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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)

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NCOILS(1)							   User Commands							 NCOILS(1)

NAME
ncoils - prediction of coiled-coil secondary structure elements SYNOPSIS
ncoils [OPTION] < [FASTA FILE] ncoils -f < /usr/share/doc/ncoils/1srya.fa DESCRIPTION
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
-f, -fasta fasta output - coils as 'x', like '-x' in seg -c concise mode - which sequences have any coils (and how many) -min_seg <int> for concise mode - only report sequence if >= min coil segments -min_P <float> minimum P to define coil segment; DEFAULT = 0.5 -win <int> window size; DEFAULT = 21 -w weight heptad positions a&d the same as b,c,e,f,g -v verbose/debug mode - print extra junk 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" ENVIRONMENT
COILSDIR - specifies the directory containing the file new.mat overriding the default /usr/share/ncoils FILES
/usr/share/ncoils/*.mat matrix data files AUTHOR
R.B. Russell, A.N. Lupas COPYRIGHT AND LICENSE
GPL Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164 SEE ALSO
coils-wrap(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 NCOILS(1)
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