Prime User Manual - ISP

Prime User Manual
Chapter 11: Command Syntax
Chapter 11
This chapter summarizes the command syntax for various programs that are part of Prime. All
the programs are executed by driver scripts, which run under the Schrödinger Job Control
facility. For more information on this facility, see the Job Control Guide. The conventions used
in describing the command syntax are outlined in the Document Conventions section at the
front of this manual.
Residue specifications are used with a number of the input file keywords for several of the
scripts. These have the format C:N, where C is a one-character chain ID (‘_’ if the chain ID is
blank) and N is the residue number and insertion code (if any). Atom specifications similarly
have the format C:N:A, where A is the 4-character PDB atom name with spaces replaced by
underscores, e.g. A:185:_SG_.
Most of these scripts accept the standard Schrödinger Job Control command line options and
other commonly used options, listed in Table 11.1. Exceptions are noted in the program
descriptions.
Table 11.1. Standard Schrödinger job control options.
Option Description
-HOST host run the job on the specified host. The default is the local host.
-LOCAL Run the job in the local directory rather than the temporary directory
-TMPDIR tmpdir Run the job in the temporary directory tmpdir
-WAIT Do no return control to the shell until the job finishes
-INTERVAL n Update the output every n seconds
-NICE Run the job at reduced priority
-DEBUG Turn on debugging for job control as well as the program
-HELP Show information on command-line usage
11.1 blast—Run Blast Searches
The blast script provides an interface to the Blast and PSIBlast programs from NCBI, while
also supporting standard Schrodinger Job Control options. All options are passed on to the
script via an input file.
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