Readme

Detailed description of the programs

<Readme>

Readme for xeasy format 2D peak list handling and 2D VNMR data conversions.

consider_correl

Label xeasy format 2D correlation assignments file with names in place of xeasy atom
numbers and deviations from the shifts given in the xeasy format atoms list (*.prot).

Usage: consider_correl xeasyfile.seq xeasyfile.prot < assignfile.peaks > outfile

Installation: Compile source with cc -o consider_correl -O consider_correl.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks), and writes a tab delimited file of 7 columns to standard output.
The seven columns are peak number, dimension 0 shift in ppm, deviation from shifts
file shift for the dimension 0 assignment, dimension 1 shift in ppm, deviation from
shifts file shift for the dimension 1 assignment, peak intensity measurement, and
assignment. Only those peaks in the original file for which assignments are given
are listed in the output. The assignments are given with each residue number
preceding its amino acid residue name. Because all correlations are presumed to
be intra-residue, the residue number and name is only given once. If inter-residue
correlations are found in the file an error message is sent to standard error, and
the program terminates. See label_correl_devs for a similar routine that gives
deviations from the average shift for an assignment in the peaks file. For best
viewing, the tab delimited text file should be read in a spread sheet application.

Example lines from labeled file:
Assignments with Deviations from Shift List Entries
peak id. Dim 0 (ppm) Dev. 0 Dim 1 (ppm) Dev. 1 Amplitude Assignment
3 8.097 0.002 4.584 -0.005 1.02e+08 17TRP:HN-HA
7 8.018 -0.022 4.538 0 6.29e+07 2SER:HN-HA
14 8.233 0.019 4.372 0.021 8.985e+06 18SER:HN-HA
17 7.922 -0.014 4.377 0.035 8.829e+06 12ALA:HN-HA
21 8.217 -0.006 4.343 0.005 1.303e+08 10SER:HN-HA






consider_nOe

Usage: consider_nOe xeasyfile.seq xeasyfile.prot < assignfile.peaks > outfile

Installation: Compile source with cc -o consider_nOe -O consider_nOe.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks), and writes a tab delimited file of 7 columns to standard output.
The seven columns are peak number, dimension 0 shift in ppm, deviation from shifts
file shift for the dimension 0 assignment, dimension 1 shift in ppm, deviation from
shifts file shift for the dimension 1 assignment, peak intensity measurement, and
assignment. Only those peaks in the original file for which assignments are given
are listed in the output. The assignments are given with each residue number
preceding its amino acid residue name. To allow for inter-residue correlations,
each assignment lists two residue number and name pairs. See label_nOe_devs for a
similar routine that gives deviations from the average shift for an assignment in
the peaks file. For best viewing, the tab delimited text file should be read in a
spread sheet application.

Example lines from labeled file:
Assignments with Deviations from Shift List Entries
peak id. Dim 0 (ppm) Dev. 0 Dim 1 (ppm) Dev. 1 Amplitude Assignment
112 8.224 0.01 4.584 -0.005 7.054e+06 18SER:HN-17TRP:HA
113 8.21 -0.013 4.584 0.024 6.939e+06 10SER:HN-9PHE:HA
114 8.104 0.002 4.581 -0.01 2.003e+06 19PHE:HN-19PHE:HA
117 8.01 -0.066 4.538 0.279 1.536e+06 22SER:HN-22SER:HA
120 8.025 0.027 4.536 0.277 1.693e+06 23ARG:HN-22SER:HA






examine

Analyze an assigned xeasy format 2D peak list and generate a list of average shifts with
RMS deviations for each of the resonances.

Usage: examine xeasyfile.seq xeasyfile.prot assignfile.peaks > outfile

Installation: Compile source with cc -o examine -O examine.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks) and writes a tab delimited file with 3 columns for resonance name,
average shift, and RMS deviation to standard output. Resonance names are given
with the residue number preceding the amino acid residue name. For resonances
for which data are not available in the .peaks file, a line with only the resonance
name is printed. For best viewing, the tab delimited text file should be read in
a spread sheet application.

Example lines from file:
atom avg. shift RMS dev.
1VAL:N
1VAL:HN
1VAL:CA
1VAL:HA
1VAL:CB
1VAL:HB 1.35233 0.00124722
1VAL:QG1 0.695 0
1VAL:QG2 0.7415 0.0045






Perl script to extract VNMR pks columns in the given order to a tab delimited file.

usage: extract_vnmr.pl col1 col2 col3 ... < infile > outfile

Reads from standard input and extracts columns from the first line of each entry
in a VNMR pks format file (type generated by the VNMR command, ll2d). Writes on
standard output a tab delimited file consisting of the column entries in the order
listed. In order, the columns read are peak number, F1 shift in ppm, F2 shift in
ppm, amplitude, and volume.

Example of use: Generate a four column file of peak number, direct dimension shift
in ppm, indirect dimension shift in ppm, and peak volume:

extract_vnmr.pl 1 3 2 5 < varianpeaks.pks > peakcolumns.txt






label_correl

Label xeasy format 2D correlation assignments file with names in place of xeasy atom
numbers.

Usage: label_correl xeasyfile.seq xeasyfile.prot < assignfile.peaks > outfile

Installation: Compile source with cc -o label_correl -O label_correl.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks) from standard input and writes a tab delimited file of 5 columns
to standard output. The five columns are peak number, dimension 0 shift in ppm,
dimension 1 shift in ppm, peak intensity measurement, and assignment. Only those
peaks in the original file for which assignments are given are listed in the
output. The assignments are given with the residue number preceding the amino
acid residue name. Because all correlations are presumed to be intra-residue,
the residue number and name is only given once. If inter-residue correlations
are found in the file an error message is sent to standard error, and the
program terminates. For best viewing, the tab delimited text file should be read
in a spread sheet application.

Example lines from labeled file:
peak id. Dim 0 (ppm) Dim 1 (ppm) Amplitude Assignment
3 8.489 4.747 0.003936 2SER:HN-HB2
10 8.476 4.508 0.006785 2SER:HN-HB3
24 8.12 4.993 0.01321 22SER:HN-HB3
75 8.02 4.622 0.0567 9PHE:HN-HA






label_correl_devs

Label xeasy format 2D correlation assignments file with names in place of xeasy atom
numbers and deviations from the average shifts for each assigned resonance in the file.

Usage: label_correl_devs xeasyfile.seq xeasyfile.prot assignfile.peaks > outfile

Installation: Compile source with cc -o label_correl_devs -O label_correl_devs.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks), and writes a tab delimited file of 7 columns to standard output.
The seven columns are peak number, dimension 0 shift in ppm, deviation from average
shift for the dimension 0 assignment, dimension 1 shift in ppm, deviation from
average shift for the dimension 1 assignment, peak intensity measurement, and
assignment. Only those peaks in the original file for which assignments are given
are listed in the output. The assignments are given with each residue number
preceding its amino acid residue name. Because all correlations are presumed to
be intra-residue, the residue number and name is only given once. If inter-residue
correlations are found in the file an error message is sent to standard error, and
the program terminates. See consider_correl for a similar routine that gives
deviations from shifts given in the shifts file. For best viewing, the tab
delimited text file should be read in a spread sheet application.

Example lines from labeled file:
Assignments with Deviations from Average Shift of Each Assignment
peak id. Dim 0 (ppm) Dev. 0 Dim 1 (ppm) Dev. 1 Amplitude Assignment
3 8.097 0.0015 4.584 0.0035 1.02e+08 17TRP:HN-HA
7 8.018 0.0005 4.538 -0.0054 6.29e+07 2SER:HN-HA
14 8.233 -0.008 4.372 -0.00166667 8.985e+06 18SER:HN-HA
17 7.922 -0.0075 4.377 0.00525 8.829e+06 12ALA:HN-HA
21 8.217 0.0015 4.343 0.000333333 1.303e+08 10SER:HN-HA
29 8.037 0.0005 4.312 0.00225 1.133e+08 14SER:HN-HA
32 7.764 0.002 4.308 -0.0045 8.896e+07 20ALA:HN-HA






label_nOe

Label xeasy format 2D nOe assignments file with names in place of xeasy atom numbers.

Usage: label_nOe xeasyfile.seq xeasyfile.prot < assignfile.peaks > outfile

Installation: Compile source with cc -o label_nOe -O label_nOe.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks) from standard input and writes a tab delimited file of 5 columns
to standard output. The five columns are peak number, dimension 0 shift in ppm,
dimension 1 shift in ppm, peak intensity measurement, and assignment. Only those
peaks in the original file for which assignments are given are listed in the
output. The assignments are given with each residue number preceding its amino
acid residue name. To allow for inter-residue correlations, each assignment
lists two residue number and name pairs. For best viewing, the tab delimited text
file should be read in a spread sheet application.

Example lines from labeled file:
peak id. Dim 0 (ppm) Dim 1 (ppm) Amplitude Assignment
15 8.031 4.656 0.001687 9PHE:HN-9PHE:HA
19 8.085 4.638 0.001396 10SER:HN-9PHE:HA
24 8.208 4.533 0.02944 14SER:HN-14SER:HB3
31 7.644 4.532 0.002276 15ILE:HN-14SER:HB3






label_nOe_devs

Usage: label_nOe_devs xeasyfile.seq xeasyfile.prot assignfile.peaks > outfile

Installation: Compile source with cc -o label_nOe_devs -O label_nOe_devs.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks), and writes a tab delimited file of 7 columns to standard output.
The seven columns are peak number, dimension 0 shift in ppm, deviation from average
shift for the dimension 0 assignment, dimension 1 shift in ppm, deviation from
average shift for the dimension 1 assignment, peak intensity measurement, and
assignment. Only those peaks in the original file for which assignments are given
are listed in the output. The assignments are given with each residue number
preceding its amino acid residue name. To allow for inter-residue correlations,
each assignment lists two residue number and name pairs. See consider_nOe for a
similar routine that gives deviations from shifts given in the shifts file. For
best viewing, the tab delimited text file should be read in a spread sheet
application.

Example lines from labeled file:
Assignments with Deviations from Average Shift of Each Assignment
peak id. Dim 0 (ppm) Dev. 0 Dim 1 (ppm) Dev. 1 Amplitude Assignment
112 8.224 0.00693333 4.584 -0.0072 7.054e+06 18SER:HN-17TRP:HA
113 8.21 -0.00484615 4.584 0.005 6.939e+06 10SER:HN-9PHE:HA
114 8.104 0.00483333 4.581 -0.00333333 2.003e+06 19PHE:HN-19PHE:HA
117 8.01 0.00257143 4.538 -0.00233333 1.536e+06 22SER:HN-22SER:HA
120 8.025 0.0152308 4.536 -0.00433333 1.693e+06 23ARG:HN-22SER:HA
122 8.019 0.0115714 4.456 -0.000571429 6.724e+06 22SER:HN-21ARG:HA
123 7.995 -0.0156364 4.456 -0.000571429 2.669e+06 21ARG:HN-21ARG:HA






possibilities

Examine an xeasy format 2D assignments file in conjunction with an xeasy format
sequence file and an xeasy format atoms file to generate a list of assignment possibilities
for unassigned shifts.

Usage: possibilities xeasyfile.seq xeasyfile.prot < assignfile.peaks > outfile

Installation: Compile source with cc -o possibilities -O possibilities.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks) from standard input and writes a tab delimited file of 6 columns
to standard output. The six columns are peak number, dimension 0 shift in ppm,
dimension 1 shift in ppm, peak intensity measurement, possible assignments for
dimension 0 shift, and possible assignments for dimension 1 shift. Only those
peaks in the original file for which at least one shift is not assigned are listed
in the output. The assignments are given with each residue number preceding its
amino acid residue name, and each possibility lists a residue number and name.
For best viewing, the tab delimited text file should be read in a spread sheet
application. Use caution in interpreting the results of this procedure.
Possible assignments are determined only by a shift being within the error
range of a shift listed in the xeasy shifts file (*.prot) without any other
considerations. One application of this is to attempt to assign parts of a larger
sequence on the basis of assignments of NMR spectra of fragments of that sequence.

Example lines from output:
peak id. Dim 0 (ppm) Dim 1 (ppm) Amplitude Potential1 Potential2
1 8.112 4.62 9.225e+06 9PHE:HN
2 8.079 4.623 1.151e+07 9PHE:HN
22SER:HN
4 8.001 4.577 7.184e+06 21ARG:HN
23ARG:HN
5 8.112 4.541 8.714e+06 9PHE:HN 6SER:HA
14SER:HA






toxeasy

Read first four columns in a tab delimited file and write an xeasy format
2D peaks file.

Usage: toxeasy < infile > outfile.peaks

Installation: Compile source with cc -o toxeasy -O toxeasy.c

Reads from standard input the first four columns of each line of a file as peak
number, dimension 0 shift in ppm, dimension 1 shift in ppm, and peak intensity
measurement. Writes on standard output a 2D xeasy format file (*.peaks) with the
color set to ? and the assignments and error set to 0.






varian2dtoazara

Create correct Azara format 2D .par and .spc files from a 2D Varian (VNMR)
curpar and datdir/phasefile pair.

Usage: varian2dtoazara phasefilepath outfilebase [sfrq]

Installation: Select proper make file and compile source with make

Reads parameters from phasefilepath/curpar and writes an azara parameters file
to outfilebase.par. Reads the 2D phasefile from phasefilepath/datdir/phasefile
and writes an azara format 2D spectrum file to outfilebase.spc. The VNMR
parameter, sfrq, is used as the frequency for the directly detected dimension.
If a third parameter is given, that parameter is used as the name of the VNMR
parameter for the indirect dimension. In the absence of a third parameter, the
VNMR parameter, dfrq, is taken as the frequency of the indirect dimension.






write_peaks

Write peak list from an xeasy format 2D assignments file with names in place of
xeasy atom numbers.

Usage: write_peaks xeasyfile.seq xeasyfile.prot < assignfile.peaks > outfile

Installation: Compile source with cc -o write_peaks -O write_peaks.c

Reads the xeasy sequence file (*.seq) for amino acid residue names and the xeasy
shifts file (*.prot) for the shift name and number. Reads the assigned 2D peaks
file (*.peaks) from standard input and writes a tab delimited file of 5 columns
to standard output. The five columns are peak number, dimension 0 shift in ppm,
dimension 1 shift in ppm, peak intensity measurement, and assignment. All
peaks in the original file are listed in the output with blanks when assignments
are missing. To allow for inter-residue correlations, every assignment lists two
residue number and name pairs. For partial assignments, the unassigned portion
is indicated by question marks. Assignments are given with the residue number
preceding the amino acid residue name. For best viewing, the tab delimited text
file should be read in a spread sheet application. This program can give very
long files.

Example lines from labeled file:
peak id. Dim 0 (ppm) Dim 1 (ppm) Amplitude Assignment
1 5.129 7.784 -210300
2 4.338 8.231 295600
3 4.366 8.223 -237400 10SER:HA-10SER:HN
4 4.354 8.22 -334200 18SER:HA-18SER:HN
5 4.325 8.224 247500




<Usage>
Entering any command without parameters will print out a description of usage.




<Installation>
Compile each C program in the utilities folder with cc -o name -O name.c
The perl script requires perl
The code for varian2dtoazara is in the varian2dtoazara folder.
Use the file Makefile.mac to make the program on Mac OS X.
Use the file Makefile.sol to make the program on Solaris 7 with Sun Workshop 5.



<Versions>
This is the first version, without any change history.



<Copyright>
Bruce D. Ray 2005



<License>
This software is distributed under the current CCPN license (see www.ccpn.ac.uk)