The three-pulse z-filter MQMAS pulse sequence generates echo and antiecho, which have the same amplitude with the same sign. In contrast, the SPAM echo/antiecho pulse program generates echo amplitude and antiecho amplitude with opposite signs. Furthermore, the first sequence involves States acquisition procedure whereas the second sequence involves the echo/antiecho procedure. As a result, the shearing AU program should be modified accordingly.
/****************************************************************/ /* xfshear2005 08.11.1996 */ /****************************************************************/ /* Short Description : */ /* */ /* Program for shearing of 2D MQMAS spectra of odd half */ /* integer quadrupolar nuclei. Data need to be aquired in */ /* States Mode */ /* Program used for shearing of ZQ-TROSY experiments */ /* like trosyzqgpphwg */ /****************************************************************/ /* Keywords : */ /* */ /* shear, odd half spin nuclei, multi quantum, mq, MQ */ /* ZQ-TROSY */ /****************************************************************/ /* Description/Usage : */ /* */ /* Program is used */ /* */ /* a) for 2D MQ experiments on nuclei with */ /* odd half integer spin for shearing-FT of 2D spectrum */ /* including 2DFT and referencing in F1 dimension */ /* according to delta(MQ)=delta(iso)+(p-R)delta(qis) */ /* It checks for the parameter "nucleus" (AMX) or "NUC1" */ /* (Avance) and sets the spin value accordingly. */ /* If the nucleus is not in the list it asks for the spin, */ /* too. Only most common nuclei are in the list. */ /* If the pulse program name matches mpxq, where */ /* x corresponds to the multiple quantum order of */ /* the experiment, then this is assumed, otherwise */ /* it is asked for by the program. */ /* Program asks if abs2 in F2 dimension is desired. */ /* If answered with yes, then a Hilbert transform */ /* is automatically done, which requires xwinnmr1.3 */ /* or later. In older versions, this command has to */ /* be eliminated from the program code. */ /* A F1 frequency shift in ppm is asked for to compensate */ /* for malchosen o1 setting. This value is stored and */ /* suggested for any repeated processing. */ /* b) for ZQ-TROSY experiments to eliminate the */ /* contribution of proton chemical shift in the */ /* F1 direction */ /****************************************************************/ /* Author(s) : */ /* */ /* Name : Christian Fernandez */ /* Organisation : Universite de Lille, CNRS-801 */ /* Email : christian.fernandez@univ.lille.fr */ /* */ /* Name : Stefan Steuernagel */ /* Organisation : Bruker Analytik */ /* Email : stefan.steuernagel@bruker.de */ /****************************************************************/ /* Name Date Modification: */ /* ste 960201 created */ /* ste 980813 check xdim's and status sizes */ /* at right time */ /* ste 980813 XHT2 included after XF1 to */ /* allow f2 phase correction after */ /* processing */ /* ste 981101 close of input data files and */ /* "mv temp-file to 2rr" etc */ /* included */ /* ste 000105 XIF2 and XFB included after */ /* shearing to allow apodisation */ /* in F2, set-up to be done prior */ /* to execution of xfshear, all */ /* handling done by this program */ /* ber/ste 010909 handling for ZQ-TROSY experiment */ /* included, allows to use strip */ /* transformation in F2 only */ /* not strip-FT for MQMAS! */ /* ste 031031 shearing and calibration */ /* of STMAS included */ /* "xf2 raw" command used to avoid */ /* error if partly processed data */ /* exist */ /* ste 040112 check pparmod for 2D, so it can */ /* be applied to planes from 3D */ /* echo/anti-echo treatment incl. */ /* ste 041224 auto function included to */ /* suppress abs2 and F1-shift query */ /* dynamic memory allocation incl. */ /****************************************************************/ /* $Id: xfshear,v 1.15.2.2 2005/02/07 14:06:38 es Exp $ */ #include <math.h> int parmode, si2, si1, outexpno, tempfile2rr, infile2rr, tempfile2ir, infile2ir; int *in2rr, *in2ir, *temp2rr, *temp2ir, *temp2rr2, *temp2ir2, *temp2rrB, *temp2irB, *temp2rrB2, *temp2irB2; int dummy, nbytes, sizeofint, nbytesread, xdim2, xdim1, loopcount4, sig, mq, nspin, wdw2, bcmod, phmod, stsr2, stsi1, stsi2, fnmode, mc2; int option1=0, option2=0; double sw1, sw2, ratio, ph, ph1, ph2, ph3, phc1, phc2, in0, sfo1, sfo12, sfo11, bf11, bf12; float Noise, spin, offset1, offset2, off2, off1, sr2, sr1, swh1; char inname2rr[PATH_LENGTH], tempname2rr[PATH_LENGTH], inname2ir[PATH_LENGTH], tempname2ir[PATH_LENGTH], imfile[8], outname[PATH_LENGTH], nucl[80], yes[20], pulprog[80], ti[80], ShearOpt[PATH_MAX]; /* select current dataset ====================== */ GETCURDATA; (void) strcpy (yes,"yes"); /* is-it a 2D spectrum and taken in States, States-TPPI or EA? ===================== */ FETCHPARS("PPARMOD",&parmode); if ( parmode != 1 ) { STOPMSG("Program is only suitable for 2D data!");} FETCHPAR1S("FnMODE",&fnmode); if ( fnmode == 0 ) { FETCHPAR("MC2",&mc2); if ( mc2 != 3 && mc2 != 4 && mc2 != 5 ) STOPMSG("mc2 must be States, States-TPPI, or Echo-Antiecho!"); } else if ( fnmode != 4 && fnmode != 5 && fnmode != 6) STOPMSG("FnMode must be in States, States-TPPI, or Echo-Antiecho!"); /* prepare for automatic execution and other ratio =============================================== */ sprintf(ShearOpt,"%s",cmd); if ( strstr(ShearOpt,"auto")) option1 = 1; if ( strstr(ShearOpt,"ratio")) option2 = 1; /* if auto selected, don't aks for ABS2 and additional F1 shift ============================================================ */ if (option1 == 1) { f1=0.; FETCHPAR1S("NOISF1",&Noise); FETCHPARS("TI",ti); if (!strcmp(ti,"shearing done")) f1=Noise; } if (option1 == 0) { /* automatic baseline correction for MQMAS and STMAS ? =================================================== */ if (mq != 1) GETSTRING("Apply ABS2 ? : ",yes); /* additional F1 shift ? ===================== */ f1=0.; FETCHPAR1S("NOISF1",&Noise); FETCHPARS("TI",ti); if (!strcmp(ti,"shearing done")) f1=Noise; if (mq != 1) GETFLOAT(" F1 shift in ppm ? : ",f1); } /* init some variables =================== */ FETCHPARS("PULPROG",pulprog); FETCHPARS("SFO1",&sfo1); FETCHPAR("WDW",&wdw2) STOREPAR("WDW",0) /* shearing ratio calculation for quadrupolar nuclei set mq and spin to 1 for 1H ==================================================*/ spin=5./2.; mq=3; FETCHPARS("NUC1",nucl) if(!strcmp(nucl,"off")) FETCHPARS ("NUCLEUS",nucl) if(!strcmp(nucl,"7Li")) spin=1.5; else if(!strcmp(nucl,"11B")) spin=1.5; else if(!strcmp(nucl,"17O")) spin=2.5; else if(!strcmp(nucl,"23Na")) spin=1.5; else if(!strcmp(nucl,"27Al")) spin=2.5; else if(!strcmp(nucl,"35Cl")) spin=1.5; else if(!strcmp(nucl,"39K")) spin=1.5; else if(!strcmp(nucl,"45Sc")) spin=3.5; else if(!strcmp(nucl,"51V")) spin=3.5; else if(!strcmp(nucl,"55Mn")) spin=2.5; else if(!strcmp(nucl,"63Cu")) spin=1.5; else if(!strcmp(nucl,"65Cu")) spin=1.5; else if(!strcmp(nucl,"69Ga")) spin=1.5; else if(!strcmp(nucl,"71Ga")) spin=1.5; else if(!strcmp(nucl,"85Rb")) spin=2.5; else if(!strcmp(nucl,"87Rb")) spin=1.5; else if(!strcmp(nucl,"93Nb")) spin=4.5; else if(!strcmp(nucl,"121Sb")) spin=2.5; else if(!strcmp(nucl,"209Bi")) spin=4.5; else if(!strcmp(nucl,"1H")) spin=1.0; else GETFLOAT(" Enter spin number : ",spin); nspin = (int) ceil ( (double)(2*spin) ); if ( nspin == 3 && !strncmp(pulprog,"mp3q",4) ) { mq = -3; ratio = 7./9.; } else { if (!strncmp(pulprog,"mp3q",4)) mq=3; else if(!strncmp(pulprog,"mp5q",4)) mq=5; else if(!strncmp(pulprog,"mp7q",4)) mq=7; else if(!strncmp(pulprog,"mp9q",4)) mq=9; else if(!strcmp(pulprog,"trosyzqgpphwg")) mq=1; else if(!strncmp(pulprog,"stmas",5)) { mq=0; if(nspin == 3) ratio=-8./9.; if(nspin == 5) ratio=7./24.; if(nspin == 7) ratio=28./45.; if(nspin == 9) ratio=55./72.; } else GETINT( " Enter the pQ order : ",mq); mq = (int) ceil ( (double)mq ); if ( mq == nspin ) mq = -mq; if ( nspin == 5 && mq == -5) ratio = 25./12.; if ( nspin == 5 && mq == 3) ratio = 19./12.; if ( nspin == 7 && mq == -7) ratio = 161./45.; if ( nspin == 7 && mq == 5) ratio = 11./9.; if ( nspin == 7 && mq == 3) ratio = 101./45.; if ( nspin == 9 && mq == -9) ratio = 31./6.; if ( nspin == 9 && mq == 7) ratio = 7./18.; if ( nspin == 9 && mq == 5) ratio = 95./36.; if ( nspin == 9 && mq == 3) ratio = 91./36.; if ( mq == 1 ) ratio = -1.; } ; if ( option2 == 1) GETDOUBLE(" Enter different shearing ratio :",ratio); /* ignore strip parameters in F1 for 1H spectra! ============================================= */ if (mq == 1 ) { FETCHPAR1("STSI",&stsi1); STOREPAR1("STSR",0); STOREPAR1("STSI",0); if (stsi1 != 0) Proc_err(0,"F1 Strip-FT not yet implemented,\nparameters disabled"); } /* ignore all strip parameters for MQMAS spectra ! =============================================== */ if ( mq != 1) { FETCHPAR("STSI",&stsi2); FETCHPAR1("STSI",&stsi1); STOREPAR("STSR",0); STOREPAR("STSI",0); STOREPAR1("STSR",0); STOREPAR1("STSI",0); if (stsi2 != 0 || stsi1 != 0) Proc_err(0,"Strip-FT not yet implemented,\nparameters disabled"); } /* calculate F2 transform ====================== */ SETCURDATA AUERR=CPR_exec( "xf2 raw",WAIT_TERM); if ( yes[0]=='y') {ABS2 XHT2} /* get required status parameters after F2 transform ================================================= */ FETCHPARS("SW_p",&sw2); FETCHPARS("SI",&si2); FETCHPARS("STSR", &stsr2); FETCHPAR1S("SWH", &swh1); FETCHPAR1S("SI",&si1); FETCHPAR1S("XDIM",&xdim1); FETCHPARS("XDIM",&xdim2); sizeofint=sizeof(int); nbytes=sizeofint*xdim2*2; /* calculate phase for shearing and scaling for MQMAS/STMAS F1 =========================================================== */ ph1= -2.*3.141529*ratio*sw2 / swh1 / (double)(si2); /* for MQMAS */ if ( mq<0 ) ph1= -ph1; d1= fabs(ratio - (double)mq); /* for TROSY */ if ( mq==1 ) d1=1.0; /* for STMAS of inner satellite */ if ( mq==0 ) d1=fabs(ratio - 1.0); sfo11=d1*sfo1; /* additional F1 shift =================== */ ph2= (double)f1; phc2= -2.*3.141529*ph2*sfo11/(double)swh1; /* compensate for strip transformation of 1H spectra ================================================= */ if ( mq == 1 ) { ph3 = - ph1 * stsr2; phc2 += ph3; } /* decide 2ii or 2ir file ====================== */ if ( fnmode == 1 ) (void)sprintf(imfile,"2ii"); else (void)sprintf(imfile,"2ir"); /* Open source file RR and IR ========================== */ (void)sprintf( inname2rr,"%s/data/%s/nmr/%s/%d/pdata/%d/2rr", disk,user,name,expno,procno); if ((infile2rr=open(inname2rr,0))==-1) { (void)sprintf(text," I/O Error (Open) \n%s ",inname2rr); STOPMSG(text);} (void)sprintf( inname2ir,"%s/data/%s/nmr/%s/%d/pdata/%d/%s", disk,user,name,expno,procno,imfile); if ((infile2ir=open(inname2ir,0))==-1) { (void)sprintf(text," I/O Error (Open) \n%s ",inname2ir); STOPMSG(text);} /* Create temporary files : 2rrtemp et 2irtemp =========================================== */ (void)sprintf( tempname2rr,"%s/data/%s/nmr/%s/%d/2rrtemp", disk,user,name,expno); if ((tempfile2rr=creat(tempname2rr,0664))==-1) { (void)sprintf(text," I/O Error (Create) \n%s ",tempname2rr); STOPMSG(text);} (void)sprintf( tempname2ir,"%s/data/%s/nmr/%s/%d/2irtemp", disk,user,name,expno); if ((tempfile2ir=creat(tempname2ir,0664))==-1) { (void)sprintf(text," I/O Error (Create) \n%s ",tempname2ir); STOPMSG(text);} (void)sprintf(text,"shear : calculating"); Show_status(text); /* allocate memory for array */ in2rr = (int*)malloc(nbytes*10); if (in2rr == 0) STOPMSG("Not enough memory"); in2ir = in2rr + nbytes/sizeofint; temp2rr= in2ir + nbytes/sizeofint; temp2ir= temp2rr + nbytes/sizeofint; temp2rr2= temp2ir + nbytes/sizeofint; temp2ir2= temp2rr2 + nbytes/sizeofint; temp2rrB= temp2ir2 + nbytes/sizeofint; temp2irB= temp2rrB + nbytes/sizeofint; temp2rrB2= temp2irB + nbytes/sizeofint; temp2irB2= temp2rrB2 + nbytes/sizeofint; /* Read data in submatrix ====================== */ TIMES(si1/xdim1) TIMES2 (si2/xdim2) TIMES3 (xdim1/2) if ((nbytesread=read(infile2rr,in2rr,nbytes))<=0) /* Read 2 rows ! */ {(void)remove(tempname2rr); STOPMSG(" 2rr file corrupted! ");} if ((nbytesread=read(infile2ir,in2ir,nbytes))<=0) {(void)remove(tempname2ir); STOPMSG(" 2ir file corrupted! ");} /* Store Sx */ for (loopcount4=0;loopcount4<xdim2;loopcount4++) { temp2rr[loopcount4]= in2rr[loopcount4]; temp2ir[loopcount4]= in2ir[loopcount4];} /* Store iSy */ for (loopcount4=0;loopcount4<xdim2;loopcount4++) { temp2rr2[loopcount4]= in2rr[loopcount4+xdim2]; temp2ir2[loopcount4]= in2ir[loopcount4+xdim2];} /* combine Sx and iSy to create ... ================================ */ for (loopcount4=0;loopcount4<xdim2;loopcount4++) { /* echo ==== */ temp2rrB[loopcount4]=(temp2rr[loopcount4] -temp2ir2[loopcount4])/2; temp2irB[loopcount4]=(temp2ir[loopcount4] +temp2rr2[loopcount4])/2; /* and antiecho ============ */ temp2rrB2[loopcount4]=(temp2rr[loopcount4] +temp2ir2[loopcount4])/2; temp2irB2[loopcount4]=(temp2ir[loopcount4] -temp2rr2[loopcount4])/2; } /* perform shearing transformation =============================== */ i1= loopcount3 +(loopcount1)*xdim1/2; for (loopcount4=0;loopcount4<xdim2;loopcount4++) { i2= loopcount4+(loopcount2)*xdim2; phc1= ph1*(double)((i2-si2/2)*i1); phc1+=phc2*(double)i1; in2rr[loopcount4]= (int)(((double)temp2rrB[loopcount4])*cos(phc1) +((double)temp2irB[loopcount4])*sin(phc1))/2; in2ir[loopcount4]= (int)(((double)temp2irB[loopcount4])*cos(phc1) -((double)temp2rrB[loopcount4])*sin(phc1))/2; in2rr[loopcount4+xdim2]= (int)(((double)temp2rrB2[loopcount4])*cos(phc1) -((double)temp2irB2[loopcount4])*sin(phc1))/2; in2ir[loopcount4+xdim2]= (int)(((double)temp2irB2[loopcount4])*cos(phc1) +((double)temp2rrB2[loopcount4])*sin(phc1))/2; } for (loopcount4=0;loopcount4<xdim2;loopcount4++) {temp2rr[loopcount4]=0.5*( in2rr[loopcount4]+in2rr[loopcount4+xdim2]); temp2ir[loopcount4]=0.5*( in2ir[loopcount4]+in2ir[loopcount4+xdim2]); temp2irB[loopcount4]=0.5*( in2rr[loopcount4]-in2rr[loopcount4+xdim2]); temp2rrB[loopcount4]=0.5*( in2ir[loopcount4]-in2ir[loopcount4+xdim2]); } for (loopcount4=0;loopcount4<xdim2;loopcount4++) {in2rr[loopcount4]= temp2rr[loopcount4]; in2ir[loopcount4]= temp2ir[loopcount4]; in2rr[loopcount4+xdim2]= temp2rrB[loopcount4]; in2ir[loopcount4+xdim2]= temp2irB2[loopcount4]; } /* Save ==== */ write(tempfile2rr,in2rr,nbytesread); write(tempfile2ir,in2ir,nbytesread); END ; /* loop3 */ END; /* loop2 */ END; /*loop1 */ close(tempfile2rr); close(tempfile2ir); close(infile2rr); close(infile2ir); /* Copy ==== */ (void)remove(inname2rr); if (rename(tempname2rr,inname2rr)!=0) Proc_err(1,"error %d",errno); (void)remove(inname2ir); if (rename(tempname2ir,inname2ir)!=0) Proc_err(1,"error %d",errno); (void)sprintf(text,"shear : finished"); Show_status(text); /* F1 Scaling for MQ MAS experiments ================================= */ if ( option2 == 0) { if ( d1 != 1.0 ) { FETCHPARS("BF1",&bf12); FETCHPARS("SR",&sr2); bf11= d1*bf12; sr1= (float)(d1*sr2); STOREPAR1S("BF1",bf11); STOREPAR1("BF1",bf11); #if 1 STOREPAR1S("SF",bf11 + sr1 * 1e-6); STOREPAR1("SF",bf11 + sr1 * 1e-6); #endif #if 0 STOREPAR1S("SR",sr1 ); STOREPAR1("SR",sr1); #endif STOREPAR1S("SFO1",sfo11); STOREPAR1("SFO1",sfo11); FETCHPAR1S("OFFSET",&offset1); offset1=offset1-ph2; STOREPAR1S("OFFSET",offset1); } } /* store TI to recall shearing and shifting ======================================== */ STOREPARS("TI","shearing done"); STOREPAR1S("NOISF1",f1); /* inverse F2 and subsequent F2+F1 transform ========================================= */ XHT2 XIF2 FETCHPAR("PH_mod",&phmod) STOREPAR("PH_mod",0) STOREPAR("WDW",wdw2) FETCHPAR("BC_mod",&bcmod) STOREPAR("BC_mod",0) CPR_exec("xfb nc_proc 0",WAIT_TERM); STOREPAR("PH_mod",phmod) STOREPAR("BC_mod",bcmod) VIEWDATA QUITMSG(" Shearing-FT done!")