[phenixbb] A Small Problem with Atom Types in AutoBuild

Dale Tronrud dale at uoxray.uoregon.edu
Sun Dec 16 23:53:42 PST 2007

    The probe model in my MR project comes from a Shelxl refinement,
and the .pdb file does not contain atom types at the end of each
ATOM statement as modern .pdb files do.  I have magnesium atoms
in my model and the atom names for these atoms are "MG" and are
properly shifted one space to the left of place where atoms with
single letter element symbols lie.

    Phaser has no problem with this .pdb file.  Resolve, however,
considers this to be a fatal error.

    and reading coordinates

  Warning...unknown atom type "M " ...this may indicate
  characters in columns 77-78 of this PDB file that are not the element ID.
  This and all similar labels ignored

  Failed to read line in PDB entry
  The PDB line is:
ATOM   2953 MG   BCL B   1      26.429   2.746 -11.155  1.00 12.03
  Sorry could not read model file

Seems a little harsh to me.  Especially since the error message doesn't
make it back to the log file monitored by the Wizard.  I was confused
about what was causing the wizard to stop until I dug into the other
files in the AutoBuild directory.

    Earlier in the log file the program worries about my atoms "NA"
and "NB" but does conclude that they are nitrogen atoms.

    In the future I'll work with .pdb files with the extra atom types
at the end of the line.

Dale Tronrud

More information about the phenixbb mailing list