Prime User Manual - ISP

Files
Chapter 11: Command Syntax
In addition to the descriptive output in the file specified by OUTPUT_FILE and the error
messages in name.err, tfm produces the following files, where the first part of the file name
is tfm by default but can be changed by other input options, and N is a serial number.
tfm.N.pdb Output structures, if applicable.
tfm.N.spair Possible strand pair assignments for unpaired strands, if automatic strandpairing
is being used.
Return Value and Errors
tfm returns a value of 0 on successful completion, 1 otherwise. All error messages are printed
to the file name.err, where name is either the STRUCT_NAME value or the SEQNAME parameter
in the file specified by INPUT_FILE. This file is empty otherwise, and all output from the
program itself is written to the file specified by OUTPUT_FILE. Output from Job Control goes
to stdout, and any errors arising before the driver script has started will likewise go to stdout or
stderr.
Examples
Sample input for tfm can be generated by running refine with the -LOCAL and -DEBUG
options. The command
refine sample
creates a directory run_sample with the input file sample.1.in (among other files determined
by the refinement type). An input file sample_tfm.inp containing the following lines can be
used to run the job from the command line
INPUT_FILE sample.1.in
OUTPUT_FILE sample.1.out
with the command
tfm sample_tfm
Environment Variables
In addition to the standard environment variables tfm recognizes the following environment
variables:
TFM_QUIET
TFM_VERBOSE
These environment variables can be set to decrease or increase the jobrelated
output in the log file. The value to which they are set is irrelevant.
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