[phenixbb] Continue from an AutoBuild job abruptly killed

Miguel Ortiz-Lombardía ibdeno at gmail.com
Thu Jan 17 04:56:58 PST 2008

Hi Ralf,

Thank you!
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.

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:

Failed to carry out AutoBuild_build_cycle:
Refinement failed...perhaps something wrong with input refinement file
or data file or the column labels for them?
Error message from phenix.refine:
Fatal problems interpreting PDB file:
  Number of atoms with unknown scattering type symbols: 22
  Number of atoms with unknown nonbonded energy type symbols: 22
  Please edit the PDB file to resolve the problems and/or supply a
  CIF file with matching restraint definitions, along with
  apply_cif_modification and apply_cif_link parameter definitions
  if necessary (see phenix.refine documentation).
  Also note that phenix.elbow is available to create restraint
  definitions for unknown ligands.

This is one line of the heavy atoms file:

HETATM    1 ZN   ZN  X   1      20.182  79.511  12.808  0.78 72.41

Can I use Zn in this way?
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?

Thank you!!


2008/1/16, Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>:
> Hi Miguel,
> Tom Terwilliger, who wrote AutoBuild, is offline until Jan 21.
> I'm guessing the intermediate states are not saved in an organized
> way, and there is no easy way to recover if your machine crashed.
> However, if you look in the temporary directories, maybe you can
> find the pdb file with the latest model before the crash, copy it
> and use that to restart AutoBuild.
> You can use the "ls -lt" command to find out which directories
> were modified last, then the same command in the directory again
> to find out which files are most recent.
> If this doesn't help, I hope Tom will assist you after the 21.
> Ralf
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!

Georges Brassens
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