> options, as the instructions in the Options window suggest.<br></blockquote><blockquote type="cite"> Specifically, if "Automatic Ligand Linking" is unchecked, but the<br></blockquote><blockquote type="cite"> "Link metals" is checked within its Options window, metal link<br></blockquote><blockquote type="cite"> restraints are still created.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> I checked the .geo file to confirm this.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Thanks,<br></blockquote><blockquote type="cite"> Engin<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> _______________________________________________<br></blockquote><blockquote type="cite"> phenixbb mailing list<br></blockquote><blockquote type="cite"> phenixbb@phenix-online.org <mailto:phenixbb@phenix-online.org><br></blockquote><blockquote type="cite"> http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote><blockquote type="cite"> Unsubscribe: phenixbb-leave@phenix-online.org<br></blockquote><blockquote type="cite"> <mailto:phenixbb-leave@phenix-online.org><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150820/427faca5/attachment-0001.htm><br><br>------------------------------<br><br>Message: 2<br>Date: Fri, 21 Aug 2015 00:45:16 -0700<br>From: Xiao Lei <xiaoleiusc@gmail.com><br>To: PHENIX user mailing list <phenixbb@phenix-online.org><br>Subject: [phenixbb] external passive 3D monitor with macbook pro or<br><span class="Apple-tab-span" style="white-space:pre"> </span>imac for coot and pymol stereo view<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><CABaNifwLZK7sGot44G5GtZNLv+8bzQ3Jwdv089HDLPds6y8-wA@mail.gmail.com><br>Content-Type: text/plain; charset="utf-8"<br><br>Dear phenixbb members,<br><br>I'm thinking to view stereo 3D structure on coot and pymol with passive 3D<br>monitor, does anyone have experience of doing this with a macbook pro or<br>imac and a external passive 3D monitor connected using HDMI port?<br><br>If mac does not support this, should I buy a PC and a passive 3D monitor to<br>do it?<br><br>Thanks ahead.<br><br>Xiao<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150821/b763e6bc/attachment-0001.htm><br><br>------------------------------<br><br>Message: 3<br>Date: Fri, 21 Aug 2015 10:41:46 -0700 (PDT)<br>From: "Jianghai Zhu" <zhu@crystal.harvard.edu><br>To: "PHENIX user mailing list" <phenixbb@phenix-online.org><br>Subject: [phenixbb] Rank-scaled map<br>Message-ID: <1440178906104.6b60500b@Nodemailer><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi,<br><br>I know PHENIX can calculate a rank-scaled density map. ?Could anyone inform me which program in PHENIX actually does this? ?<br><br><br>Thanks.<br><br><br>Best,<br><br>?<br>?--Jianghai<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150821/467922b2/attachment-0001.htm><br><br>------------------------------<br><br>Message: 4<br>Date: Fri, 21 Aug 2015 10:58:41 -0700<br>From: Pavel Afonine <pafonine@lbl.gov><br>To: Jianghai Zhu <zhu@crystal.harvard.edu>,<span class="Apple-tab-span" style="white-space:pre"> </span>PHENIX user mailing list<br><span class="Apple-tab-span" style="white-space:pre"> </span><phenixbb@phenix-online.org><br>Subject: Re: [phenixbb] Rank-scaled map<br>Message-ID: <55D766D1.30406@lbl.gov><br>Content-Type: text/plain; charset="utf-8"; Format="flowed"<br><br>Hi Jianghai,<br><br>it is available in cctbx and it is used as part of FEM, phenix.fem [*], <br>and phenix.map_comparison [**] but there is no standalone <br>user-accessible program that would take your map and turn it into <br>rank-scaled one.<br><br>It is trivial to add so I'm adding it right now and chances are you will <br>have it in tomorrow's nightly build.<br><br>All the best,<br>Pavel<br><br>[*]<br>Acta Cryst. (2015). D71, 646-666.<br>FEM: feature-enhanced map<br>P. V. Afonine, N. W. Moriarty, M. Mustyakimov, O. V. Sobolev, T. C. <br>Terwilliger, D. Turk, A. Urzhumtsev and P. D. Adams<br><br>[**]<br>Acta Cryst. (2014). D70, 2593-2606.<br>Metrics for comparison of crystallographic maps<br>A. Urzhumtsev, P. V. Afonine, V. Y. Lunin, T. C. Terwilliger and P. D. Adams<br><br><br><br>On 8/21/15 10:41, Jianghai Zhu wrote:<br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I know PHENIX can calculate a rank-scaled density map. Could anyone <br></blockquote><blockquote type="cite">inform me which program in PHENIX actually does this?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite">? ?--Jianghai<br></blockquote><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150821/d380ddfa/attachment-0001.htm><br><br>------------------------------<br><br>Message: 5<br>Date: Fri, 21 Aug 2015 17:08:27 -0700<br>From: Pavel Afonine <pafonine@lbl.gov><br>To: phenixbb@phenix-online.org<br>Subject: Re: [phenixbb] on the starting mtz file for phenix refine<br>Message-ID: <55D7BD7B.8060805@lbl.gov><br>Content-Type: text/plain; charset=windows-1252; format=flowed<br><br>Experimental data in both *data.mtz and any other *.mtz from <br>phenix.refine are identical. What's in *.mtz file is described in <br>details in phenix.refine documentation:<br><br>http://phenix-online.org/documentation/reference/refinement.html<br><br>You can use any of the two files as input to phenix.refine and that will <br>not make any difference.<br><br>Pavel<br><br>On 8/17/15 06:28, Smith Lee wrote:<br><blockquote type="cite">Dear All,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In the on-line phenix document, there is,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">"Should I use the MTZ file output by phenix.refine as input for the next round of refinement?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The only time this is necessary is when you refined against a dataset that did not include R-free flags, and let phenix.refine generate a new test set. In this case, you should use the file ending in "_data.mtz" for all future rounds of refinement. You do not need to update the input file in each round, as the actual raw data (and R-free flags) are not modified".<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">When we have phenic adding R-free flgas in the first time we process the mtz data by phenix.refine, besides the *data.mtz, phenix also create a *.mtz. In the future phenix.refine, can I refine by always using the *.mtz created in the R-free flag adding step, rather than refine by always using the *data.mtz created in the R-free flag adding step? What is the difference between that *data.mtz and that *.mtz? And what is the side-effect if in the future steps I refine by always using the *.mtz created in the R-free flag adding step?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best regards.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Smith<br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite">phenixbb@phenix-online.org<br></blockquote><blockquote type="cite">http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote><blockquote type="cite">Unsubscribe: phenixbb-leave@phenix-online.org<br></blockquote><br><br><br>------------------------------<br><br>Message: 6<br>Date: Sun, 23 Aug 2015 23:14:24 -0400<br>From: Manoj saxena <mks131@gmail.com><br>To: phenixbb@phenix-online.org<br>Subject: [phenixbb] Ligand addition in COOT for later refinement in<br><span class="Apple-tab-span" style="white-space:pre"> </span>Phenix.refine<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><CAEwpOy7GDq=N_ySw5cdnQvkW7vuQddp=TDQGrpW28PNNiPOBiw@mail.gmail.com><br>Content-Type: text/plain; charset="utf-8"<br><br>Greetings<br> I am trying to place a ligand (CIT) in<br>a protein model that already have some citrate ligands placed. I am doing<br>this using Coot's option "get monomer", and after the fitting of ligand in<br>the density I tried to refine the model using the ligand and the protein<br>pdb as input models. Refinement did not start and I got an error message in<br>Phenix- "Number of groups of duplicate atom labels:....."<br>Could someone please explain how could I get past this error message and<br>what is the correct way to add a ligand to a model that already has some of<br>the ligands<br>of the same type.<br><br>Many thanks in advance<br><br>Regards<br><br>Manoj Saxena<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150823/b3158a4b/attachment-0001.htm><br><br>------------------------------<br><br>Message: 7<br>Date: Mon, 24 Aug 2015 10:14:27 -0700<br>From: Oleg Sobolev <osobolev@lbl.gov><br>To: Manoj saxena <mks131@gmail.com><br>Cc: "phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br>Subject: Re: [phenixbb] Ligand addition in COOT for later refinement<br><span class="Apple-tab-span" style="white-space:pre"> </span>in<span class="Apple-tab-span" style="white-space:pre"> </span>Phenix.refine<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><CADd3otFzEtGR0jaCRYOHBpuwaLZ4Tgdkuq3p54Efa_D_La5ypA@mail.gmail.com><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi Manoj,<br><br>The error says that chain id, residue id and atom name are the same for<br>several atoms. And there should be listing of such atoms after the error.<br>You may try to change chain id or residue number of your new ligand, if<br>this is the case.<br><br>Best regards,<br>Oleg Sobolev.<br><br>On Sun, Aug 23, 2015 at 8:14 PM, Manoj saxena <mks131@gmail.com> wrote:<br><br><blockquote type="cite">Greetings<br></blockquote><blockquote type="cite"> I am trying to place a ligand (CIT) in<br></blockquote><blockquote type="cite">a protein model that already have some citrate ligands placed. I am doing<br></blockquote><blockquote type="cite">this using Coot's option "get monomer", and after the fitting of ligand in<br></blockquote><blockquote type="cite">the density I tried to refine the model using the ligand and the protein<br></blockquote><blockquote type="cite">pdb as input models. Refinement did not start and I got an error message in<br></blockquote><blockquote type="cite">Phenix- "Number of groups of duplicate atom labels:....."<br></blockquote><blockquote type="cite">Could someone please explain how could I get past this error message and<br></blockquote><blockquote type="cite">what is the correct way to add a ligand to a model that already has some of<br></blockquote><blockquote type="cite">the ligands<br></blockquote><blockquote type="cite">of the same type.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Many thanks in advance<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Regards<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Manoj Saxena<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite">phenixbb@phenix-online.org<br></blockquote><blockquote type="cite">http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote><blockquote type="cite">Unsubscribe: phenixbb-leave@phenix-online.org<br></blockquote><blockquote type="cite"><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150824/4cd110ad/attachment-0001.htm><br><br>------------------------------<br><br>Message: 8<br>Date: Tue, 25 Aug 2015 15:00:08 +0000<br>From: Nigel Moriarty <nwmoriarty@lbl.gov><br>To: PHENIX user mailing list <phenixbb@phenix-online.org>, cctbx<br><span class="Apple-tab-span" style="white-space:pre"> </span>mailing<span class="Apple-tab-span" style="white-space:pre"> </span>list <cctbxbb@phenix-online.org>,<span class="Apple-tab-span" style="white-space:pre"> </span>industry@phenix-online.org,<br><span class="Apple-tab-span" style="white-space:pre"> </span>developers@phenix-online.org<br>Subject: [phenixbb] Computational Crystallography Newsletter - Volume<br><span class="Apple-tab-span" style="white-space:pre"> </span>6,<span class="Apple-tab-span" style="white-space:pre"> </span>Number 2<br>Message-ID: <1440514809861-9080b291-d7469201-2e4a7309@lbl.gov><br>Content-Type: text/plain; charset="utf-8"<br><br>I am pleased to announce the publication of the latest issue of the<br>Computational Crystallography Newsletter:<br><br> http://www.phenix-online.org/newsletter/<br><br>A listing of the articles and short communications is given below. Please <br>note that the newsletter accepts articles of a general nature of interest <br>to all crystallographers. Please send any articles to me at <br>NWMoriarty@lbl.gov noting that there is a Word Template on the website to <br>streamline production.<br><br>July 2015 <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf><br><br>Articles<br>- A context-sensitive guide to RNA & DNA base-pair & base-stack geometry <br><http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=22><br><br>Short Communications<br>- New Phaser-MR search panel in Phenix <br><http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=7><br>- Quantum chemical techniques for minimising ligand geometries in the <br>active site <br><http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=10><br>- 13 typical occupancy refinement scenarios and available options in <br>*phenix.refine* <br><http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12><br><br>Fitting tips #10 ? How do your base pairs touch and twist? <br><http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=3><br><br>Cheers<br><br>Nigel<br><br>---<br>Nigel W. Moriarty<br>Building 33R0349, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : CCI.LBL.gov<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150825/4073fb69/attachment-0001.htm><br><br>------------------------------<br><br>Message: 9<br>Date: Thu, 27 Aug 2015 03:30:02 +0000<br>From: Tristan Croll <tristan.croll@qut.edu.au><br>To: "phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br>Subject: [phenixbb] Starting structure as reference model - crashing<br><span class="Apple-tab-span" style="white-space:pre"> </span>in<span class="Apple-tab-span" style="white-space:pre"> </span>1.10-2142<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><BY1PR0101MB1174A17E69C643EC5DC88E27DD6F0@BY1PR0101MB1174.prod.exchangelabs.com><br><span class="Apple-tab-span" style="white-space:pre"> </span><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br><br><br>When I attempt to run a refinement in Phenix 1.10-2142 using the starting structure as a reference model, it crashes with the complaint that the reference (actually, the error states NCS - despite no NCS being present or enabled. I guess internally it's using the same code?) is too dissimilar to the model, and a calculated RMSD of >90 (degrees? I'm using torsion-angle restraints in any case). The same settings work without complaint on the same structure in dev-2006. I'm running from the GUI, checking "Reference model restraints" in the main phenix.refine window, and then "use starting model as reference" under "All parameters... Reference model restraints...".<br><br><br>Thanks,<br><br><br>Tristan<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150827/e03ad9da/attachment-0001.htm><br><br>------------------------------<br><br>Message: 10<br>Date: Wed, 26 Aug 2015 21:42:24 -0700<br>From: Pavel Afonine <pafonine@lbl.gov><br>To: Tristan Croll <tristan.croll@qut.edu.au>,<br><span class="Apple-tab-span" style="white-space:pre"> </span>"phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br>Subject: Re: [phenixbb] Starting structure as reference model -<br><span class="Apple-tab-span" style="white-space:pre"> </span>crashing in 1.10-2142<br>Message-ID: <55DE9530.7090800@lbl.gov><br>Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br><br>Hi Tristan,<br><br>could you please send me files (off list) and tell how to reproduce the <br>problem?<br><br>Thanks,<br>Pavel<br><br><br>On 8/26/15 20:30, Tristan Croll wrote:<br><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">When I attempt to run a refinement in Phenix 1.10-2142 using the <br></blockquote><blockquote type="cite">starting structure as a reference model, it crashes with the complaint <br></blockquote><blockquote type="cite">that the reference (actually, the error states NCS - despite no NCS <br></blockquote><blockquote type="cite">being present or enabled. I guess internally it's using the same <br></blockquote><blockquote type="cite">code?) is too dissimilar to the model, and a calculated RMSD of >90 <br></blockquote><blockquote type="cite">(degrees? I'm using torsion-angle restraints in any case). The same <br></blockquote><blockquote type="cite">settings work without complaint on the same structure in dev-2006. I'm <br></blockquote><blockquote type="cite">running from the GUI, checking "Reference model restraints" in the <br></blockquote><blockquote type="cite">main phenix.refine window, and then "use starting model as reference" <br></blockquote><blockquote type="cite">under "All parameters... Reference model restraints...".<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Tristan<br></blockquote><blockquote type="cite"><br></blockquote><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150826/dceec17a/attachment.htm><br><br>------------------------------<br><br>_______________________________________________<br>phenixbb mailing list<br>phenixbb@phenix-online.org<br>http://phenix-online.org/mailman/listinfo/phenixbb<br><br><br>End of phenixbb Digest, Vol 117, Issue 9<br>****************************************<br></div></blockquote></div><br></div></body></html>