Hi,
> What is the correct syntax for using talos_tools.tcl
The only procedure in xplor/tcl/talos_tools.tcl that you need to
worry about is readTalos. An example of its use is in
xplor/eginput/marvin/cvn/sa_pass1.tcl. Briefly, you call it like this
package require talos
set talosPot [create_XplorPot CDIH]
readTalos \
-fileName talos_pred.tab \
-scale 200.0 \
-widthScale 1.0 \
-segName "abcd"
where
talosPot is just a TCL name for the classic xplor constraints
dihedral potential, which we'll use to hold the TALOS restraints
talos_pred.tab is a TALOS pred.tab file (an example of which is in
eginput/marvin/cvn/cvn_talos_pred.tab)
scale is the force constant to be used with the TALOS restraints (via
the classic xplor restraints dihedral scale statement)
widthScale is a scaling factor, which is multiplied by the width of
each restraint in the pred.tab file (in case you think TALOS has
created overly-tight estimates)
and segName is the name of the segment to apply these TALOS
restraints to (in case the pred.tab file doesn't contain segment names)
Only the fileName flag needs to be defined. All the others have
reasonable default values.
One last point regarding the readTalos procedure--only lines that are
marked "Good" in the pred.tab file will be used as restraints. In my
work,
I've only used those residues that Talos could identify as "good"
without any human intervention, since I wanted to avoid bias. But
Gabriel Cornilescu
assures me that things work better if you go through his manual
inspection procedure with the TALOS GUI, as explained in the TALOS
documentation.
> and for using import_nmrdraw.tcl to read noe peak lists into xplor-
> nih for use with PASD
Right now, I only have two procedures in xplor/tcl/
import_nmrdraw.tcl, but that's likely to change in the future.
process3dCnmrDrawPeakTable is actually just a wrapper around
process3dCPippPeakTable, because the two programs' syntaxes are nearly
identical in this case. So the flags I use in xplor/eginput/marvin/
cvn/initialMatch3dC.tcl are exactly those that need to be defined in
using
process3dCnmrDrawPeakTable. Specifically,
package require nmrdraw
set noe [create_MarvnNOEPotential marv]
process3dCnmrDrawPeakTable \
-fileName aFile.tab \
-peakIDcolumnName PkID \
-fromProtonColumnName X \
-fromCarbonColumnName Z \
-toProtonColumnName Y \
-intensityColumnName Intensity \
-pot $noe \
-remarksVariableName peakRemarks
where
-pot gives the name of a MarvinNOEPotential
-fileName gives the name of an nmrDraw .tab file.
-peakIDcolumnName gives the name (given in the .tab file's VARS line)
of the column that contains the peak ID numbers
-fromProtonColumnName gives the name of the column that contains the
peak's chemical shift along the from proton dimension
-fromCarbonColumnName gives the name of the column that contains the
peak's chemical shift along the from heavyatom dimension (ie., is
bonded to the from proton dimension's proton)
-toProtonColumnName gives the name of the column that contains the
peak's chemical shift along the to proton dimension
-intensityColumnName gives the name of the column that contains the
peak's intensity
and -remarksVariableName just gives the name of a TCL variable
that'll hold a bunch of remarks generated by this procedure, which
will end up tacked onto the top of the .peaks file
All but the last flag must be defined.
(The second procedure in import_nmrdraw.tcl is
process3dNnmrDrawPeakTable, which is identical to
process3dCnmrDrawPeakTable,
except that the -fromCarbonColumnName flag becomes -
fromNitrogenColumnName. See xplor/eginput/marvin/cvn/
initialMatch3dN.tcl)
> Does the nmrpipe peak file have to be the long version produced by
> the default settings of the peak detection window or can it be the
> shorter version produced by the pkFilter.tcl command?
Either the long or short versions should work, as long as all of the
columns referenced by the other flags exist
One last point about using nmrDraw files: they generally don't
contain the information about the spectral range that exists at the
top of PIPP's PCK tables.
(Take a look at xplor/eginput/marvin/cvn/3dc_capp_def.PCK for an
example.)
Therefore, you can't use the readSpectralRangeFromPippPeakTable
procedure later on in the initialMatch script (in the call to match3d).
Therefore, you'll need to work out by hand exactly what the actual
highest and lowest possible values are along each dimension of your
spectrum.
(At first, I tried to determine this by asking for the carrier and
spectral width, but different programs' treatment of the first point
in the FT creates small
differences in the highest and lowest possible values.) So you'll
need to replace the calls to [readSpectralRangeFromPippPeakTable ] with
something like [list 10.013 -1.124], where the highest possible shift
along one dimension of your spectrum might be 10.013ppm, and the lowest
possible value along that same dimension might be -1.124 ppm.
> After reading the dihedral restraints and noe peak lists into xplor-
> nih how can one write them (in order to verify that they were read
> correctly)?
Since the Marvin readTalos procedure is just a wrapper around the
classic xplor restraints dihedral statement, you
could use
XplorCommand "print threshold 0.0 cdih end"
to see all the restraints it created.
To write out a Marvin-formatted NOE peak table from TCL, use the TCL
procedure
writeMarvinPeaks \
-fileName aFileName.peaks \
-pot $noe \
-remarks $peakRemarks
where
-fileName defines the name of the output file
-pot defines the name of the MarvinNOEPotential you referenced in
process3dCnmrDrawPeakTable
-remarks defines the TCL variable that holds the remarks generated by
(among many other procedures) process3dCnmrDrawPeakTable
All but the last argument need to be defined.
The syntax of the file generated by writeMarvinPeaks is detailed in
another piece I wrote for the xplor-nih list, which is in the list
archives.
But it's extremely easy to read.
Good luck, and let me know if you run into any snags.
--JK
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