*** abstree.c	2005/07/16 14:40:23	1.2
--- abstree.c	2005/07/16 14:47:46
***************
*** 1353,1359 ****
      ay = atm2->yorg - atm1->yorg + atm2->fyorg - atm1->fyorg
           + (double)(atm2->ytrl - atm1->ytrl)/40.;
      az = atm2->zorg - atm1->zorg + atm2->fzorg - atm1->fzorg
!          - (double)(atm2->ztrl - atm1->ztrl)/40.;
      if( !ax && !ay && !az )
          return 0.0;
  
--- 1353,1359 ----
      ay = atm2->yorg - atm1->yorg + atm2->fyorg - atm1->fyorg
           + (double)(atm2->ytrl - atm1->ytrl)/40.;
      az = atm2->zorg - atm1->zorg + atm2->fzorg - atm1->fzorg
!          + (double)(atm2->ztrl - atm1->ztrl)/40.;
      if( !ax && !ay && !az )
          return 0.0;
  
***************
*** 1362,1368 ****
      by = atm3->yorg - atm2->yorg + atm3->fyorg - atm2->fyorg
           + (double)(atm3->ytrl - atm2->ytrl)/40.;
      bz = atm3->zorg - atm2->zorg + atm3->fzorg - atm2->fzorg
!          - (double)(atm3->ztrl - atm2->ztrl)/40.;
      if( !bx && !by && !bz )
          return 0.0;
  
--- 1362,1368 ----
      by = atm3->yorg - atm2->yorg + atm3->fyorg - atm2->fyorg
           + (double)(atm3->ytrl - atm2->ytrl)/40.;
      bz = atm3->zorg - atm2->zorg + atm3->fzorg - atm2->fzorg
!          + (double)(atm3->ztrl - atm2->ztrl)/40.;
      if( !bx && !by && !bz )
          return 0.0;
  
***************
*** 1371,1377 ****
      cy = atm4->yorg - atm3->yorg + atm4->fyorg - atm3->fyorg
           + (double)(atm4->ytrl - atm3->ytrl)/40.;
      cz = atm4->zorg - atm3->zorg + atm4->fzorg - atm3->fzorg
!          - (double)(atm4->ztrl - atm3->ztrl)/40.;
      if( !cx && !cy && !cz )
          return 0.0;
  
--- 1371,1377 ----
      cy = atm4->yorg - atm3->yorg + atm4->fyorg - atm3->fyorg
           + (double)(atm4->ytrl - atm3->ytrl)/40.;
      cz = atm4->zorg - atm3->zorg + atm4->fzorg - atm3->fzorg
!          + (double)(atm4->ztrl - atm3->ztrl)/40.;
      if( !cx && !cy && !cz )
          return 0.0;
  
***************
*** 1567,1573 ****
        y = (double)(ptr->atm->yorg + ptr->atm->fyorg + OrigCY)/250.0
           +(double)(ptr->atm->ytrl)/10000.0;
        z = (double)(ptr->atm->zorg + ptr->atm->fzorg + OrigCZ)/250.0
!          -(double)(ptr->atm->ztrl)/10000.0;
  
  #ifdef INVERT
        sprintf(eptr, "\n  Coordinates: %9.3f %9.3f %9.3f\n",x,-y,-z);
--- 1567,1573 ----
        y = (double)(ptr->atm->yorg + ptr->atm->fyorg + OrigCY)/250.0
           +(double)(ptr->atm->ytrl)/10000.0;
        z = (double)(ptr->atm->zorg + ptr->atm->fzorg + OrigCZ)/250.0
!          +(double)(ptr->atm->ztrl)/10000.0;
  
  #ifdef INVERT
        sprintf(eptr, "\n  Coordinates: %9.3f %9.3f %9.3f\n",x,-y,-z);
*** infile.c	2005/07/16 14:40:23	1.2
--- infile.c	2005/07/16 14:45:10
***************
*** 3050,3056 ****
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 -(double)(aptr->ztrl)/10000.0;
   
  #ifdef INVERT
              fprintf(DataFile,"%8.3f%8.3f%8.3f",x,-y,-z);
--- 3050,3056 ----
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 +(double)(aptr->ztrl)/10000.0;
   
  #ifdef INVERT
              fprintf(DataFile,"%8.3f%8.3f%8.3f",x,-y,-z);
***************
*** 3137,3143 ****
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 -(double)(aptr->ztrl)/10000.0;
  #ifdef INVERT
  #ifdef __STDC__
              fprintf(DataFile,"%10.4f%10.4f%10.4f ",x,-y,-z);
--- 3137,3143 ----
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 +(double)(aptr->ztrl)/10000.0;
  #ifdef INVERT
  #ifdef __STDC__
              fprintf(DataFile,"%10.4f%10.4f%10.4f ",x,-y,-z);
***************
*** 3290,3296 ****
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 -(double)(aptr->ztrl)/10000.0;
   
              /* Apply Current Viewpoint Rotation Matrix */
              xpos = (float)(x*RotX[0] + y*RotX[1] + z*RotX[2]);
--- 3290,3296 ----
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 +(double)(aptr->ztrl)/10000.0;
   
              /* Apply Current Viewpoint Rotation Matrix */
              xpos = (float)(x*RotX[0] + y*RotX[1] + z*RotX[2]);
***************
*** 3368,3374 ****
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 -(double)(aptr->ztrl)/10000.0;
  
  #ifdef INVERT
              fprintf(DataFile," %8.3f %8.3f %8.3f",x,-y,-z);
--- 3368,3374 ----
              y = (double)(aptr->yorg + aptr->fyorg + OrigCY)/250.0
                  +(double)(aptr->ytrl)/10000.0;
              z = (double)(aptr->zorg + aptr->fzorg + OrigCZ)/250.0
!                 +(double)(aptr->ztrl)/10000.0;
  
  #ifdef INVERT
              fprintf(DataFile," %8.3f %8.3f %8.3f",x,-y,-z);
*** render.c	2005/07/16 14:40:23	1.2
--- render.c	2005/07/16 14:48:21
***************
*** 2015,2021 ****
             y = (double)(QAtom->yorg + QAtom->fyorg + OrigCY)/250.0
                 +(double)(QAtom->ytrl)/10000.0;
             z = (double)(QAtom->zorg + QAtom->fzorg + OrigCZ)/250.0
!                -(double)(QAtom->ztrl)/10000.0;
  
  #ifdef INVERT
             sprintf(buffer, "  Coordinates: %9.3f %9.3f %9.3f\n",x,-y,-z);
--- 2015,2021 ----
             y = (double)(QAtom->yorg + QAtom->fyorg + OrigCY)/250.0
                 +(double)(QAtom->ytrl)/10000.0;
             z = (double)(QAtom->zorg + QAtom->fzorg + OrigCZ)/250.0
!                +(double)(QAtom->ztrl)/10000.0;
  
  #ifdef INVERT
             sprintf(buffer, "  Coordinates: %9.3f %9.3f %9.3f\n",x,-y,-z);
*** script.c	2005/07/16 14:40:23	1.2
--- script.c	2005/07/16 14:54:20
***************
*** 1397,1403 ****
          fprintf(OutFile," P %g %g %g\n", 
            (src->xorg + src->fxorg + src->xtrl/40. + OrigCX)/250.0, 
            RestoreY((src->yorg + src->fyorg + src->ytrl/40. + OrigCY))/250.0,
!           -(src->zorg + src->fzorg - src->ztrl/40. + OrigCZ)/250.0 );
      }
  
      if( col1 != col2 )
--- 1397,1403 ----
          fprintf(OutFile," P %g %g %g\n", 
            (src->xorg + src->fxorg + src->xtrl/40. + OrigCX)/250.0, 
            RestoreY((src->yorg + src->fyorg + src->ytrl/40. + OrigCY))/250.0,
!           -(src->zorg + src->fzorg + src->ztrl/40. + OrigCZ)/250.0 );
      }
  
      if( col1 != col2 )
***************
*** 1405,1411 ****
            (src->xtrl + dst->xtrl)/40. + OrigCX + OrigCX)/500.0;
          y = (src->yorg + dst->yorg + src->fyorg + dst->fyorg +
            (src->ytrl + dst->ytrl)/40. + OrigCY + OrigCY)/500.0;
!         z = (src->zorg + dst->zorg + src->fzorg + dst->fzorg -
            (src->ztrl + dst->ztrl)/40. + OrigCZ + OrigCZ)/500.0;
  
          fprintf(OutFile,"{} L %g %g %g\n", x, RestoreY(y), -z );
--- 1405,1411 ----
            (src->xtrl + dst->xtrl)/40. + OrigCX + OrigCX)/500.0;
          y = (src->yorg + dst->yorg + src->fyorg + dst->fyorg +
            (src->ytrl + dst->ytrl)/40. + OrigCY + OrigCY)/500.0;
!         z = (src->zorg + dst->zorg + src->fzorg + dst->fzorg +
            (src->ztrl + dst->ztrl)/40. + OrigCZ + OrigCZ)/500.0;
  
          fprintf(OutFile,"{} L %g %g %g\n", x, RestoreY(y), -z );
***************
*** 1420,1426 ****
      fprintf(OutFile," L %g %g %g\n", 
        (dst->xorg + dst->fxorg + dst->xtrl/40. + OrigCX)/250.0,
        RestoreY((dst->yorg + dst->fyorg + dst->ytrl/40. + OrigCY))/250.0,
!        -(dst->zorg + dst->fzorg - dst->ztrl/40. + OrigCZ)/250.0 );
  
      MagePrev = dst;
      MageCol = col2;
--- 1420,1426 ----
      fprintf(OutFile," L %g %g %g\n", 
        (dst->xorg + dst->fxorg + dst->xtrl/40. + OrigCX)/250.0,
        RestoreY((dst->yorg + dst->fyorg + dst->ytrl/40. + OrigCY))/250.0,
!        -(dst->zorg + dst->fzorg + dst->ztrl/40. + OrigCZ)/250.0 );
  
      MagePrev = dst;
      MageCol = col2;
***************
*** 1837,1843 ****
              y = (double)(aptr->yorg + aptr->fyorg)/250.0 
                  + (double)(aptr->ytrl)/10000.;
              z = (double)(aptr->zorg + aptr->fzorg)/250.0 
!                 - (double)(aptr->ztrl)/10000.;
  #ifdef __STDC__
              fprintf(OutFile,"object {sphere {<%g, %g, %g> %g}\n",
  #else
--- 1837,1843 ----
              y = (double)(aptr->yorg + aptr->fyorg)/250.0 
                  + (double)(aptr->ytrl)/10000.;
              z = (double)(aptr->zorg + aptr->fzorg)/250.0 
!                 + (double)(aptr->ztrl)/10000.;
  #ifdef __STDC__
              fprintf(OutFile,"object {sphere {<%g, %g, %g> %g}\n",
  #else
***************
*** 1927,1933 ****
                      y = (double)(aptr->yorg + aptr->fyorg)/250.0
                        + (double)(aptr->ytrl)/10000.;
                      z = -(double)(aptr->zorg + aptr->fzorg)/250.0
!                       + (double)(aptr->ztrl)/10000.;
  
                      fputs("    Translation { translation ",OutFile);
                      WriteVRMLTriple(x-ox,RestoreY(y-oy),z-oz);
--- 1927,1933 ----
                      y = (double)(aptr->yorg + aptr->fyorg)/250.0
                        + (double)(aptr->ytrl)/10000.;
                      z = -(double)(aptr->zorg + aptr->fzorg)/250.0
!                       - (double)(aptr->ztrl)/10000.;
  
                      fputs("    Translation { translation ",OutFile);
                      WriteVRMLTriple(x-ox,RestoreY(y-oy),z-oz);
***************
*** 2006,2012 ****
                  y = (double)(dst->yorg + dst->fyorg)/250.0
                    + (double)(dst->ytrl)/10000.;
                  z = -(double)(dst->zorg + dst->fzorg)/250.0
!                   + (double)(dst->ztrl)/10000.;
  
                  fputs("        ",OutFile);
                  WriteVRMLTriple(x,RestoreY(y),z);
--- 2006,2012 ----
                  y = (double)(dst->yorg + dst->fyorg)/250.0
                    + (double)(dst->ytrl)/10000.;
                  z = -(double)(dst->zorg + dst->fzorg)/250.0
!                   - (double)(dst->ztrl)/10000.;
  
                  fputs("        ",OutFile);
                  WriteVRMLTriple(x,RestoreY(y),z);
***************
*** 2023,2029 ****
                        +(double)(src->ytrl + dst->ytrl)/20000.;
                  z = -(double)(src->zorg + dst->zorg +
                        src->fzorg + dst->fzorg)/500.0
!                       +(double)(src->ztrl + dst->ztrl)/20000.;
                  
                  fputs("        ",OutFile);
                  WriteVRMLTriple(x,RestoreY(y),z);
--- 2023,2029 ----
                        +(double)(src->ytrl + dst->ytrl)/20000.;
                  z = -(double)(src->zorg + dst->zorg +
                        src->fzorg + dst->fzorg)/500.0
!                       -(double)(src->ztrl + dst->ztrl)/20000.;
                  
                  fputs("        ",OutFile);
                  WriteVRMLTriple(x,RestoreY(y),z);