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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
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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 ************************************************************************

Modified: Fri May 13 16:00:00 1994 GMT
Page accessed 5350 times since Sat Apr 17 21:34:57 1999 GMT