-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
CSHIFT and several related utilities (PROTSHIFT and CSCON) translate
a MORASS NMRD (simul.out) file into the FELIX .mat format. These
utilities were written by Howard Robinson, Dan Severance and Rob
Meadows who are entirely responsible for their contents. I have attempted
to add some more organization to how they go together. If all else
fails, read the code and/or contact one of them. Good luck.
1> CSHIFT requires 2 input files, a chemical shift assignment file and an
MORASS simul.out file of simulated NOESY volumes:
1) myfile.asg which contains some FELIX header info, residue info and
chemical shifts for each proton in each residue in ppm.
2) simul.out contains the 'NMRD' information contained in the output file
from the SIMUL module of MORASS (which will require a .pdb file).
You will be prompted interactively for the actual names of both files
when you run the program.
2> PROTSHIFT will construct the chemical shift portion of a .asg file for a
protein from the XYZ coordinates. These can be in either amber, charmm
or midas formats. PROTSHIFT also requires a file called 'atoms.dtb' which
contains a list of amino acids and their individual proton chemical shifts.
This file is provided. Note that PROTSHIFT randomizes the shifts and line
widths a little to provide a more natural spectra.
For an RNA or DNA one could use a protein .asg file as a template and
put in the actual individual nucleoside proton chemical shift I suppose.
3> CSCON will take the raw output from PROTSHIFT, add the appropriate header
info and pop out a complete .asg file suitable for CSHIFT. You will be
prompted interactively for all file names.
Bruce A. Luxon
Chemistry Dept.
Purdue University
W. Lafayette, IN
email bruce@dggpi2.chem.purdue.edu
7/93
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
The following are the original comments in the program cs.c:
cs.c written by Howard Robinson to produce an intensity matrix in
Dennis Hare's felix .mat format from Morass output file .nmrd and an
assignment file. The calculation of the lorentzian surfaces is from
Dan Severance and Rob Meadows at Purdue University, W. Lafayette IN.
Gaussian, sums of lorentian and gaussian and product of lorentian and
gaussian are also produced. In all cases, the linewidths specified in the
assignment file will be accurately produced, and volumes are in scale to
each other. The entire 2D simulated data set will need to be scaled to the
empirical 2D data set.
The following line compiles this code.
cc cs.c -o cs -lm
I get one warning about pointers when compiling this on the SGI 4D irix 3.2.
A sample assignment file appears below. The comments in the first 9 lines
are optional but the order and number of parameters are fixed. After the first
9 lines, the assignments are read until EOF. The parameters can be obtained
from felix with the rmx command. The volumes come from inspection of the
.nmrd file of Morass. The cuttoff radius is in Hz. The felix plot scale
factor may need adjustment. The apodization is either lorentian or
gaussian or a sum of (r * lorentian) * ((1-r) * gaussian) with the
ratio r appended to the linetype entry (lor+gauss 0.4), or a product
of lorentian and gaussian curves (lor*gauss).
The assignments must all be unique atom labels with the chemical shift in ppm
and the linewidth in Hz.
512 512 number of points (from felix rmx command)
500.1 500.1 spectrometer frequency
4329.0 4329.0 sweep width in hertz
243.5 243.5 reference point
2470.5 2470.5 hertz for reference point (fix alignment here)
.001 1.0 min max volume (inspect the .nmrd file)
100.0 100.0 5*linewidth for cuttoff radius
1000000000.0 felix plot scaling (may need adjusting)
lorentian line type (lorentian) (gaussian) (lor+gauss 0.3) (lor*gauss)
1 C H5' 3.694 9.0
1 C H5D 3.573 9.0
1 C H4' 4.437 9.0
1 C H3' 4.555 9.0
1 C H2' 0.933 9.0
1 C H2D 2.159 9.0
1 C H1' 6.124 9.0
1 C H5 5.661 9.0
1 C H6 7.298 9.0
A sample Morass .nmrd file appears below. The first 7 lines are ignored.
The program compares the residue number and atom label for an exact
match with the assignment file. You will be notified if there is a failure.
The only information abstracted from this file is the volume for each cross
peak. Morass produces this file with only the lower half and diagonal cross
peaks so cs also produces symmetry related peaks.
MORASS OUTPUT FILE FROM SIMUL
SPINS TAU TIME SFRQ VOL0
108 3.000 0.200 500.100 1.000
-------------------------------------------------------------------------------- I J VOLUME ATOM (I) ATOM (J) RATE RIJ PPM(I) PPM(J)-------------------------------------------------------------------------------- 1 1 0.3549 C 1 H5' C 1 H5' 10.83478
2 1 0.3289 C 1 H5D C 1 H5' -8.92160 1.631
2 2 0.3400 C 1 H5D C 1 H5D 11.31420
3 1 0.1184 C 1 H4' C 1 H5' -0.90033 2.390
3 2 0.1214 C 1 H4' C 1 H5D -1.02868 2.338
3 3 0.5831 C 1 H4' C 1 H4' 2.92666
To execute: if the assignment file above is named t.ass and the .nmrd file
is named t.nmrd, and the output felix intensity matrix file name will be
t.mat, then the following execution line may be used:
cs t.ass t.nmrd t.mat
Only the real part of the intensity matrix is produced.
Any questions: robinson@b.scs.uiuc.edu or for bitnet robinson@uiucscs
Original comments in PROTSHIFT.F by Rob Meadows:
C ************************************************************************
C shift: READS A COORDINATE FILE IN CHARMM, MIDAS OR AMBER FORMAT,
C SEARCHES A DATABASE FOR THE CORRECT CHEMICAL SHIFTS FOR
C THE PROTONS IN THAT COORDINATE FILE AND CREATES A NEWF
C FILE CONTAING THE ATOM IDS, CHEMICAL SHIFTS AND LINE
C WIDTHS FOR USE WITH THE CS PROGRAM.
C
C THE SHIFTS AND LINEWIDTHS ARE RANDOMIZED BY A SMALL
C AMOUNT IN ORDER TO SIMULATE THE CHEMICAL SHIFT
C DEVIATIONS USUALLY FOUND IN A PROTEIN OR PEPTIDE MOLECULE.
C
C CURRENT LINE WIDTHS ARE 8.0 HERTZ.
C
C rpm; 1991
c ************************************************************************
|
