[phenixbb] A Small Problem with Atom Types in AutoBuild

Tom Terwilliger terwilliger at lanl.gov
Mon Dec 17 07:04:44 PST 2007

Hi Dale,

Yes, I agree this is a little harsh, and the message should have been 
made clear as well.  The problem is having a totally general way to 
read atom types uniquely, which I have not solved.  This particular 
stop comes because your pdb file has an ATOM record with a metal atom 
in it (MG) and resolve will stop with anything like that to prevent 
confusion between atoms like CA and calcium.

The current version of phenix should solve this particular problem 
for you because it will pull the non-protein atoms out of your PDB 
file and put them back in as HETATM records, which resolve will 
interpret correctly (I hope).

Also if you simply rename your MG records as HETATM instead of ATOM 
that should (I hope) fix the problem in your version as well.

I'm sorry for the trouble!
All the best,
Tom T

At 12:53 AM 12/17/2007, Dale Tronrud wrote:

>     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.
>   Opening
>   MR.1.pdb
>     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
>   MR.1.pdb
>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
>phenixbb mailing list
>phenixbb at phenix-online.org

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
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