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.
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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB