The user may enter several options when starting the
LEAP program. If the option "-h" is used
(e.g., xleap -h), then the program
will print a list of start-up options and then exit.
A directory may be added to the program's search path
by using the option: "-I dir". This
will cause the program to search dir whenever
a file is requested. If the user would like to execute
LEAP commands at start-up, they should use the option:
"-f file". Finally, if the user enters the command
option "-s", the "leaprc" file will not be executed
at start-up.
A file called "leaprc" is executed as a script file at the start of the LEAP session unless the user suppresses it with a command line option. The file is used to customize the operation of the LEAP program. For example, in the "leaprc" file included in the distribution, commands have been added to load the standard AMBER force field parameter library and the TIP3P water residue, the main chain and terminating amino acid residue UNITs, and the nucleic acid residue UNIT libraries. The file also sets up PDB Name maps and creates aliases. The user can copy and customize the file included in the distribution. LEAP will look for this file in the user's current directory during start-up.
The verbosity command is used to control how much output
LEAP displays to the user. A verbosity level of 0 tells
LEAP to print the minimum amount of information. A verbosity level
of 1 tells LEAP to print all information it can, and a verbosity
level of 2 tells LEAP to print all information and to display
each line read from source files executed using the source command.
The command line interface allows the user to specify a
log file that is used to log all input and output within the command
line environment. The log file is named using the logFile
command. The file has two purposes: to allow the user to see a
complete record of operations performed by LEAP, and to help recover
from (and recreate) program crashes.
Output from LEAP commands is written to the log file at a verbosity
level of 2 regardless of the verbosity level set by the user using
the verbosity command. Each line in the log file that was
typed in by the user begins with the two characters "> "
(a greater-than sign followed by a space). This allows the user
to extract the commands typed into LEAP from the log file to
create a script file that can be executed using the source command.
This provides a type of insurance against program crashes by
allowing the user to regenerate their interactive sessions. An
example of a command that works on UNIX systems and that will
create a script to reenact a LEAP session is:
Note that changes via graphical and table interfaces (xleap) are not captured by command-line traces.