<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Gino,<div><br></div><div>I'm sorry for the trouble! Try this:</div><div><br></div><div><span class="Apple-style-span" style="font-family: verdana, helvetica, arial, sans-serif; font-size: 16px; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><pre>yum install tcsh</pre><pre><br></pre><pre>The problem is that ubuntu does not have csh. I will be changing autosol to use sh but I haven't done that yet.</pre><pre><br></pre><pre>All the best,</pre><pre>Tom T</pre><pre><br></pre></span><div><div>On Aug 17, 2010, at 10:54 AM, Gino Cingolani wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi All,<br><br>I came back from synchrotron with some good SAD/MAD data.<br>Running some quick autosolve jobs at the beamline already gave interesting Se-mets peaks. At the beamline they use an old version of Phenix (1.3.... I believe).<br><br>Strangely, at home my latest version of Phenix finds absolutely nothing and quickly end with the following error message:<br><br>********************************************************************************<br>Failed to carry out AutoSol_scale_and_analyze_mad:<br><br>None of the solve versions worked<br>********************************************************************************<br><br>To test is the problem is in our data, I quickly re-run 3 old mad/sad datasets of structures previously solved in the lab <br>using the old (good) Solve and/or older Phenix versions.<br>Sadly, all SAD/MAD searches quickly end with the same error message.<br><br>I then tested the 'p9_se_w2.sca' that comes with Phenix.. and once again the same premature failure.<br><br>Is there something wrong with my Phenix? <br>I'm using version 1.6.4-486 on an XPS 420 Quad running Ubuntu 10.04.<br><br>Thanks,<br><br>Gino<br><br>PS everything else in Phenix seems to work (e.g. refinement, validation, elbow, utilities, etc.)<br><br><br>******************************************************************************<br>Gino Cingolani, Ph.D.<br>Associate Professor<br>Thomas Jefferson University<br>Dept. of Biochemistry & Molecular Biology<br>233 South 10th Street - Room 826<br>Philadelphia PA 19107<br>Office (215) 503 4573<br>Lab (215) 503 4595<br>Fax (215) 923 2117<br>E-mail: <a href="mailto:gino.cingolani@jefferson.edu">gino.cingolani@jefferson.edu</a><br>******************************************************************************<br>"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"<br>("You were not born to live like brutes, but to follow virtue and knowledge")<br>Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) <br><br><br>---- Original message ----<br><blockquote type="cite">Date: Fri, 13 Aug 2010 10:44:40 -0700<br></blockquote><blockquote type="cite">From: Nathaniel Echols <<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>> <br></blockquote><blockquote type="cite">Subject: Re: [phenixbb] geometry weight and rmsd bonds - angles <br></blockquote><blockquote type="cite">To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> On Fri, Aug 13, 2010 at 10:20 AM, Lionel Costenaro<br></blockquote><blockquote type="cite"> <<a href="mailto:lcocri@ibmb.csic.es">lcocri@ibmb.csic.es</a>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> So hydrogens were not added (find_and_add_hydrogens =<br></blockquote><blockquote type="cite"> False) and none was in the input pdb, but refined as<br></blockquote><blockquote type="cite"> riding (hydrogens.refine=riding), solvent was not<br></blockquote><blockquote type="cite"> updated (ordered_solvent = False) -there is already<br></blockquote><blockquote type="cite"> 510 waters almost all well defined.<br></blockquote><blockquote type="cite"> To my knowledge, parameters were fine (including<br></blockquote><blockquote type="cite"> refining riding hydrogens) except maybe for the<br></blockquote><blockquote type="cite"> anisotropy of waters for which Pavel recommend<br></blockquote><blockquote type="cite"> isotropy at this resolution.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> This is a common point of confusion, especially for<br></blockquote><blockquote type="cite"> people used to REFMAC. The "riding" model only<br></blockquote><blockquote type="cite"> specifies how existing hydrogen atoms<br></blockquote><blockquote type="cite"> should be treated; it does not actually model hydrogens<br></blockquote><blockquote type="cite"> in those positions if they are not present in the input<br></blockquote><blockquote type="cite"> file. So if there weren't any hydrogens in the input<br></blockquote><blockquote type="cite"> file, it was being refined hydrogen-free. To actually<br></blockquote><blockquote type="cite"> place the hydrogens, you need to click the box labeled<br></blockquote><blockquote type="cite"> "Automatically add hydrogens to model", which will run<br></blockquote><blockquote type="cite"> phenix.ready_set to place the new atoms. The<br></blockquote><blockquote type="cite"> find_and_add_hydrogens option is more specialized<br></blockquote><blockquote type="cite"> anyway and should be left alone unless you are working<br></blockquote><blockquote type="cite"> at ultra-high resolution or doing neutron<br></blockquote><blockquote type="cite"> crystallography.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> - bond outlier CAD - OAC model 1.26 - ideal:<br></blockquote><blockquote type="cite"> ProDRG single 1.36, readyset deloc 1.30, eLBOW<br></blockquote><blockquote type="cite"> deloc 1.429, smiles deloc 1.269<br></blockquote><blockquote type="cite"> - bond outlier CBC - OBD model 1.30 - ideal:<br></blockquote><blockquote type="cite"> ProDRG deloc 1.23, readyset double 1.23, <br></blockquote><blockquote type="cite"> eLBOW aromatic 1.768, smiles double 1.234<br></blockquote><blockquote type="cite"> - angle outlier CAG CAF CAD model 99 - ideal:<br></blockquote><blockquote type="cite"> ProDRG 111, readyset 117, eLBOW 109, smiles<br></blockquote><blockquote type="cite"> 117<br></blockquote><blockquote type="cite"> - dihedral outlier CBC NBB CAY CAZ model 2.2 -<br></blockquote><blockquote type="cite"> ideal: ProDRG 180, readyset 131.66, eLBOW<br></blockquote><blockquote type="cite"> 62.5, smiles 68<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> It seems to me that chemistry clearly depends on the<br></blockquote><blockquote type="cite"> software used, amazing.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> This shouldn't be a huge surprise - the programs use<br></blockquote><blockquote type="cite"> different methods to specify (or guess) molecule<br></blockquote><blockquote type="cite"> parameters, some of which are more effective than<br></blockquote><blockquote type="cite"> others, and different approximations when optimizing the<br></blockquote><blockquote type="cite"> geometry, most of which are optimized for speed rather<br></blockquote><blockquote type="cite"> than theoretical rigor (unless you are running quantum<br></blockquote><blockquote type="cite"> chemical calculations like the AM1 optimization in<br></blockquote><blockquote type="cite"> eLBOW). As a general rule, it is very difficult to<br></blockquote><blockquote type="cite"> accurately guess the chemistry of a molecule based on a<br></blockquote><blockquote type="cite"> PDB file alone; I suspect that CIFs may have similar<br></blockquote><blockquote type="cite"> problems, but Nigel can clarify.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Which method to obtain a "correct" ligand and link<br></blockquote><blockquote type="cite"> definition from scratch should I use?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> I think the correct answer is: use eLBOW with a SMILES<br></blockquote><blockquote type="cite"> string for the ligand, then run ready_set to generate<br></blockquote><blockquote type="cite"> the link, but be sure to supply the CIF file for your<br></blockquote><blockquote type="cite"> ligand to ready_set (instead of letting ready_set create<br></blockquote><blockquote type="cite"> one from scratch based on coordinates). I need to<br></blockquote><blockquote type="cite"> double-check what the GUI returns in a situation like<br></blockquote><blockquote type="cite"> this, because I have not tested this particular case.<br></blockquote><blockquote type="cite"> However, if ready_set tries to make a new CIF with<br></blockquote><blockquote type="cite"> just ligand restraints (*not* the link information), you<br></blockquote><blockquote type="cite"> probably want to ignore that, and keep the rest of the<br></blockquote><blockquote type="cite"> output files. Feel free to email me if you have<br></blockquote><blockquote type="cite"> difficulty running it. (And as mentioned before, you<br></blockquote><blockquote type="cite"> should definitely update to the newest version, because<br></blockquote><blockquote type="cite"> the behavior of some programs has changed, and the eLBOW<br></blockquote><blockquote type="cite"> GUI is relatively new anyway.)<br></blockquote><blockquote type="cite"> -Nat<br></blockquote><blockquote type="cite">________________<br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote><blockquote type="cite"><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:<a href="http://www.phenix-online.org">www.phenix-online.org</a><br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>