<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Tom<div><br></div><div>Thanks for the quick reply. Now I get this error. </div><div><br></div><div><br></div><div><div>chem171-152-dhcp:RBD_rebuild_xtalclear_SG76 francisreyes$ phenix.autobuild after_autosolPHENIX VERSION: 1.3 of 26-05-2008</div><div><br></div><div><br></div><div><br></div><div> PHENIX autobuild Fri Jun 27 13:44:38 2008</div><div><br></div><div><br></div><div> The PHENIX developers include:</div><div><br></div><div>P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung,</div><div>T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo,</div><div>J.C. Sacchettini, N.K. Sauter, L.C. Storoni, T.C. Terwilliger, P.H. Zwart</div><div><br></div><div><br></div><div> If you use PHENIX please cite:</div><div><br></div><div>Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.-W., Ioerger, T.R., McCoy, A.J.,</div><div>Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., Terwilliger, T.C.</div><div>(2002). PHENIX: building new software for automated crystallographic structure</div><div>determination. Acta Cryst. D58, 1948-1954.</div><div><br></div><div> </div><div><br></div><div>------------------------------------------------------------ </div><div>Starting AutoBuild with the command:</div><div><br></div><div>phenix.autobuild after_autosol=True </div><div><br></div><div>Sending output to AutoBuild_run_4_/AutoBuild_run_4_1.log </div><div><br></div><div><br></div><div>No matching array: scaling.input.xray_data.obs_labels=ScalAveragedSG_76_30_PHX</div><div><br></div><div>Possible choices:</div><div> AutoBuild_run_4_/refinement_PHX.mtz:S,SIGS</div><div> AutoBuild_run_4_/refinement_PHX.mtz:FP,SIGFP</div><div> AutoBuild_run_4_/refinement_PHX.mtz:PHIB</div><div> AutoBuild_run_4_/refinement_PHX.mtz:FOM</div><div><br></div><div>Please use scaling.input.xray_data.obs_labels</div><div>to specify an unambiguous substring of the target label.</div><div><br></div><div><br></div><div>********************************************************************************</div><div>Failed to carry out AutoBuild_set_up_build:</div><div><br></div><div>failure</div><div>********************************************************************************</div><div><br></div><div><div>On Jun 27, 2008, at 1:11 PM, Tom Terwilliger wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Francis,<div><br></div><div>Thanks! I think the problem is here in your cif_def_file_list parameter file:</div><div><br></div><div> anomalous_scatterers {<br> group {<br> selection = "name I"<br> f_prime = -0.5783<br> f_double_prime = 6.8299<br> }<br> }</div><div><br></div><div>where you are specifying the name I for anomalous scatterers...which seems perfectly reasonable, but....</div><div><br></div><div>unlike what you might expect, the anomalously-scattering atoms are not added to the PDB file created by AutoSol, so the I atom is not present during refinement and you get the error you show.</div><div><br></div><div>In AutoBuild, this should be added automatically, and if not, you can add it with</div><div><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;">input_lig_file_list=my_ha_file.pdb</span></font></pre><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;"><br></span></font></pre><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;">So yes, just go on to AutoBuild. The build in AutoSol is really just to see if everything is working ok...not to do a real build. The default now is to use "helices_strands_only" so that this build goes very fast.</span></font></pre><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;">I hope that helps!</span></font></pre><pre><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; white-space: normal;">-Tom T</span></font></pre><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></div></div></div></div></div></div></span><br class="Apple-interchange-newline"> </div><br><div><div>On Jun 27, 2008, at 12:20 PM, Francis E Reyes wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br>------------------------------------------------------------<br>Starting AutoSol with the command:<br><br>phenix.autosol data=ScalAveragedSG_76_30.ref <br>seq_file=seq_from_pdb.dat \<br>refine_eff_file_list=./refinement/non_default.eff sites=2 <br>atom_type=I \<br>f_prime=-0.582314 f_double_prime=6.84299 res_phase=3.4 <br>resolution_build=3.0 \<br>resolution=3.0 wavelength=1.5418 ha_sites_file=./ha_sites.pdb<br><br>Sending output to AutoSol_run_7_/AutoSol_run_7_1.log<br><br><br>********************************************************************************<br>Failed to carry out AutoSol_build:<br><br>Refinement failed...perhaps something wrong with input refinement file<br>or data file or the column labels for them?<br>Error message from phenix.refine:<br>Empty atom selection:<br> refinement.refine.anomalous_scatterers.group.selection="name I"<br>********************************************************************************<br><br><br>Cuts out in the first round of refinement (after initial Build_1.pdb) .<br><br>I guess I should not have specified anomalous scatterers (at least to <br>autosol).<br><br>Does it refine anomalous automagically in the autobuild when doing a <br>SAD via autosol?<br><br>How do I recover from this error? (continue with the autobuild <br>without anomalous scattering it now seems).<br><br><br>Thanks<br><br>FR<br>---------------------------------------------<br>Francis Reyes M.Sc.<br>215 UCB<br>University of Colorado at Boulder<br><br>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D<br><br>8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D<br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></div></blockquote></div><br></div></div>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://www.phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div> <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>---------------------------------------------<br>Francis Reyes M.Sc.<br>215 UCB<br>University of Colorado at Boulder<br><br>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D<br><br>8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D</div></div></span> </div><br></div></body></html>