Prime User Manual - ISP

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Chapter 11: Command Syntax
Syntax
Options
$SCHRODINGER/fr jobname [options]
The -DEBUG and -HOST options are recognized by fr. See Section 2.3 of the Job Control
Guide for more information.
Command Input File
The command input file is named jobname.inp. This input file contains keyword-value pairs,
one pair per line separated by one or more spaces. The keywords are given in Table 11.4.
Table 11.4. Keywords for the fr script.
Keyword syntax Description
QUERY_NAME name Name of the query sequence
QUERY_FILE filename Query sequence file, in FASTA format
ALIFORMAT value Select format of alignments file. Default is Maestro format. For “normal”
format set value to dev.
BGNRES n The first residue of the query that is used in search for homologs. Default: 1
(the first residue).
ENDRES n The last residue of the query that is used. Default: the last residue of the
complete query
PREDSS[_i] filename Secondary structure prediction file of the query sequence, in CASP format.
One occurrence of this keyword is required for each file, and there must be
at least one SSP. If only one prediction is used, the keyword is PREDSS; if
more predictions are used, the keyword is suffixed with an index, starting
from zero: PREDSS_0, PREDSS_1, and so on.
Files
• Input file—named jobname.inp. Contains keywords for running the program.
• Query sequence file—File containing the complete sequence of the query, in FASTA format.
Specified in the input file.
• Secondary structure prediction files in CASP format for the query sequence. See below
for an example of CASP format.
• Output Ranking File—File named jobname.out containing a list of templates ranked
according to the FR scoring function as described above.
Prime 2.1 User Manual