gencoil(1) [debian man page]

GENCOIL(1)							   User Commands							GENCOIL(1)

NAME

       gencoil - Generates a virtual coil suitable for sequence simulation in ODIN

DESCRIPTION

       gencoil: Generates a virtual coil suitable for sequence simulation in ODIN

   Usage and options:
	      Generate a radially inhomogenous coil:

	      gencoil -rad -n <inplane-size> -fov <FOV> -R <radial-inhomogeneity[%]> -o <Coil-file>

	      Generate an array coil by rotating pre-existing image file:

	      gencoil -rot -n <inplane-size> -fov <FOV> -nc <numof-rotated-subcoils> -i <input-image> -sl <selected-slice> -o <Coil-file>

	      Generate an array coil consisting of simple loops:

       gencoil -arr -n <inplane-size> -nc <numof-rotated-loops>
	      -fov <FOV> -R <array-radius> -o <Coil-file>

	      Generate coil with a B1 gradient:

	      gencoil -grad -n <inplane-size> -fov <FOV> -g <B1-gradient-endpoint> -o <Coil-file>

   Other options:
       -v  <loglevel>  or  <component:loglevel>  for  debugging/tracing  all  components  or a single component, respectively. Possible values for
	      loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog).

       -h, --help, -help, --version : Print help text or version information

gencoil 1.8.5							    March 2012								GENCOIL(1)

COILS-WRAP(1)							   User Commands						     COILS-WRAP(1)

NAME

       coils-wrap - runs ncoils three times to give you a three-window output

SYNOPSIS

       coils-wrap [OPTION]

DESCRIPTION

       coils-wrap runs ncoils three times to give you a three-window output.

       ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By
       comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that
       the sequence will adopt a coiled-coil conformation.

OPTIONS

       -i  input file in FASTA format

       -o  output file

       -r  raw output file, default: `<output file>_raw'

       -m  matrix type; set matrix (MTK or MTIDK)

       -w  weight a&d = b,c,e,f&g (boolean)

EXAMPLES

       "coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out -r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt"

       "ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa"

FILES

       /usr/share/coiledcoils/*.mat
	   matrix data files

AUTHOR

       R.B. Russell, A.N. Lupas, 1999

COPYRIGHT AND LICENSE

       GPL

       Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164

SEE ALSO

       ncoils(1), "usr/share/doc/coils/README", http://www.russelllab.org/cgi-bin/coils/coils-svr.pl <http://www.russelllab.org/cgi-
       bin/coils/coils-svr.pl>

       A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996
       A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991

2002								    2011-10-29							     COILS-WRAP(1)