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.\" ========================================================================
.\"
.IX Title "NCOILS 1"
.TH NCOILS 1 "2020-11-29" "2002" "User Commands"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
ncoils \- prediction of coiled\-coil secondary structure elements
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
ncoils [\s-1OPTION\s0] < [\s-1FASTA FILE\s0]
.PP
ncoils \-f < /usr/share/doc/ncoils/1srya.fa
.SH "DESCRIPTION"
.IX Header "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.
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\-f, \-fasta" 4
.IX Item "-f, -fasta"
fasta output \- coils as 'x', like '\-x' in seg
.IP "\-c" 4
.IX Item "-c"
concise mode \- which sequences have any coils (and how many)
.IP "\-min_seg <int>" 4
.IX Item "-min_seg <int>"
for concise mode \- only report sequence if >= min coil segments
.IP "\-min_P <float>" 4
.IX Item "-min_P <float>"
minimum P to define coil segment; \s-1DEFAULT\s0 = 0.5
.IP "\-win <int>" 4
.IX Item "-win <int>"
window size; \s-1DEFAULT\s0 = 21
.IP "\-w" 4
.IX Item "-w"
weight heptad positions a&d the same as b,c,e,f,g
.IP "\-v" 4
.IX Item "-v"
verbose/debug mode \- print extra junk
.SH "EXAMPLES"
.IX Header "EXAMPLES"
\&\f(CW\*(C`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\*(C'\fR
.PP
\&\f(CW\*(C`ncoils \-win 14 < /usr/share/doc/ncoils/1srya.fa\*(C'\fR
.SH "ENVIRONMENT"
.IX Header "ENVIRONMENT"
\&\s-1COILSDIR\s0 \- specifies the directory containing the file new.mat overriding the default \fI/usr/share/ncoils\fR
.SH "FILES"
.IX Header "FILES"
.IP "\fI/usr/share/ncoils/*.mat\fR" 4
.IX Item "/usr/share/ncoils/*.mat"
matrix data files
.SH "AUTHOR"
.IX Header "AUTHOR"
R.B. Russell, A.N. Lupas
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
\&\s-1GPL\s0
.PP
Based on Lupas, Van Dyck & Stock (1991) Science 252,1162\-1164
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBcoils\-wrap\fR\|(1), \*(L"usr/share/doc/coils/README\*(R", <http://www.russelllab.org/cgi\-bin/coils/coils\-svr.pl>
.IP "A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513\-525, 1996" 4
.IX Item "A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996"
.PD 0
.IP "A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162\-1164, 1991" 4
.IX Item "A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991"