calcPr
Given a PDB, compute the P(r) due to adding MTSL tags at the specified residues.
Usage: calcPr [option] segid1:resid1 segid2:resid2 <pdb files>
where option is one or more of:
-compare <filename> - read a comparison P(r) from a file with lines
consisting of r P(r). In this case, the values
of r are used in
computation of the new P(r). and both
curves are plotted.
-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.
-probWidth <val> - width of contribution to probability
distribution of a
single pair of rotamers (0.7 Angstromif not
specified here or in the tagCoords file)
-distanceSigmoidWidth <val> - distance sigmoid value (2.5 Angstrom
if not specified here or in the tagCoords
file)
-paraAtomRadius <val> - radius of the paramagnetic atom (3 Angstrom
if not specified here or in the tagCoords
file)
-makePlot - If specified, make a plot of the P(r)
-plotFilename <filename> - name for a 2D plot file including a P(r).
When specified, -makePlot is assumed.
[Default: the plot is to the screen
Residues to be tagged are identified by segid:resid
Options:
-selection - atoms included in the calculation of tag occlusion.
["name C CA N O"]
-writeTaggedPDB - write out a PDB including tag atoms in the file named
``tagged.pdb''.
-rMin <val> - minimum value of r - used if -compare is not
specified.
-rMax <val> - maximum value of r - used if -compare is not
specified.