Prime User Manual - ISP

Chapter 11: Command Syntax
• Output alignment file—File named jobname.ali containing pairwise alignment between
the query and a template. By default, the alignment is in Maestro format (m2io). In order
to view alignments in normal format (i.e. aligned residues from query and template are
placed on top of each other), add the keyword ALIFORMAT to the input file with value set
to dev.
• Log file—File named jobname.log containing progress of the program, including warnings
and error messages.
Return Value and Errors
The script returns 0 for success and 1 for failure.
In case of failure, check the log file for details on what might be have caused the program to
fail. To turn on debugging output use the -DEBUG command line option as follows:
$SCHRODINGER/fr -DEBUG jobname
Examples
The following file demonstrates the use of three SSPs.
QUERY_NAME HypProtein_furiosus_truncated
QUERY_FILE HP.seq
PREDSS_0 prime_foldrecog_run1_HP-ssp1.casp
PREDSS_1 prime_foldrecog_run1_HP-ssp2.casp
PREDSS_2 prime_foldrecog_run1_HP-ssp3.casp
BGNRES 1
ENDRES 197
The following is an example of a CASP format file. The CASP format has a minimum of 2
columns per line, with the first being the one-letter code for the amino acid and the second
being the secondary structure type. An optional third column gives the confidence level of the
prediction.
PFRMAT SS
TARGET 1HL6:A
AUTHOR xxxx-xxxx-xxxx
REMARK written by Schrodinger LLC Software
METHOD not applicable
MODEL 1
M C 1.00
A C 1.00
D H 1.00
V H 1.00
...
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