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