Using PROG_PATH /S1/Apps/Dan/bin
/s/Apps/DanBin/stapp.sgi5 help
Documentation: stapp.help Program: stapp.c and pipp.c
Date Editted: June 1997 Purpose: Assign Peaks in Any Exp
See Also: stapp_exp.par, By: Dan Garrett
peptide_def2.par, pipp.help


Program requires a minimum of three arguments:

stapp <Data File> <Shift File> <Parameter File>

Do NOT invoke the program using
source stapp.com
as this will pass the environment variables from the stapp.com shell back
to the parent shell (ie the variables become defined in your window).
Make the stapp.com file executable as in:
chmod +x stapp.com
and then execute using:
stapp.com


The <Data File> is the file name for the 2D, 3D or 4D NMR data files
which may be stored in a single file or a series of files in which each
file has a single 2D plane or 3D cube. Each file must have a 512 float
parameter header followed by a series of 32 bit floating point numbers
consisting of only the real points. If the NMR data are stored in a
series of 2D files then <Data File> should be the base name to the files
ie HNCA. The format for file names for a 3D experiment stored as a series
of 2D files is the base name appended with a three digit number indicating
the slice number (ie third dimension data point) with the extension .DAT,
ie HNCAzzz.DAT. The format for file names for a 4D experiment stored
as a series 2D files is the base name appended with a two digit number
indicating the fourth dimension data point and a three digit number indicating
the third dimension data point with the extension .DAT, ie HNCAaazzz.DAT.
The <Abs. Threshold> is the minimum absolute value for calculating contours.
The <Level Multiplier> specifies the separation between successive contour
levels to give exponentially increasing levels.

*** Byte-Swap Variables *** Controls Byte-swapping of data
Floating point and integer representation differs between PC's
running Linux and Unix (ie Sun and SGi). Both float and int are
4 bytes in length. Only non-ASCII files such as NMR data,
*.XTRMA and *.CNTR files need to be byte-swapped when the
data was recorded under Linux and viewed under Unix.
The byte swapping is: ABCD <--> DCBA

***********************************************************
*** set BYTE_SWAP variables in stapp.com NOT stapp.par ***
*** MUST use setenv in stapp.com for these variables ***
***********************************************************

DIAG_BYTE_SWAP 0 When set to non-zero show byte-swap diagnostics.
This will let you know whether byte-swapping
is taking place or not for each file.
BYTE_SWAP_AUTO 1 When possible automatically sense if byte-swapping
should be performed. Note NMRi data can NOT
automatically be sensed for byte-swapping.
BYTE_SWAP_RD_ACQ, BYTE_SWAP_RD_CNTR and
BYTE_SWAP_RD_XTRMA take precedence, ie
overide this, if they are set.
BYTE_SWAP_RD_ACQ - When set to non-zero force byte-swapping to
take place when reading processed NMR data.
If explicitly set to 0 then byte-swapping will
NOT occur when reading processed NMR data.
When BYTE_SWAP_RD_ACQ is not explicitly set
and auto-sense is enabled then byte-swapping
is determined when the header params are
read from the first plane only, ie byte-swapping
is NOT determined on a plane by plane basis.
BYTE_SWAP_RD_XTRMA - When set to non-zero force byte-swapping to
take place when reading extrema files.
If explicitly set to 0 then byte-swapping will
NOT occur when reading extrema files. When
BYTE_SWAP_RD_XTRMA is not explicitly set and
auto-sense is enabled then byte-swapping
is determined when the extrema file is read in.



**** Notes Specific to STAPP ****

The stapp program is used for assigning NMR datasets and/or updating peak pick
tables from one dataset to another dataset, ie using a .PCK file to direct a
new peak pick. The stapp program will assign any nD NMR experiment for which
there is an entry in the stapp_exp.par file and assignments are in a shifts
file of the correct format (see example il4_hd1.shifts in 3d_example). Stapp
does not use the raw NMR data files directly, but instead determines all local
extrema above an absolute threshold and stores these in a file
<Base Name>.XTRMA (where Base Name is base name to NMR files). The size of
the .XTRMA file depends strongly on how low of a threshold is specified in the
stapp parameter file. Virtually all of the parameters that stapp requires,
except <Data File> and <Shift File>, are specified in the parameter file,
which I will call stapp.par.

Pipp allows users to determine assignments interactively using the same
parameters and procedures that stapp uses, ie the same parameter file that
is read into stapp for an HNCA dataset is read into pipp for making
assignments. It is easier to set up the stapp.par file within pipp instead
of stapp. This is because pipp will give information more quickly than
stapp. For, instance when determining DATA_OFFSET, see below, pipp will tell
you how far away and in which direction this peak is from the assignment
table. Also when setting EXP_NAME, see below, you must not only get the
correct experiment, but you must get the one whose Transpose state matches
your dataset. This requirement will change when the acquisition parameters
are stored in a separate ascii text file.


The stapp program is controlled by a set of paramaters given in the stapp.par
file and listed below. However, default values will be used for parameters
that are not set. To set parameters use the format:
<Parameter-Name> <Value of Parameter>
A # at the begining of the line means that that line gets ignored.
Always use the same variable type as shown in the default, ie integer, real
or string.

All the parameters that stapp uses are listed below, ie there are no
inherited parameters from ps_contour, capp or pipp except for
byte-swap parameters listed above.

Parameter Default Purpose of Parameter
Value


EXP_NAME - Identifies the type of experiment being looked
at. This is a required parameter and is
used to find the experiment in the
stapp_exp.par file.
DIM_COUNT - The number of dimensions for this experiment.
This is a required parameter and must match
what the DIM_COUNT in EXP_NAME in
stapp_exp.par.
THRESHOLD 5.0e5 Minimum absolute threshold for selecting extrema. When
stapp.par is used in pipp must make sure that this
matches the contouring threshold (if this is higher
that what the contouring was done at then you would
be able to click on a peak but that peak would not
be in the .XTRMA file and therfore not found).
PK_FILE_NAME - Base name to the Peak-Pick table (.PCK file) that stapp
will create, ie pipp does not use this parameter.
In addition to the .PCK file 3 other files may be
created: .ASG, .DEG and .LOST. The .ASG file is the
file format that gets read into pipp. The .DEG file
is in the same format as the .PCK file, but contains
degenerate assignments, ie one peak with more than one
possible assignment. The .LOST file is in the same
format as the .PCK file, but contains peaks which
would be lost when SEARCH_PCK_FILE is TRUE which
means a .PCK file drives the peak picking instead
of the assignments driving the peak picking.
SEQUENCE - Amino acid sequence. Within the Assignment
table the parameter FIRST_RES_IN_SEQ can be
used to specify the residue number the first
amino acid. By default the first amino acid
is 1. Must use the single letter amino acid
code that is given in peptide_def2.par.
Spaces and tabs are permitted. Multiple
lines may be used if the line continuation
char \ is used. Note due limititations of
word sizes within the program do not wite
the SEQUENCE as 1 long word (max word size
is 64 characters; ie USE spaces).
DATA_OFFSET 0.0 DIM_COUNT number of floats to indicate a consistent
offset between shifts from this current experiment
and the assignment table. The DATA_OFFSET for
each axis is the number to add to the nD experiment
to make it match the corresponding value in the
assignment table. In Inform mode in pipp the
deviation for each axis can be used directly in
DATA_OFFSET, ie if deviation is less than ERROR_RANGE
than pipp will give the magnitude and direction of
the offset. Units are in PPM.
ACQ_BASE_PHASE POSITIVE A string identifiing wheteher the base phase of the
peaks are are positive, negative or unknown. Must
be one of: POSITIVE, NEGATIVE, or UNKNOWN. This
gets used to fold assignments into the spectrum.
UNKNOWN means that you do not know a priori whether
an assignment will be positive or or negative. The
only information that stapp uses to determine the
sign of peaks is folding therefore experiments such
as CBCANH that have negative CB from peaks not from
folding will not be handled correctly unless
ACQ_BASE_PHASE is set to UNKNOWN.
ANTIPHASE_FOLDOVER TRUE Boolean that indicates whether peaks at the edge of the
Z axis have their sign flipped when going across
the edge. This is redundant with the folding
information in stapp_exp.par, but is left in for
compatibility with pipp.
ERROR_RANGE DLTA_HZ DIM_COUNT number of floats which indicate the maximum
error accepted for each axis, ie if absolute
difference between experiment and assignment table
is greater than ERROR_RANGE for any axis that
assignment is not considered. This should be set
at the digital resolution of this experiment or the
uncertainty of the assignment table, whichever is
higher. Units are in PPM.
DEG_PROX_LIMIT - DIM_COUNT number of floats which indicate if 2 values
are within this range they can not be discriminated
between, ie this is a DEGenerate PROXimity LIMIT.
This should be set at about 1/2 of ERROR_RANGE.
Units are in PPM.
DEG_INTENS_FCTR 5.0 Float indicating that if 2 peaks are within
DEG_PROX_LIMIT of each other and the peak that
is closer to the assignments is DEG_INTENS_FCTR
is a crude way to get around some sinc wiggles.
DIST_FROM USE_NONE String indicating where distances are to come from
for use in distance filtering. Options are:
USE_NONE, and USE_PDB_FILES. USE_PDB_FILES
requires that PDB_FILES also be read in.
This may be absent and the program will
set it if PDB_FILES is set.
PDB_ATM_NM_FILTER * String indicating what type of atoms should be
read from the PDB_FILES. Normally this is
set to H* to only read in the protons for
distance calculation.
PDB_FILES - Space delimited list of PDB file names that are
read in for distance filtering. List may
extend over many lines by using the line
continuation char \
XPLR_FILE_NAME - String indicating the Xplor contraint file that should
be read in. This allows pipp to report whether
an NOE is already in the constraint table or not.
SMW_FILTER - Space delimited string indicating which type of NOEs you
are looking for. By default all possible NOEs are
allowed. This can be used to restrict stapp searches
to only those peaks that you have not already found.
WRITE_NOE_DIST FALSE Boolean flag to indicate whether distances
should be written to the .PCK with the assignments.
MIN_NOE_DIST -1.0 Float indicating the minimum distance allowed
between selected pairs of protons. This is
a good way to see what parts of the
structure are far from each other
but also show NOEs in the spectra.
MAX_NOE_DIST 20000.0 Float indicating the maximum NOE distance
allowed between potential assignments.
Default allows everything.
NOE_KEAP_INTRA - Boolean indicating whether intraresidue NOEs should be
kept independent of their distance. Default is
whatever was used in the stapp_exp.par file.
ACQ_PRMS_TABLE - Table of reference parameters which includes:
SIZE, SW, SF, First-Hz, and Units. SIZE is
number of points. SW is the Sweep Width in
Hz. SF is the Spectrometer Frequency in
MegaHz. First-Hz is the Hz value of the
first point. Units is the desired output
units for the .PCK file. All of these can
be obtained from any .PCK generated by pipp
on this experiment. When stapp.par is used
in pipp this is ignored. Normally only the
Z_AXIS neads to be specified since the X and
Y are obtained from the NMRi header. See
also ACQ_PRM_FRMT for a method to read all
params from the nmrPipe header (which
requires that the data has been processed
using Frank Delaglio's nmrPipe program).
ACQ_PRM_FRMT NMRI2D A string identifiing whether the header should
be read in the old NMri 2D format or in the
nmrPipe format. Must be on of NMRI2D or
NMRI_PIPE. Note to read in the NMRI_PIPE
format the data must be processed using
Frank Delaglio's nmrPipe program.
AXIS_ON_PLANE "X_AXIS Y_AXIS" Which two axis are used to define the plane.
This decides what plane is contoured and displayed.
For 3D data can choose X_AXIS Z_AXIS and also
Y_AXIS Z_AXIS. This create a new subdirectory
using the basename with the extension
.XZ or .YZ. If DATA_GROUPED is SINGLE_DATA_FILE
then the name of contour subdirectory for XY
will also have the extension .XY.
DATA_HEADER_SZ 2048 Number of bytes in header.
DATA_GROUPED 2D_FLS Specifies the arrangement of NMR data. Options
are: 2D_FLS 3D_FLS 4D_FLS SINGLE_DATA_FILE.
The Zant format is similar to SINGLE_DATA_FILE,
but has not been tested, ie may be slight
differences in header parameters.
SP_AXIS - A string indicating which axis strip plots are
along. See below in stapp_exp.par
RESID_START - Integer specifiing which residue to start at.
This is used only for Strips.
IGNR_RES_OFST_SHFTS FALSE Boolean indicating whether assignments with
residue offsets should be ignored. This should
be set when the assignments are complete and
otherwise errors will occur when peak-picking
NOE type data.
SEARCH_PCK_FILE FALSE Boolean indicating whether a .PCK file should
be used to direct the search instead of the
assignment table. If set to TRUE then MUST
also set PCK_IN_FILE, PCK_KEAP_SIGN,
PCK_DO_ASSIGN, PCK_SHOW_LOST, PCK_DO_INTERP.
If set to FALSE then these PCK_* parameters
are ignored. A .PCK directed search
allows you to keap the same Peak-ID number
between different experiments, or will let
you run capp on a 4D dataset and use capp's
.PCK file in stapp so that only good peaks
are kept.
PCK_IN_FILE - This is the full name, ie include .PCK, of the
peak pick table that will direct the search.
The extension must be included in the name
but does not have to .PCK. You may have
more than one peak pick table, but there are
no provisions for correcting the same Pk-ID
number in the 2 input peak pick tables.
PCK_KEAP_SIGN - Boolean indicating that the sign of the peak must
remain the same in the input peak pick table and
the output peak pick table, ie if peak was
positive then new peak must be positive if this
is set to TRUE. If set to FALSE then the closest
peak in the .XTRMA independent of sign will
be chosen.
PCK_DO_ASSIGN - Booelan indicating whether assignments should be done on
the peak. If TRUE then any previous assignment
will be ignored and a new assignment will be made
making use of distance filters and SMW filters.
If this is FALSE then an assignment table is not
required and not read in.
PCK_DO_INTERP - Boolean indicating whether the intensity and position
should be re-interpolated in the new experiment.
If TRUE then the shift and intensity are found in
the .XTRMA file. If FALSE then the .XTRMA file is
not neaded.
PCK_SHOW_LOST - Boolean indicating whether peaks that are not found
in the current experiment should be kept tracked
of in the .LOST file.
KEAP_DEG_PCK_ID FALSE Boolean indicating whether peak degeneracy from *.DEG
is used within PIPP. When set to FALSE then
PIPP can NOT define an ambigous NOE. When set
to TRUE PIPP can maintain a list of assignmenmts
for each peak, ie degeneracy. The degenerate
assignments for all the peaks are stored in the
text file *.DEG.
SIAD_STRING - Space delimited string indicating the SIAD to use for
each axis. See SIAD_STRING below for stapp_exp.par
for more details.
C12_RES_START - Integer specifiing the first residue that is
unlabelled. For this to work correctly you must
set SEQUENCE to have both the labelled and
unlabelled polymer, ie use BLNK residues to separate
the 2 so that the unlabeled starts at 101 and
continues to the number of residues. Also, must
use and EXP_NAME in which the C12_EDITTED
parameter is set.
C12_RES_END - Integer specifiing the last residue that is unlabelled.
MAX_PK_BUFFER 3000 Integer indicating maximum number of peaks to keap
in memory before writing to file. Default is
good enough.
INTERP_INTENS FALSE Boolean indicating whether the intensity should be
interpolated using a 3 point parabolic interpolation.
So far this has not given any difference in
intensity. If FALSE then uses the highest point
as the intensity of the peak.
PK_TBL_FRMT %7.2f String indicating output format for each axis. May use
one format for all axis or specify a space delimited
array formats for each axis,
e.g. %7.4 %7.4 %6.2.
USE_AA_CODE_3 FALSE Boolean indicating whether user wishes to converse using
the 3 letter code or the single letter code.
DO_METHYL_FILTER TRUE Boolean indicating whether non-stereo assigned methyls
should be filtered based on the order of atoms.
For example the assignment L80.CG1|CG2.HG1#|HG2# is
allowed but L80.CG2|CG1.HG1#|HG2# will be filtered
out when this is set to TRUE. The purpose of this
is to allow LEU and VAL methyls to be non-stereo
assigned but keap track of which proton shift
belongs with which carbon shift. The assignment
table should therefor have an entry for CG1|CG2
and HG1#|HG2# and the user must make certain that
the atoms are bonded.
DO_SIGN_FILTER FALSE Boolean indicating whether the peak being picked should
be filtered by it's sign or not. Currently only the
effect of folding on the peaks sign is used to
determine the expected sign of a peak based upon
the number of folds for the shift. If ACQ_BASE_PHASE
is set to UNKNOWN then the sign filter is NOT done.
COMPLETE_ASGNMTS TRUE Boolean indicating whether the assignment table is complete.
When set to TRUE no new assignemnts will be created.
When set to FALSE PIPP/STAPP will attempt to make new
assignments in the assignment table. This should
always be set to TRUE when working with NOE data, ie
can NOT use NOE to determine assignments.
REQ_ND_SYM TRUE Boolean indicating whether nD symmetry should be required
for all assignments or not. nD symmetry can only
be checked if SYM_ATOMS has been correctly defined
in stapp_exp.par.
SYM_ERROR - DIM_COUNT number of floats indicating Maximum error
range to use for nD symmetry checking. Default
is higher of DEG_PROXIM_LIMIT for 2 axis involved
and ERROR_RANGE for axis not involved in symmetry,
ie Z. Default seems ok.
PK_EXCLUDE_XY_DIAG TRUE Boolean indicating that any assignments within
PK_WDTH_XY_DIAG. of the diaganol should be
ignored. This is functionally different
than EXCLUDE_AUTO_PK.


In order to determine assignments in pipp or in stapp four default parameter
tables are read from the directory specified in the parameter PROG_PATH, if
not specified then the directory specified in PROG_PATH in the shell script
which calls the executable is used. The default files in the program path
can be ignored and user defined files read in its place by setting the Alt.
File parameter to the name of a file the user wishes to use. This allows
a single default table for everyone and lets individuals modify the default
file for specialized experiemnts. The parameter names given under the
Alt. File in the table below require a complete pathname that is absolute,
ie begins with a /, or relative to the current directory. These four
parameter tables are breifly described below followed by the required format
of each file:

Default File Name Alt. File Description
peptide_def2.par AA_PAR_FL Contains definitions for All the atom
names and amino acids so that
assignments and PDB files can be used
in stapp and pipp.
stapp_exp.par EXP_PAR_FL Contains definitions for ALL experiments to
be used by stapp and pipp. This how
stapp knows what atoms are observed
along each axis.
stapp_def.par STAPP_PAR_FL Contains default definitions for stapp
parameters that will be overriden by
settings in stapp.par. This file can
be modified for site specific defaults.
smw.par SMW_PAR_FL Contains definitions for strongh, medium,
weak and very weak NOE so that pipp can
read in and Xplor constraint table and
correctly classify the NOE constraint
into S, M, W, VW respectively.

File format for peptide_de2.par:
In order for this description to make sense you should look at a
the default example.
Contains 3 records: ATOM_NAMES, RESIDUE_NAMES and AA_DEFINITIONS.
ATOM_NAMES: complete list of all atom names, including ALIAS's, that
make up the amino acids. Each line has any number of atom names
separated by spaces or tabs. A blank line ends the ATOM_NAMES
record.
RESIDUE_NAMES: complete list of all residue names that make up the
amino acids. Note the file peptide_dna.par contains definitions
that are usuable for protein DNA complexes, ie has
deoxy-oligonucleotide definitions. Each line has a variable number
of amino acid residue names separated by spaces or tabs. The
residue BLNK is ESSENTIAL for the program to run and must be the
first residue in the list, otherwise the order is unimportant. A
blank line ends the RESIDUE_NAMES record.
AA_DEFINITIONS: complete list of definitions for each amino acid with
6 records: CHAR_CODE, VALID_ATOMS, EXCHANGEABLE, SIDE_CHAIN,
BOND_ATOMS, and AVRG_ATOM_TBL. The keyword AMINO_ACID followed by
the amino acid residue name begins each amino acid record. A blank
line ends each amino residue definition.
CHAR_CODE: The single amino acid character code for this amino
acid. For dna we opted for lower case single letter codes.
VALID_ATOMS: Complete list of atom names that are valid for
this amino acid. If line is too long then MUST use line
continuation symbol \ at end of line.
EXCHANGEABLE: List of all exchangeable atoms.
SIDE_CHAIN: List of all side chain atoms.
BOND_ATOMS: Pairwise list of all atoms that are bonded to
each other. Again use \ at end of line if line extends
beyond carriage return.
AVRG_ATOM_TBL: Tabular list of methyls, methylenes and
aliased atoms. This lets stapp and pipp know that position
of individual protons of a methyl ar not important, but
there average position is impoortant. This record is not
required, ie it may be ommitted, but if it is used it must
be the LAST record on the list because a blank line ends
the AVRG_ATOM_TBL record and a blank line ends the
AMINO_ACID record.
AVRG_ATOM: required Header for AVRG_ATOM_TBL record.
FAST: Average type used for methyls.
SLOW: Average type used for methylenes.
ALIAS: Average type used for defining alias's.

File format for stapp_exp.par:
In order for this description to make sense you should look at a working
example. Contains any number of experiment definitions which begin with
EXP_NAME and end with a blank line. After EXP_NAME the name(s) for the
experiment is(are) given. This name must not contain any spaces or tabs
and this is how the stapp program identifies each experiment which is
being used. Multiple experiment names are allowed (separated by spaces or
tabs) on the EXP_NAME line so that users may call the same experiment by
different names. A # at the beginning of line means that that line gets
ignored. There are currently 23 defineable parameters for each experiment,
but only 3 are required. The optional parameters are very important
in defining specific types of experiments as will be seen below.

Required Parameters:
AXIS_ATOM_TABLE: Defines which atoms are observed along each axis.
Currently, the axis are defined by X, Y, Z and A (ie the order in
the NMR dataset). In the future the axis will be defined by
F1, F2, F3, and F4 so that the dimension order of the NMR dataset
will not affect the experiment definition. The header line to table
is required, but is not read in. The AXIS_ATOM_TABLE ends with a
blank line. The AXIS_ATOM_TABLE must be the last record for each
experiment and ends the experiement entry. The keyword X_AXIS,
Y_AXIS, Z_AXIS or A_AXIS are required to define the atoms along the
respective axis. The order of which axis get defined first is
unimportant since the keyword are read in for each axis. The order
of information on each line for each axis is fixed as:
AXIS: Identifies axis being read in.
This must be one of: X_AXIS, Y_AXIS, Z_AXIS, A_AXIS.
ATOM_NAME: Name of atom observed for this axis. A single wild
card, *, may be used. A residue group, ie .i or .j, may be
used to differentiate the same type of atom on different
residues (if missing then .i is assumed). If the ATOM_NAME
does not include a VALID_ATOM that is listed in the
peptide_def2.par file then the parameter ATOM_SET must be
used to define a set of atoms for an axis.
FOLD_TYPE: Type of folding expected for this axis. Can be
one of IGNORE, NEG_PHASE, or POS_PHASE. If set to IGNORE
then no folding will be done to shifts read in from the
assignment table. NEG_PHASE implies that shifts are folded
in with opposite sign. POS_PHASE implies that shifts are
folded in with same sign. The stapp.par parameter
ACQ_BASE_PHASE indicates whether the base phase for a
specific experiment is positive, negative or unknown.
FOLD_FUNC: How to do the folding. Can be one of NONE or SW. SW
implies that folding is by an integral amount of the sweep
width. NONE implies that folding is ignored. May at some
later date include other fold functions.
DIM_COUNT: Number of dimensions for this experiment. This must match
the number of axis given in AXIS_ATOM_TABLE.
SORT_ATOMS: Which atoms/axis to use for sorting the .XTRMA file and
searching for assignments. All other atoms/axis are depended (or
constrained by) by the SORT_ATOMS in some way, ie may be bonded to
sort or in same residue or adjacent residue. For NOE experiments
there should be 2 SORT_ATOMS since there are 2 independent
atoms/axis. The number of the SORT_ATOMS plus the number of
constrained atoms must equal the number of observed atoms in
AXIS_ATOM_TABLE else an error message will be given. See also
ATOMS_BONDED and RESID_RELAT.

Optional Parameters:
ATOM_SET: Lists atom names for a specific axis. Allows there to be
a set of atoms for a given axis without using wild cards. Format
for this is: "ATOM_SET Cz CA CB" where Cz is being defined to be
CA or CB. Cz must also appear in the AXIS_ATOM_TABLE for the correct
axis, ie "Z_AXIS Cz POS_PHASE SW". There should be separate
ATOM_SET definitions for each axis, but not more than one ATOM_SET
definition for each axis. See the definition for the CBCANH
experiment for an example. Unless specified there are no
ATOM_SETs created.
ATOMS_BONDED: Pairwise list of which atoms are bonded. List should
contain the same ATOM_NAME in the AXIS_ATOM_TABLE, ie C* or Cz but
not Z_AXIS. Since this is used to constrain one of the atoms/axis
it is not allowed to have 2 SORT_ATOMS bonded to each other, ie
this restricts what can be selected for the SORT_ATOMS. See almost
any experiment for an example. Unless specified there are no
ATOMS_BONDED used as a constraint.
RESID_RELAT: Explicitly defines how one residue group relates to
another residue group. This requires that the ATOM_NAMES in the
AXIS_ATOM_TABLE use at least 2 residue groups such as .i and .j.
Any single letter can be used to signify a group. An ATOM_NAME
omitting the . will be put into the .i residue group. Format for
this is: "RESID_RELAT *.j *.i 0 -1", which means that the .j group
is in the same residue as .i or the i-1 residue. Since this is
used to constrain the .j residue group, no axis/atoms may in the .j
residue group may be used as SORT_ATOMS, ie this restricts what can
be selected for the SORT_ATOMS. See the CBCANH experiment for
examples. Unless specified no RESID_RELAT are made.
SIAD_STRING: List of which atoms you are interested along each
axis separated by spaces or tabs. The format for the SIAD
(Sequence Independent Atom Designator) for each axis is:
{RES1|RES2.}ATM1{|ATM2:OFFSET1|RNG1-RNG2} where the RES1, RES2,
ATM2, OFFSET1 and OFFSET2 which are between the brackets { and }
are optional. No spaces are allowed within the SIAD and the
brackets { and } are not part of the definition they only indicate
what part of the definition is optional, ie do not type in the
brackets { or }. The only part of the definition that is required
is ATM1 which must be a valid atom name with at most one wild card
such as HA* but not Hy.i, ie this should not be from
AXIS_ATOM_TABLE in stapp_exp.par but from VALID_ATOMS in
peptide_def2.par. The * is a wild card except if it is alone,
ie *, then this indicates that you do not care about that axis.
The | indicates an or that allows multiple atoms, multiple residue
types or multiple offsets. The . separates the residue
specification from the atom name specification. The : separates
the atom specification from the offset specification. RES1 and RES2
may be written using the single letter amino code or 3 letter.
OFFSET1 is a signed offset from the current residue number, which
gets defined somewhere else. RNG1-RNG2 specifies a range of
offsets. This gets used in pipp to jump by residue number instead
of the slice number or chemical shift. SIADS are also being
used within the Assignment Table.
NEW_ASGNMT_FROM: List of ATOM_NAMEs that indicate which atoms
new assignments can come from when stapp is used to generate
an assignment table. Atoms that are missing from this list will
be used to generate new assignments. This is required so that
if in a CBCANH experiment a chemical shift with a new HN and N shift
and a Cb is that is close to a previous shift is NOT used to
predict the HN:+1 and N:+1 shift, ie there is more information in
in the HN and N shift to determine the spin-system than
in the Cb shift alone. This allows stapp to create a new
spin system for the HN and N shift.
AVERAGE_SHIFT: List of ATOM_NAMEs that indicate which shifts can
be used in the average for determining the assignment table value.
AUTO_AXIS: Pair of axis that the diaganol will appear across,
ie X_AXIS and Y_AXIS for C-13 edited NOESY. This is used in
conjuntion with EXCLUDE_AUTO_PK and PK_EXCLUDE_XY_DIAG to
eliminate diaganol peaks.
EXCLUDE_AUTO_PK: Boolean value, ie TRUE or FALSE. Determines if Auto
peaks should be excluded. Uses AUTO_AXIS to determine what axis to
filter on. When TRUE this will filter out HA - HA if the two HA's
are on the same residue.
EXCLUDE_EXCHANGEABLE: Boolean value, ie TRUE or FALSE. If TRUE will
not assign any ATOMs that are defined as EXCHANGEABLE, ie excludes
them from being searched.
SYM_ATOMS: Pair of ATOM_NAMEs that the symmetry is around. Must use
same ATOM_NAME as used in AXIS_ATOM_TABLE, ie H*.i H*.j not
Y_AXIS Z_AXIS. If this is not set then the experiment can NOT do
any type of 3D symmetry filtering or looking.
LBL_PEAK_WITH: List of ATOM_NAMEs to label the peak with in pipp,
ie can give assignment for only one axis. Must use same ATOM_NAME
as used in AXIS_ATOM_TABLE, ie H*.i not Y_AXIS. In pipp.com file
must "setenv XVW_LBL_FRMT 2" and "setenv PK_WR_ASSIGN 1" in order
to see the assignment on the screen and have it written in the
peak-pick table. If LBL_PEAK_WITH is absent then pipp will write
the full assignment over the peak which is usually too large.
See any experiment for examples.
NOE_RELAT: Pair of ATOM_NAMEs involved in the NOE. Must use same
ATOM_NAME as used in AXIS_ATOM_TABLE, ie H*.i or Hy.i not X_AXIS.
If this is absent then you will not be able to use distances within
pipp or stapp to filter out improbable assignments. See any NOE
experiment for examples.
RESID_PRIO: Defines a residue priority for one residue group relative
to another. This was intended to help stapp differentiate in
NOE type spectra between multiple assignments based on sequential
NOEs and adjacent NOEs being more likely than long range NOEs, but
so far it does not help.
C12_EDITTED: List of ATOM_NAMEs that are editted by C12, ie bonded to
a C12 atom. This will be used in conjunction with the C12_RES_START
and C12_RES_END stapp.par parameters. Must use same ATOM_NAME as
used in AXIS_ATOM_TABLE, ie H*.j not Y_AXIS. See 12C,13C-NOESY
experiment for an example.
SP_AXIS: Specifies which axis is has Strip Plots along it (this is
also known as Sequence Projected axis). Alows a 3D dataset to looked
at as if it were a 2D dataset. A separate program by Stephan
Grzesiek will take a 3D N-15 edited NOESY and create a single 2D
were one axis has strips taken at the N-15 and HN position of all
the backbone amides. For more info on Sequence Projected data see
pipp.help. If this is set then MUST also set SP_ATOMS and
NON_SP_EXP.
SP_ATOMS: What atoms make up the Sequence Projected axis. Usually it is
N and HN, but may also be CA and HA.
NON_SP_EXP: Identifies another entry in stapp_exp.par which is the
non Sequence Projected Experiment. The NON_SP_EXP must exist and
the ATOM_NAMEs in SP_ATOMS must be the same as given in the
AXIS_ATOM_TABLE of the NON_SP_EXP.



Version 4.3.2 ( 03/15/00 )


more /S1/Apps/Dan/bin/stapp.help