Given a PDB, compute the DEER trace arising from signal due to adding a pair of MTSL tags added at the specified residues.
Usage: calcTrace [option] <pdb files>
where option is one or more of:
-pair <a> <b> <filename> - Specify two residues on which to place
paramagnetic tags in the "a" and "b"
arguments and a filename containing the
corresponding DEER trace in space-
separated format
-selection <atom selection> - atoms included in the calculation of tag
occlusion. ["name C CA N O"]
-writeTaggedPDB - If specified, write out a PDB including tag
atoms in the file named 'tagged.pdb'.
-makePlot - If specified, make a plot of the DEER trace
-plotFilename <filename> - name for a 2D plot file including a P(r).
When specified, -makePlot is assumed.
[Default: the plot is to the screen
-rMin <val> - minimum value of r used in computation of the
P(r) [10]
-rMax <val> - maximum value of r used in computation of the
P(r) [100]
-rDelta <val> - spacing of r used in computation of the P(r)
[0.5]
-probWidth <val> - width of contribution to probability
distribution of a
single pair of rotamers [None].
-addUnrecognized - add in unrecognized PDB entries. HETATM records
are always read, but will be ignored if they
don't specify standard residue names. With this
option, any atom which is not recognized will
be added to the structure.
-tagCoords <filename> - filename containing coordinates for the
rotamer coordinates.
-distanceSigmoidWidth <val> - distance sigmoid value (2.5 Angstrom)
-paraAtomRadius <val> - radius of the paramagnetic atom (4 Angstrom)
-zeroFit - if specified, scale experiment and shift input
time values such that
initial maximum is approximately 1
at time zero.
-dropInterval <val> - time interval (in micro sec) of the input
experimental curve to omit at the end of the
DEER trace ({dropInterval}).
Residues to be tagged are identified by segid:resid