Prime User Manual - ISP

SKA has difficulty aligning to multiple chains.
Chapter 11: Command Syntax
• scan mode—SKA searches a database of protein structures and identifies potential structural
analogues. By default a non-redundant database of protein chains from the PDB is
searched.
Syntax
$SCHRODINGER/ska [options] jobname
By default the input is read from the file jobname.inp and the output is written to
jobname.out.
ska does not generate output other than the explicitly defined database and a log file in
dbcreate mode—see below for details.
Options
The only option accepted by ska is -DEBUG, which turns on debugging mode for both Job
Control and the SKA program.
Command Input File
The input file consists of lines containing keyword-value pairs, one per line. The keywords are
described in Table 11.8. The set of allowed and required keywords depends on the mode,
which is determined by the MODE keyword.
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/ska -DEBUG jobname
Environment Variables
The ska program handles all required environment variables internally and requires only that
the environment variable SCHRODINGER be set. Should the environment variable TROLLTOP
exist in the current environment it will be overwritten.
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