Sorry for the bother, but I can't figure this out for the life of me... I'm attempting to do a 2d alignment of the R2R3 region of AtTT2 with the MYB 1MSF. However, when I try to run the align2d command (script below), it says that I am using a malformed pdb file. I am certain that is not the case, as I just recently got the file directly from the pdb. If anyone could help me out with this, it would be much appreciated.

____ <every ATOM definition in the pdb file, same as below> iup2crm_279W> IUPAC atom not found in topology library; residue type index: C4 25 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. fndatmi_285W> Number of residues <> number of atoms; atom code: 127 105 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 127 105 CA openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 dispers_247E> Internal error: 126 127 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Dynamically allocated memory at finish [B,kB,MB]: 5936909 5797.763 5.662 Starting time : 2003/05/08 17:50:17.028 Closing time : 2003/05/08 17:50:26.897 Total CPU time [seconds] : 0.00

_____ The .top: SET OUTPUT_CONTROL 1 1 1 1 1 READ_TOPOLOGY FILE = '/home/osu3233/bin/modeller6v2/modlib/top_allh.lib' READ_MODEL FILE = '1MSF' SEQUENCE_TO_ALI ALIGN_CODES = '1MSF' ALIGN_CODES = '1MSF' #GENERATE_TOPOLOGY SEQUENCE = '1MSF' #SEQUENCE_TO_ALI ALIGN_CODES = '1MSF' READ_ALIGNMENT FILE = 'test.ali', ALIGN_CODES = 'AtTT2', ADD_SEQUENCE = ON ALIGN2D WRITE_ALIGNMENT FILE='AtTT2-1msf.ali', ALIGNMENT_FORMAT='PIR' WRITE_ALIGNMENT FILE='AtTT2-1msf.pap', ALIGNMENT_FORMAT='PAP'

Thanks, Mike Kurtz