InSane: Wit!P commands
Example of a typical InSane command sequence in Wit!P
Input:
foobar_1214_*.pdb : ensemble of known structures
foobar.ppm : file with resonance assignments
foobar_noesy.mat : 3D NOE spectrum
foobar_noesy.xpk: crosspeak list for foobar_noesy.mat
Output:
insane.xpk : annotated crosspeak list.
insane.tbl : X-Plor distance constraints generated from insane.xpk
User input is shown in bold text. Commands annotated using
Wit!P comments (--> ...). Responses of the programs, other than command
prompts are not shown. '$' is the shell-prompt, '#' is the shell comment
character.
$ witnotp
Wit!P> nmr foobar --> create new NMR set, call
it foobar
NMR> structure --> bring up structure menu to read
structures from PDB files:
NMR structure option: read pdb foobar_1214_?.pdb foobar_1214_??.pdb
NMR structure option: fit average * --> fit whole ensemble
to structure average
[0 atoms selected] template atoms: *_87-*_122/ca -->
using C-alphas of residues 87 to 122
NMR structure option: end --> return to NMR main menu
NMR> shift read foobar.ppm --> read resonance
assignments from file
NMR> spectrum open foobar_noesy.mat -> open noesy
spectrum file
spectrum> noise foobar_noesy.mat 2.5e4 -> set
the noise level
spectrum> --> set the references for C and N
spectrum> reference foobar_noesy.mat C 150.856 4620 23.195 54.6
spectrum> reference foobar_noesy.mat N 60.795 4620 59.0 123.02
spectrum> peaks read foobar_noesy.mat foobar_noesy.xpk -->
read peaklist
spectrum> --> set filter
criteria:
spectrum> structures * --> use whole ensemble of structures
spectrum> class include all --> include all classes
of pseudoatom pairs
spectrum> intensity greater 1.0 --> allow only pairs
with NOE intensity > noise
spectrum> contribution average 0.9 --> define parameters
for contribution filter
spectrum> distance average 10.0 --> allow only pairs
with average distance < 10 Å
spectrum> distance minimum infinity --> don't filter
by minimum distance
spectrum> distance maximum infinity --> don't filter
by maximum distance
spectrum> tolerance 1.5 --> pair must be with 1.5 points
of peak to be assignment candidate
spectrum> peaks assign reset foobar_noesy.mat --> clear
old assignments
spectrum> peaks assign insane foobar_noesy.mat -->
run InSane procedure
spectrum> peaks write felix foobar_noesy.mat insane.xpk-->
new peak file
spectrum> end --> return to NMR menu
NMR> end --> return to Wit!P main menu
Wit!P> exit y --> exit to DOS (or Unix, Linux, Windows...)
# Convert the new crosspeak file insane.xpk to X-Plor distance constraints
(insane.tbl):
$ xpk2xpl -p insane.xpk -v foobar_noesy.vol
-o insane.tbl
A.Widmer,
NIBR/CPC/CSG-SB