I would like to provide BALBES a set of locally-generated models to use as MR probes. These files contain SEQRES records and an arbitrary CRYST1 record CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 followed by the usual ATOM records.
I created a subdirectory ./myprobes containing the models, and invoked BALBES using balbes -o `pwd` -f 182-3-h32.mtz -s Lm3759.pir -l myprobes/ However, balbes apparently could not interpret the PDB files. In the top level output it says #-----------------------------------------------------------# # Model Database Analysis # #-----------------------------------------------------------# number of amino acids in the input sequence file is 113 4 structures found to be above 15% identity with the given sequence, Error message : no structure was found In process_details/get_structure*log it gave messages like: -- monomers start ---- =================================== ====== structure 1 ======== INFO: Nmod= 3 Percent of volume: 25.7 Limit: 0.80 =================================== ------ monomers ------ ==:U__1___u ERR: Number of atoms = 0 ERROR: in READPDB read user pdb file =================================== ====== structure 2 ======== INFO: Nmod= 3 Percent of volume: 25.7 Limit: 0.80 =================================== ------ monomers ------ ==:U__5___u ERR: Number of atoms = 0 ERROR: in READPDB read user pdb file Do I need to pre-process the PDB files somehow before giving them to BALBES? I notice that its own database is not really in PDB format. I used BALBES_1.1.4 (Linux) Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742