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
