Hi Ralf,<br><br>Thank you!<br>I have managed to sort of continue from where it was by giving the wizard the overall_best.pdb model, the overall_best_refine mtz as map coefficients, asking not to rebuild_in_place the model (due to the presence of residues not assigned to the sequence) and changing group_ca_length to 4. Finally, I also provided the last NCS specification file, which was more complete than the one generated from the original heavy atom sites. This seems to be a reasonable option.
<br><br>However, in the meantime, I thought I would like to add the heavy atoms to the refinement, since the option exists. These are Zn atoms (the protein contains two Zn fingers) However, if I try to do so, when the heavy atoms are merged to the model I get this error:
<br><br>Failed to carry out AutoBuild_build_cycle:<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>Fatal problems interpreting PDB file:
<br> Number of atoms with unknown scattering type symbols: 22<br> Number of atoms with unknown nonbonded energy type symbols: 22<br> Please edit the PDB file to resolve the problems and/or supply a<br> CIF file with matching restraint definitions, along with
<br> apply_cif_modification and apply_cif_link parameter definitions<br> if necessary (see phenix.refine documentation).<br> Also note that phenix.elbow is available to create restraint<br> definitions for unknown ligands.
<br>************************************************************<br><br>This is one line of the heavy atoms file:<br><br>HETATM 1 ZN ZN X 1 20.182 79.511 12.808 0.78 72.41 <br><br>Can I use Zn in this way?
<br>I read that I can use phenix.elbow to prepare a cif file for Zn, but not understand how... Could you please give me a clue?<br><br>Thank you!!<br><br><br>Miguel<br><br><div><span class="gmail_quote">2008/1/16, Ralf W. Grosse-Kunstleve <
<a href="mailto:rwgk@cci.lbl.gov">rwgk@cci.lbl.gov</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Miguel,<br>Tom Terwilliger, who wrote AutoBuild, is offline until Jan 21.
<br>I'm guessing the intermediate states are not saved in an organized<br>way, and there is no easy way to recover if your machine crashed.<br>However, if you look in the temporary directories, maybe you can<br>find the pdb file with the latest model before the crash, copy it
<br>and use that to restart AutoBuild.<br>You can use the "ls -lt" command to find out which directories<br>were modified last, then the same command in the directory again<br>to find out which files are most recent.
<br>If this doesn't help, I hope Tom will assist you after the 21.<br>Ralf<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org
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