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Install.doc for:
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** MULTICOIL (version 1.0) **
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Copyright 1997 MIT **
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The multicoil program is described in:
Ethan Wolf, Peter S. Kim, Bonnie Berger, "MultiCoil:
A Program for Predicting Two- and Three-stranded Coiled
Coils", Protein Science 6:1179-1189, June 1997.
Website:
http://theory.lcs.mit.edu/multicoil
The multicoil program predicts the location of coiled-coil regions in
amino acid sequences and classifies the predicted regions as dimeric
or trimeric. It is based upon the paircoil program, released in 1995.
This document contains information on obtaining and installing a copy
of the multicoil program on your system. Please read the file
"Instruction.doc" that accompanies the program before running the
program.
When using the multicoil program in your research, please cite the
paper listed above.
For further correspondence please email:
multicoil-help@theory.lcs.mit.edu
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GETTING THE PROGRAM
To install a copy of the multicoil program you must first obtain a
copy of the file "MULTICOIL.tar" in your home directory. You should
then follow the rest of the instructions in this document
(Install.doc). There are two ways to obtain MULTICOIL.tar:
1.
Through the worldwide web at address:
http://theory.lcs.mit.edu/multicoil.html
Follow the instructions at that site for downloading
the file.
2.
Via anonymous ftp from:
address: theory.lcs.mit.edu
directories: /pub/multicoil/SUN
or
/pub/multicoil/SGI
or
/pub/multicoil/DEC_mips
/pub/multicoil/DEC_alpha
depending on your machine type.
(For those of you unfamiliar with ftp, an example of what
to do is given at the end of this document).
IMPORTANT:
Make sure you take the MULTICOIL.tar file that is
compatible with your system type (SUN, SGI,
DEC_alpha, or DEC_mips).
The program will not work if it is not designed
for your machine.
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INSTALLING THE PROGRAM
Once you have a copy of MULTICOIL.tar in your home directory, type the
command:
"tar -xvf MULTICOIL.tar"
This command creates a directory ~/MULTICOIL containing the
following files:
0.
1.
2.
3.
4.
5.
6.
The documents:
Install.doc and Instruction.doc
The program: multicoil
The file:
multicoil_config
The directory:
CONVERSION_FILES/
containing the files:
gauss_param21+
gauss_param28+
likeilhood_cctb21
likelihood_cctb28
The directory:
PROGRAM_DATA/
containing the files:
cctb28.Z
tritb28.Z
genbnk.Z
sampled-pir.seq.Z
The example sequence file:
test.seq
The empty directory:
TEST_RUNS/
which is set as the default location for the program output
in the multicoil_config file.
NOTE: You can change the names of the output files by editing the
multicoil_config file. You can also turn off an output option
by commenting that line out of the multicoil_config file (by
preceding the line with a "#" symbol).
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RUNNING THE PROGRAM
Before running the program make sure you read the documentation in
"Instruction.doc". Additionally, when running the program, please
click on the "help" button in the graphical user interface for a
summary of the commands.
You should also have a look at the file "multicoil_config". This file
contains information that the program requires, including where your
output files will be written. Detailed information on the contents of
"multicoil_config" and how you may want to modify its contents to
control the program is available in "Instruction.doc". If you make
modifications, make sure that the locations of the files needed by the
program in the CONVERSION_FILES and PROGRAM_DATA/ directories are
listed correctly in "multicoil_config".
NOTE that the multicoil program MUST be able to locate the
"multicoil_config" file in order to run. By default it looks for
"~/MULTICOIL/multicoil_config".
You can also move the "multicoil_config" file to any location (for
example, if you want to have multiple copies of "multicoil_config",
each specifying different output files and options for running the
program). However, you must then set the environment variable
MULTICOIL_CONFIG to give the file's location.
For example:
If you move the multicoil_config file into:
"~/multicoil_config"
then before running the program you would type:
"setenv MULTICOIL_CONFIG ~/multicoil_config".
You can also put such a setenv command in your .login file, so
that you do not have to set it each time you log on.
In any case, read the "Instruction.doc" file, and then you are ready to
run your copy of multicoil.
After reading "Instruction.doc", you can type:
"cd ~/MULTICOIL"
"multicoil test.seq"
for a test run of the multicoil program.
Output files will be created in the directory ~/MULTICOIL/TEST_RUNS/
according to the default settings in multicoil_config.
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