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!!
Miguel
2008/1/16, Ralf W. Grosse-Kunstleve <
rwgk@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
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