contactMap
Generate contact map from one or more pdb files.
Usage: contactMap [options] <structure files>
where options are one or more of:
-cutoff <val> -- default distance cutoff used to determine contacts
[default: 4 angstroms]
-psf <psf file> -- optional psf file
-xticks <vals> -- colon-separated xtick values
-yticks <vals> -- colon-separated ytick values
-selection <atom selection>
-selection2 <atom selection>
-selPair <sel1> <sel2> <color[:cutoff]>
-- specified instead of -selection and
-selection2. Display contacts between
residues in the specified pair of
atom selections using the specified
color. Currently supported colors are
red, green and blue. A per-selection pair distance
cutoff can be optionally specified by appending a
colon-separated value to the color specification.
-printTable -- print out a texual representation of the table
-includeZeros -- if specified, include zero values in the output table.
-printContacts -- print contacts for each file processed.
-printAtomContacts -- print the identity of all atom pairs which are within
cutoff, and the associated distance.
-ensWeightRegexp=value -- regular expression used to extract ensemble
weights from remarks section of the PDB header.
The weight for contacts from a pdb file is
taken from all characters on the matched remark
after the ensWeightRegexp.
-absolute -- for the color shading: make the darkest color
be relative to the absolute number of weighted
contacts divided by number of structures. By default
it is relative to the maximum contact value.
-popEnumerated <spec>- enumerate which colors to use for a specific
population range. The colors and ranges are specified
by a space, or column separated list of values
'val1 color1 ... valN colorN'
where colorI is displayed for populations between
val(I-1) and valI, and so on.
-cmpPDB <pdb file> -- if specified, denote the contact map for a comparison
-cmpPSF <psf file> file as a green contour. -cmpPSF should be specified
for non-standard structures.
-suppressDiag <num> -- do not display contacts for which |i-j| <= num,
where i and j are residue numbers. For instance,
specifying -suppressDiag 0 will prevent contacts
for which i==j
-noPlot -- don't create plot.
-outFile <filename> -- plot filename
Specific MODEL records within a pdb file can be chosen using the syntax file.pdb:2 where the integer following the colon specifies the MODEL record. A range of MODELs can be chosen using a model specifier BEG-END, where BEG and END specify start and end record numbers, respecitvely.