-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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 ************************************************************************