From: Piero Ugliengo <[email-masked]>
Date: Mon, 27 Jan 1997 11:20:16 +0200 (IST)

Unfortunately the MOLDRAW manual is still under development. However,
together with the code I also include a file MOLDRAW.MAN where you can
find enough description of the input file format.  I also take this
opportunity to inform anybody interested in MOLDRAW that a minor (but
significative)  upgrade has been done and version (1.0d) is now
downloadable free of charge at: 

http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html

Thanks to all of you  interested in MOLDRAW.
Piero Ugliengo

----------------------------------------------------------------------------
Prof. Piero Ugliengo
Dip. Chimica Inorganica, Chimica Fisica
e Chimica dei Materiali
Via P. Giuria, 7
I-10125 Torino

Voice: +39-11-6707515
FAX:    +39-11-6707855
E-mail: [email-masked]
MOLDRAW program at:
http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html

------------------Message 3-------------------------
Date: Tue, 28 Jan 1997 10:47:35 +0200 (IST)
From: Piero Ugliengo <[email-masked]>

Here is the promised file. Keep in mind that this
was the manual for the old DOS version and that
only parts dealing with input file format are still
significative in the present version.
I am working hard to make both an HTML and 
standard help file and as soon as I will have 
something significant I will let you know
Ciao

--=====================_854473616==_
Content-Type: TEXT/PLAIN; CHARSET=iso-8859-1
Content-Transfer-Encoding: QUOTED-PRINTABLE
Content-ID: <[email-masked]>
Content-Description: 

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           =B3                                                   =B3
           =B3          M O L D R A W  User Manual               =B3
           =B3                                                   =B3
           =B3           Release 4.5 (20/12/1991)                =B3
           =B3                                                   =B3
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                                                                =20
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     by  P. Ugliengo D. Viterbo - Dipartimento di  Chimica  Inorganica,=20
     Chimica Fisica e Chimica dei Materiali, Universit=A0, Via P.  Giuria=20
     7, I-10125 Torino, Italy (EARN address: U102@ITOCSIVM)
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     and  G. Chiari - Dipartimento di Scienze Mineralogiche e  Petrolo-
     giche, Universit=85, Via Valperga Caluso 37, I-10125 Torino, Italy.
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     Reference: P.  Ugliengo,  G.  Borzani  & D.  Viterbo  -  J.  Appl.     =
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                Cryst. 21, 75, (1988).
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           =B3            INSTALLATION   INSTRUCTIONS            =B3
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          The  diskette (3.5" 720 Kb) contains all the files needed  to=20
     run  MOLDRAW  as well as some test examples (MOL files).  All  the=20
     files  are stored in a compressed form by means of  the  shareware=20
     program  PKZIP  (PKUNZIP  to explod the zipped  archives  is  also=20
     included). In addition, the following files are provided:
     MOLDRAW.MAN  the printable ASCII user manual.
     MOLDXR.EXE  a program to convert coordinate files  retrieved  from=20
     the Cambridge Structural Database (using the Daresbury CSSR format=20
     only)  into  MOL type files. At least one file with  XR  extension=20
     should be present in the same subdirectory where MOLDXR is execut-
     ed. Standard communication programs may be used to download the XR=20
     files from the host (resulting from a successful search and stored=20
     by means of the command SCON) to the PC.=20
    =20
     MOLDCRY.EXE  is  a program to convert coordinate  files  retrieved=20
     from the CRYSTIN Inorganic Database.
    =20
     Installing MOLDRAW onto hard-disk
    =20
          To  install MOLDRAW onto hard-disk, at least 1 Mbyte of  free=20
     disk  space  is needed in order to store all  the  executable  and=20
     example  files.  Two directories need to be present  on  the  hard=20
     disk:  MDRAW to store all the executable files and GEOM  to  store=20
     all the coordinates MOL files. The generation of these two  direc-
     tories is left to the user: from the DOS root, type MD GEOM and MD=20
     MDRAW and then, after inserting the diskette in drive A: (or  B:),=20
     type  A:(B:)INSTALL. If the two directories were already  present,=20
     the old files having the same names of the new ones will be  over-
     written.  If  this is the case, the safer procedure is  to  backup=20
     your important data before starting the installation.=20
    =20
     Running MOLDRAW form floppies.
    =20
          It  is possible to run MOLDRAW from floppies as long as  some=20
     optional  files are not copied. The smallest subset needed to  run=20
     MOLDRAW, contains the following files:
    =20
                         MOLD.EXE
                         MOLDPAR.DTA
                         MOLDPLUT.DTA
                         MOLDRAW.HLP
                         MCONFIG.DTA
    =20
     If really short of disk space, delete also MOLDRAW.HLP and do  not=20
     use  the HELP command. The floppy with the input MOL files may  be=20
     placed  in  the  last available drive and  the  MCONFIG.DTA  files=20
     should be changed to match this new configuration.  =20
    =20
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           =B3         CONFIGURING   MOLDRAW                     =B3
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          Before running MOLDRAW, the proper configuration must be  set=20
     up by running the MOLDCONF.EXE file. The following graphic  boards=20
     are available: color graphic adapter (CGA, 640x200 b/w),  enhanced=20
     graphic  adapter (EGA with 256Kb video ram, 640x350, 16 colors,  2=20
     graphic pages) and video graphic array (VGA, 640x480, 16 colors, 1=20
     graphic  page).Internal  hard-copy  is only  implemented  for  two=20
     different  protocols: IBM like (Proprinter, Graphic  Printer)  and=20
     Epson like (EPSON LQ-500 and others) or fully compatible. Internal=20
     hard-copy is becoming obsolete, due to the new standard facilities=20
     provided with MS-DOS 5.0. Accessible disks are a: through d:.  Two=20
     DOS path have to be specified: the path where the MOLDRAW executa-
     ble  files are stored, and that in which the input MOL  files  are=20
     stored.  For  instance,  if the user has the  MOLD.EXE  and  other=20
     utility  files stored in a DOS path C:\MDRAW, the first path  will=20
     be C:\MDRAW and if he has three geometry files named A.MOL,  B.MOL=20
     and C.MOL stored in the directory C:\GEOM, the second path will be=20
     C:\GEOM.  The  file  MCONFIG.DTA will  contain  the  configuration=20
     parameters  which have been set by the MOLDCONF.EXE program.  This=20
     file  can also be edited directly by the user (make a backup  copy=20
     of  the  original file before editing). Make sure that  your  text=20
     editor  does not add extra control characters to  the  MCONFIG.DTA=20
     file.
          In  order to run the program, simply type MOLDRAW.  The  file=20
     MOLDRAW.BAT will be executed. In this file a record  MOLD xxxx  is =20
     present;  xxxx is the maximum number of atoms the user can handle.=20
     With  the present release (4.5) a maximum of 2500 atoms  and  5000=20
     bonds  can  be manipulated (at least 640 Kbytes  of  RAM  needed).=20
     Different  numbers of atoms may be specified to fit the  available=20
     hardware facilities, by editing the MOLDRAW.BAT file.
    =20
     General MOLDRAW functionality
    =20
          At start MOLDRAW looks for a file named DIREC.TXT, containing=20
     the  list of the available MOL files sorted in  alphabetic  order.=20
     The total number of MOL files is stored as header of the file.  If=20
     the  DIREC.TXT file does not exist, MOLDRAW  automatically  create=20
     it, and the list is immediately displayed on the screen. Due to  a=20
     bug  in the program, the very first time trying to pick up a  file=20
     from  that list, will result in an unrecoverable error, with  pro-
     gram abortion; simply run MOLDRAW again. Any time a new coordinate=20
     MOL  file is typed in, it is necessary to inform MOLDRAW that  the=20
     new  file is now available: the command REWDIR should be  used  to=20
     this  purpose, in order to update the DIREC.TXT contents with  the=20
     new  file name. In order to read  some MOL files stored in a  sub-
     directory different from that indicated in MCONFIG.DTA, issue  the =20
     DOS  command to switch temporally to the DOS prompt and CD to  the=20
     new sub-directory; type EXIT to return to MOLDRAW, then issue  the=20
     command  NEWDIR to enable the program to read the MOL files  using=20
     the new selected sub-dir.
    =20
     =20
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           =B3   MOLDRAW  INPUT   FILE    DESCRIPTION            =B3
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          All  the input information contained in the MOL files are  in=20
     free  format  and case insensitive. Spaces or TAB may be  used  as=20
     separators  of  different  fields in the  same  record.  Different=20
     records are separated by carriage return.
    =20
          Any name for the file is allowed, as long as it is compatible=20
     with the DOS syntax, completed with the MOL extension. When  read-
     ing  a file for the first time, MOLDRAW writes at the end  of  the=20
     input  deck information about the center of gravity (BARICE),  the=20
     connectivity  (CONNB), the number of bonds for each  atom  (BONDS)=20
     and the number of fragments (FRAG) of the corresponding  molecular=20
     system.  These  quantities  are read in in  all  subsequent  runs.=20
     Whenever  a manual modification of the geometry  specification  is=20
     performed (deletion of an atom or change of the value of a coordi-
     nate) all the added connectivity information  must be deleted from=20
     the input file; the geometry modification are then correctly taken=20
     into account in the subsequent runs. It is unlikely that the  user=20
     change manually any connectivity information, which can be altered=20
     by  means  of the LINK and UNLINK commands. However, a  brief  de-
     scription of this information in a MOL file follows:
    =20
       CONNB
       12        ----> number of pair of atoms directly linked
       1 2 3 4 5 6 7 8 8 9 10 11 ....... ---> atom 1 link to 2
                                         ---> atom 3 link to 4
                                         ---> atom 4 link to 5
       BONDS
       3  2  1  1  1  4  3 ... ---> atom 1 linked to 3 atoms                =
                   =20
                               ---> atom 2 linked to 2 atoms
                               ---> atom 3 linked to 1 atom
       FRAG
       2                       ---> number of different fragments
       1  1  1  1  2  2  2 ... ---> atoms 1,2,3,4 in fragment 1
                               ---> atoms 5,6,7   in fragment 2
    =20
     IMPORTANT  NOTE:  MOLDRAW release 4.5  calculates and  stores  the =20
     connectivity  information in a format different from that  of  the=20
     previous releases. For instance, the 1-2-3 connectivity list is no=20
     longer stored in the MOL file, but is computed as needed. In order=20
     to  be  able  to process the old MOL files  (those  obtained  form=20
     previous  version of MOLDRAW) two files CONV.BAT and  MOLDCONV.EXE=20
     are  included. Copy these two files in the subdirectory where  the=20
     old  format files are stored and type CONV. This operation  simply=20
     deletes the connectivity information previously stored in each MOL=20
     file.
    =20
     Molecular plots on plotter and Laser-printer
    =20
          From  release  4.2 on, facilities to  get  standard  PLUTO-78=20
     plots  on  plotters  and Laser-Printers have  been  included.  The=20
     required files are:
    =20
                         PLU90.BAT
                         P90.EXE
                         PL90.EXE=20
                         LP.EXE
                         PLUTO1.PS
    =20
          From  within MOLDRAW, issue the SAVEP command to  generate  a=20
     PLUTO78  compatible  input  file  (extension  PLI,  default   name=20
     PLUTO.PLI),  which  contains the coordinates and  all  the  needed=20
     information to keep the same view and connectivity of the original=20
     MOLDRAW  view  also in the plotted picture. If some  bonds  result=20
     unlinked, icrease the parameter in the TOL record at the bottom of=20
     the  PLI file. The PLI file is stored in the same directory  where=20
     the  corresponding MOL file is stored. After quitting MOLDRAW,  at=20
     the DOS prompt type:
    =20
                    PLU90 \GEOM\PLUTO.PLI
    =20
     in  order  to produce a plot file named  PLUTO.PLT  or  PLUTO.POS,=20
     depending  if  an HP-GL (pl90 vga h) or a  PostScript  description=20
     (pl90  vga p) of the image is desired. Please edit  the  PLU90.BAT=20
     content  in order to set the preferred options. A preview  on  the=20
     screen of the resulting image (as close as possible to the printed=20
     image)  will be produced, using EGA (option e) or VGA  (option  v)=20
     graphic  boards. The files PLT and POS are easily included in  any=20
     word  processor  supporting these graphic  protocols.  A  Hewlett-
     Packard facility LP.EXE and its parameter file PLUTO1.PS, is  also=20
     included, to rasterize the HP-GL format into a PCL one, which  can=20
     be directly printed on any Hewlett-Packard compatible laser print-
     er.  The HP-GL PLT file can be sent as such, to the  new  HP-Laser=20
     Printers Series III, after issuing the correct escape sequence  to=20
     the  printer, in order to turn it to plotter mode. Make  a  backup=20
     copy of the PLU90.BAT file, before modifying  it.

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           =B3       MOL    FILES     KEYWORDS                   =B3
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    =20
          In  the following, the complete list of the allowed  keywords=20
     which can be specified in a MOL file is reported. The meaning  and=20
     a short example is also included. As a general rule, the  informa-
     tion  to which any keyword refers is on a record immediately  fol-
     lowing the keyword itself.
    =20
     -TITLE : any string not exceeding 70 characters.
    =20
     Example:
                   TITLE
                   n-butane with standard geometry
    =20
     -CELL  : a, b, c  axial lengths in =8F and alpha, beta, gamma angles=20
     in degrees,  defining the crystallographic unit cell are given. If=20
     the  atomic  positions  are  expressed  as  orthogonal   cartesian =20
     coordinates, then this record should be 1 1 1 90 90 90. If one  of=20
     the  axial lengths is negative, the program will not display  that=20
     particular  axis, when the cell contents will be required  through=20
     the  CELLG command (useful for displaying slices of planar  struc-
     tures).  =20
     Example:
                   CELL
                   10.034    8.456  12.341    90.0   97.31  90.0
    =20
     Molecular Geometry Specification
    =20
           Molecular geometry can be specified in three different ways:=20
    =20
     -COORD  : the atomic number and the three X, Y, Z  (fractional  or=20
     cartesian in =8F) coordinates are provided. A final line  containing=20
     all zero values is required to end geometry input.
     Example:
                           COORD
                           6   0.3456  0.9876  -.3334
                           6   0.1234  0.5678  -.7896
                           7   0.5631  -.3300   .2340
                           .   ......  ......   .....
                           .   ......  ......   .....
                           0     0       0        0

     -COORDAU : the atomic number and the three X, Y, Z coordinates  in=20
     atomic units (1 a.u.=3D 1 bohr =3D 0.5291771 Angstrom) are provided. A=
=20
     final line containing all zero values is required to end  geometry=20
     input. This is useful to enter geometry as resulting from  quantum=20
     mechanical calculation (TURBOMOLE, CRYSTAL and GAMESS codes).
     Example:
                           COORDAU
                           .   ......  ......   .....
                           6   0.1234  0.5678  -.7896
                           7   0.5631  -.3300   .2340
                           .   ......  ......   .....
                           .   ......  ......   .....
                           0     0       0        0
    =20
     -COSYMB  : the sequence number (even in random order  but  without=20
     omissions),  the  atomic  symbol  and the three  X,  Y,  Z  atomic=20
     coordinates are supplied. A final line containing all zero  values=20
     is  required to end geometry input. The atomic symbol is a  string=20
     of  characters; the first two (one) characters are  recognized  as=20
     standard  atomic symbol, therefore the user must  avoid  ambiguous=20
     notations  (for instance do not indicate by HO3 an  hydrogen  atom=20
     attached  to oxygen O3, because the atom would then be  recognized=20
     as  an holmium!). Spaces are not allowed within the atomic  symbol=20
     string.
     Example:
                    COSYMB
                    .    .        ......  .......  .....
                    3    C        0.3456   -.1234  0.4554
                    5    N34      -.4444   1.2344  0.8999
                    7    C(12')   0.3456   -.1232  0.4545
                    9    N(1a)    -.4444   1.2343  0.2343
                   10    HA3'     0.89     0.7346  1.234=20
                    .    .        ......    ......   .....
                    .    .        ......    ......   .....
                    0    0        0         0        0
    =20
     -MATZ  :  the geometry is given in terms of  internal  coordinates=20
     (bond distances, bond angles and torsion angles). The same  format=20
     adopted  in the AMPAC program (Dewar et al., JACS,1977, 99,  4899)=20
     is used. The atom type is specified by the atomic number.
     Example: ethane molecule in staggered conformation, in which atoms=20
     1,6,5,8,7 and 4 are hydrogens and 2 and 3 are carbons. Bonds  are:=20
     1-2, 2-6, 2-5, 2-3, 3-8, 3-7, 3-4.
    =20
                  1          8           in which 1-2-3-4 are
                                7        in the same plane
                     2 ---- 3=20
                 6
                    5          4
    =20
                  MATZ
                    1     0.0     0     0.0   0    0.0   0   0  0  0
                    6     1.08    0     0.0   0    0.0   0   1  0  0
                    6     1.54    0   109.5   0    0.0   0   2  1  0
                    1     1.08    0   109.5   0  180.0   0   3  2  1
                    1     1.08    0   109.5   0   60.0   0   2  3  4
                    1     1.08    0   109.5   0  -60.0   0   2  3  4
                    1     1.08    0   109.5   0   60.0   0   3  2  1
                    1     1.08    0   109.5   0  -60.0   0   3  2  1
                    0       0     0     0     0    0     0   0  0  0
    =20
     The first number is the atomic number followed by the bond length,=20
     the  bond  angle  and  the torsion angle.  The  digit  after  each=20
     geometrical parameter will not be used by MOLDRAW, and it is given=20
     in  order  to keep compatibility with the AMPAC format.  The  last=20
     three numbers are the sequential numbers of the atoms in terms  of=20
     which the preceding geometrical parameters definition is possible.=20
     The forth line in MATZ indicates that hydrogen number 4 is  linked=20
     to  carbon  3 with a bond length of 1.08=8F, with  angle  4-3-2   of=20
     109.5=F8 and torsion angle 4-3-2-1 of 180=F8. The last line containing=
=20
     all  zero values is required to end geometry input. The  algorithm=20
     used  to transform from Z-matrix to cartesian coordinates is  such=20
     that  the first four atoms should be in the sequence 4-3-2-1.  Any=20
     other starting sequence can cause unpredictable results.
    =20
     -GROUP:   space group symbol.
     Example:
                    GROUP
                    P21/C
    =20
     Only the following most common space groups are internally handled=20
     by MOLDRAW, without any further supply of symmetry data:
    =20
     P1  P-1  P21  C2  PC  CC  P21/C  P212121  PCA21  PNA21  P21/A
     P21/N    PBCN     PBCA   C2/C   PNA21   PNMA
    =20
     For different space groups, after the GROUP specification  (needed=20
     to set the lattice centering), the symmetry operators are given by=20
     one of the two following keywords:
    =20
     -SYMNUM:  the  components  of the translation vectors  T  and  the=20
     elements  of  the rotation matrices R are  given.  (CRYSTIN  files=20
     generated  specifying  the  SMAT option are  compatible  with  the=20
     SYMNUM format). Each operator takes one record:
    =20
          T1 T2 T3  R11 R12 R13  R21 R22 R33  R31 R32 R33
    =20
     The last record is a line with T1=3DT2=3DT3=3D-1 and Rij=3D0.
     Example:
              SYMNUM
              0.   0.   0.    1  0  0   0  1  0   0  0  1
              0.5  0.   0.5  -1  0  0   0  1  0   0  0 -1
             ............................................
             -1.  -1.  -1.    0  0  0   0  0  0   0  0  0
    =20
     -SYMSIM:  the symmetry operators are given following the  notation=20
     of  the  International Tables for X-Ray Crystallography,  Vol.  I.=20
     Each symmetry operator requires one record and the input is termi-
     nated by a record containing the  END keyword.
     Example:
            SYMSIM
             x,y,z
            -x,1/2+y,1/2-z
            -x,-y,-z
             x,1/2-y,1/2+z
            END
    =20
     -CHARGE: net atomic charges as resulting from a previous  quantum-
     mechanical calculation. Sequence numbers (even in random order but=20
     without omission) and charge values are required.
     Example:
                    CHARGE
                    1      0.1234
                    2     -.2345
                    3      1.098
                    .      .....
    =20
     -SCAN   :  to define a series of selected geometrical  degrees  of=20
     freedom  to be scanned through the SCAN command. This  option  may=20
     only  be used when the geometry is input via the  MATZ  directive.=20
     The SCAN keyword requires the following records: i) the number  of=20
     degrees  of freedom to be scanned; ii) for each degree of  freedom=20
     the  number  of the row of the Z-matrix where it is  defined,  its=20
     type (bond, angle or torsion), the initial, the final and the step=20
     values to be used in the scan and a reference user defined  label.=20
     For each point an energy evaluation is carried out and is reported=20
     at the bottom of the screen, together with the new geometry. Three=20
     files  are also created, COULOMB.DAT, TOTALEN.DAT and  VDWAALS.DAT=20
     containing  the value of the geometrical degree of  freedom  being=20
     scanned and the corresponding value of the energy, partitioned  as=20
     pure electrostatic, total and non-bonded exp-6 contributions. This=20
     option  is useful to move monomers defining an hydrogen bond  com-
     plex  in  order   to look at the most  favorable  conformation.  A=20
     complete example follows:
    =20
     Given  the  Z-matrix  (atomic number 101  and  100  indicate  lone=20
     pairs):
    =20
     MATZ
     101    0.00000  0     0.000   0    0.000   0   0  0  0
       8    0.9423   0     0.000   0    0.000   0   1  0  0
       6    1.39872  0   109.63    0    0.000   0   2  1  0
       1    1.08191  0   107.32    0  180.000   0   3  2  1
       1    1.0882   0   112.131   0  118.78    0   3  2  4
       1    1.0882   0   112.131   0 -118.78    0   3  2  4
     100    0.67136  0   121.35324 0  104.32801 0   2  3  1
     100    0.67136  0   121.35324 0 -104.32801 0   2  3  1
      99    1.0      0    90.000   0    0.000   0   1  2  3
       8    2.01     r    90.000   a  175.600  t2   1  9  2
       6    1.39872  0   112.82    b -115.000  t1  10  1  9
       1    1.08191  0   107.32    0   52.000  t4  11 10  1
       1    1.0882   0   112.131   0  118.78    0  11 10 12
       1    1.0882   0   112.131   0 -118.78    0  11 10 12
       1    0.9423   0   109.630   0  180.000   0  10 11 12
     100    0.67136  0   121.35324 0  104.32801 0  10 11 15=20
     100    0.67136  0   121.35324 0 -104.32801 0  10 11 15
       0    0.00000  0     0.000   0    0.000   0   0  0  0
    =20
     the following SCAN records can be given:
    =20
     SCAN=20
     2                 ---->  number of degrees to be scanned
     12 3  0. 90. 5.  T4=20
     !  !  !   !  !   !
     !  !  !   !  !   ----->  label of the degree of freedom
     !  !  !   !  --------->  increment
     !  !  !   ------------>  final value
     !  !  ---------------->  initial value
     !  ------------------->  1 (bond)  2 (angle) 3 (torsion)
     ---------------------->  row of the Z-matrix=20
    =20
     10 1  1.5  2.5  .1  R  ---> row 10, bond, from 1.5 to 2.5
                                 step 0.1 =8F label R
    =20
    =20
    =20
           =DA=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=BF
           =B3          DESCRIPTION  OF  OTHER  FILES            =B3
           =C0=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=D9
    =20
     MOLDPAR.DTA  - Contains, for each atom, a record with the  default=20
     values of:=20
     1-atomic number.
     2-covalent radius: used to establish atom-atom connectivity.
     3-graphic radius: used to define the size of the displayed  atomic     =
 =20
       sphere.
     4-van  der  Waals  radius: used to define the size  of  the  atomic=20
       sphere in a van der Waals display.=20
     5-tolerance   of   covalent  radius:  used  as  a   tolerance   in=20
       establishing an atom-atom connection.
     6-atomic  symbol.
     7-atomic weight.
     This sequence of records is ended by one with -1 in each field and=20
     is  followed by a set of records, each with the  following  energy=20
     calculation parameters:=20
     1-atomic number.
     2-Buckingham  parameters  A, B, C: used  for  energy  calculations=20
       [M.A. Spackman, J. Chem. Phys., 85(11), 1986].
     This sequence is eneded by a record with a 0 in each field.=20
     Finally  the  internal  color codes for the  different  atoms  are=20
     listed  both for EGA and VGA graphic boards. The user  may  change=20
     all  but the energy parameters while running MOLDRAW  through  the=20
     PARAM  command;  the  new  set  of  parameters  is  saved  in  the=20
     MOLDNEW.DTA file. If this has to be used as standard set the  user=20
     must perform the following sequence of DOS commands:
    =20
          RENAME MOLDPAR.DTA MOLDPAR.BAK   <-- save old file
          RENAME MOLDNEW.DTA MOLDPAR.DTA   <-- rename new file
    =20
     MCONFIG.DTA -  Contains the data for the system specifications.
    =20
     SPOOL.LOG  - This is the default name of the output log file  used=20
     by  MOLDRAW  to store important results (see below). The  user  is=20
     prompted  for a name whenever a new MOL file is read in.  The  LOG=20
     file  is  an  ASCII  file which can be  edited  or  imported.  The=20
     information written on this file may be:
     a) all  the  geometric  (after an ANG or DIST  or  TORS  or  PGEOM     =
=20
        command) and energetic data (after ENER, ENERG);
     b) possible errors in the input file;
     d) two forms of Z-matrix suitable for AMPAC and MOLDRAW input.
    =20
     PLUTO.PLI - This is the default name of a file which is  generated=20
     after  a SAVEP command. It contains the input stream to be  passed=20
     to  the PLUTO78 program. The same orientation and connectivity  of=20
     the  molecule  present onto the screen should be obtained  in  the=20
     final PLUTO78 plot.
    =20
     FRAGM.MOL - This is the default name of a file which is  generated=20
     after a FRAG command. It contains the coordinates and connectivity=20
     of  the molecular fragment actually saved. Being a MOL file it  is=20
     directly  readable  by MOLDRAW and is available  after  issuing  a=20
     REWDIR command.

    =20
           =DA=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=BF
           =B3      DESCRIPTION  OF  INTERACTIVE  COMMANDS       =B3
           =C0=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=C4=
=C4=C4=C4=C4=C4=C4=D9
    =20
    =20
          This  section  describes all the keywords that the  user  can=20
     specify in the command area, during an interactive run.                =
     =20
    =20
     -*  :  to repeat the last command.
     Syntax:   *
     %
    =20
     -ADD  :  to add atoms to the current structure. The user can enter=20
     default value for bond length, bond angle and torsion angle to  be=20
     used in all the subsequent steps. The user should enter the atomic=20
     symbol  to  add, followed by three numbers relative to  the  atoms=20
     needed  to define the bond length, bond angle and  torsion  angle.=20
     These  three values can be explicitly entered or referred  to  the=20
     default values by means of the * symbol. Press enter to exit  this=20
     option.
     Syntax:   add
     Example:  add
               *,*,*        <----- answer to default values
               H,3,4,2,1.54,109,123  <--- add an hydrogen forming
                                     a bond length of 1.54 with atom
                                     3, a bond angle of 109 with atoms
                                     3-4, and a torsion of 123 with
                                     atoms 3-4-2
               O,5,7,6,*,*,90 <--- use defaults for length and angle
                                   but 90 for torsion with 5-7-6
     %
     -ANG  :  to  compute the bond angle defined by  three  atoms.  The=20
     program  automatically prompts for the three atom sequential  num-
     bers. The sequential numbers must be separated by commas. To  exit=20
     this  command press carriage return without entering  any  number.=20
     The angle is also written into the LOG file.
     Syntax:  ang
    =20
                   1,6,8 to compute angle formed by atoms 1,6,8
                   ............................................
     %
    =20
     -ASPE  :   to obtain real circles for the atomic  spheres  on  the=20
     hard-copy  printout changing the axial ratio. Default  values  are=20
     0.417 for  EGA, 0.8 for CGA and .4 for VGA.
     Syntax: aspe 0.9  to change the axial ratio to 0.9.
             aspe      without argument resets the aspect ratio to  the=20
                       default values.
     %

     -BALL : to display the atoms as spheres. The radius of an atom  is=20
     determined by the its graphic radius. If EGA or VGA are available,=20
     different colors, with illumination spots, for different atoms are=20
     used.  Atoms which are closer to the observer are  enlarged  while=20
     those which are further away are reduced in size according to  the=20
     FATS command.
     Syntax:  ball
     %
    =20
     -BARICE   :  to compute and display the center of  masses  of  the=20
     current  structure in fractional coordinates with respect  to  the=20
     original definition of axes origin.
     Syntax:  barice
     %
    =20
     -BROT : to rotate a moiety of the molecule around a selected bond.=20
     The  sequence numbers of the two atoms defining the rotation  bond=20
     are  required.  A check is performed in order  to  avoid  rotation=20
     along bonds which are part of a cyclic structure. The four  atoms,=20
     defining  the torsion angle to be monitored, must then  be  input.=20
     Step  rotation (user controlled rotation) or  continuous  rotation=20
     (program controlled rotation) are both allowed. Calculation of the=20
     conformational  energy,  employing a  simple  electrostatic  model=20
     (when  charges  are  supplied)  and  Buckingham  model  potentials=20
     (limited  to the atoms included in the MOLDPAR file) can  be  per-
     formed.  The  data are written into the LOG file, and  the  energy=20
     profile  is  displayed at the end of the rotational  scan  on  the=20
     screen.
     Syntax:  brot 3,5   to rotate around  the  bond  defined by atoms
                         3 and 5 (3---5).
     %
    =20
     -CELLG  :   to generate the unit cell contents together  with  the=20
     cell  box.  For the following most common spaces groups,  P1   P-1 =20
     P21  C2  PC  CC  P21/C  P212121  PCA21  PNA21  P21/A  P21/N   C2/C  =20
     PNA21    PNMA    PBCN  PBCA, only the symbol (in capital  letters)=20
     can  be given either in the input file (cf. GROUP record) or as  a=20
     command.  All other space groups can be handled by  supplying  the=20
     symmetry  operators  via the SYMNUM or SYMSIM keywords.  Atoms  in=20
     special  positions  will be duplicated by the  symmetry  operators=20
     and, the user must eliminate the duplicated atoms by answering "y"=20
     to  the "check atomic duplication " question. For molecular  crys-
     tals the asymmetric unit is treated as a whole, for ionic crystals=20
     it is treated atom by atom.
     Related  commands: ECELL, WCELL, NOCELL, NEIGH, NEXT.
     Syntax:  cellg
     %

     -CLEAN   :  to delete atoms with coincident  spatial  coordinates.=20
     This is always the case when some atoms in the asymmetric unit lie=20
     on  symmetry elements (an atom on the inversion center or  seating=20
     on a reflection plane will be repeated on itself). This option may=20
     be  used  when the same atomic site is occupied by more  than  one=20
     atomic species with fractional occupation number.
     Syntax:  clean
     %
    =20
     -CLS  :  to clear the screen. It may be useful after an  incorrect=20
     input in the command line.
     Syntax:   cls
     %
    =20
     -COL  : to change the default atomic color table. This  option  is=20
     not allowed when the CGA board is used.
     Syntax:  col
     %
    =20
     -CROT : to rotate in a continuous mode, the whole molecule  around=20
     one  of  the  three reference axes. The Z axis is  assumed  to  be=20
     perpendicular to the display plane. The user can press "s" to slow=20
     down  the  motion, "f" to speed it up and space bar  to  stop  the=20
     rotation. "e" will exit the CROT option.
     Syntax: crotx  5 for    clockwise   rotation in  5=F8 steps around X=20
             croty -5  "  anti-clockwise     "     "  "    "     "    Y
             crotz 10  "     clockwise       "     "  10=F8  "     "    Z
             crot 2  interactive  rotation  in  2=F8 steps, using the=20
                     arrow keys in the numerical keypad.
    =20
     The default rotation angle is 10 deg. Both stick and stick & balls=20
     displays may be rotated. Smooth rotation, using two graphic pages,=20
     is only possible with the EGA board. =20
     %
    =20
     -DIST  : to compute the distance between two atoms.  The   program=20
     automatically  prompts for two atoms. The input  sequence  numbers=20
     must  be  given separated by a comma. To exit this  command  press=20
     carriage  return without any input. The distance is  also  written=20
     into the LOG file.
     Syntax:  dist
    =20
                    1,6   to compute distance between atoms 1 & 6
                    3,14  "    "        "       "       "   3 & 14=20
                    ..............................................
     %
    =20
     -DOS   :  to temporally switch to the DOS shell. Any  DOS  command=20
     can then be issued provided it is compatible with the free  memory=20
     left by MOLDRAW. Type "exit" to return to the MOLDRAW session.
     Syntax    dos
     %
     -DRAW  :  to draw the molecule using the  last  specified  zooming=20
     factor.=20
     Syntax: draw
     %
    =20
     -ECELL  :   to  erase the unit cell box displayed  after  a  CELLG=20
     command. Only the unit cell contents is displayed.
     Related commands:  CELLG, WCELL.
     Syntax: ecell
     %
    =20
     -ELETT  :   to compute the electrostatic  energy  using  Coulomb's=20
     expression. The atomic charges must be present in the input  file.=20
     The energy can be displayed or written into the LOG file.
     Syntax:    elett
     %
    =20
     -ENANT  :  to generate  the enantiomorphic molecule of that  actu-
     ally displayed, by changing the signs of all its coordinates.
     Syntax  : enant
     %
    =20
     -END  :  to terminate a MOLDRAW session. All the files are closed.=20
     The user can then print or edit the LOG file.
     Syntax:  end
     %
    =20
     -ENERG  :   to  compute both the non-bonded  energy,    based   on =20
     Buckingham model potentials (limited to the atoms included in  the=20
     MOLDPAR  file) and the electrostatic energy by means of  Coulomb's=20
     formula. The values are written into the LOG file.
     Syntax:   energ
     %
    =20
     -ENERI  :   to  compute both the non-bonded  energy,   based    on   =
=20
     Buckingham model potentials (limited to the atoms included in  the=20
     MOLDPAR file)  and the electrostatic energy by means of  Coulomb's=20
     formula. The values are displayed interactively.
     Syntax:   eneri
     %
    =20
     -ENFRAG   :  to unlabel the different molecular fragments  and  to=20
     return  to default display, i.e. to clear the action of the  NFRAG=20
     command.
     Syntax  :  enfrag
     %
    =20
     -FATB :  to scale the values of atomic radii. This command can  be=20
     used to improve perspective effects.
     Syntax:  fatb 5    atomic radii are magnified by a factor of 5.
     %
    =20
     -FATS  :  to enhance the perspective by changing the ratio between=20
     the closest and the farthest displayed atomic sphere.
     Syntax:  fats 3  the nearest ball will be 3 times bigger than  the     =
            =20
     farthest away.=20
    =20
     %=20
     -FRAG  :   to generate a new .MOL file with a  molecular  fragment=20
     obtained  from the geometry in core. The program prompts  for  the=20
     fragment  file-name.  The  user can save  any  previously  defined=20
     fragment(s)  (option 1) or delete any number of atoms (option  2).
     In  order  to properly run option 1, the user must issue  a  NFRAG=20
     command  before the FRAG command. Global deletion of  atomic  type=20
     are  allowed  through the "allsymbol" string. The syntax  used  to=20
     delete atoms is:
           "allh" to delete all the hydrogen atoms;
           "allc" to delete all the carbon atoms;
           "allsi" to delete all the silicon atoms;
           "3-12" to   delete   all  the  atoms   in   the   sequence      =
=20
                  3,4,5,6,...,12.
     It is not possible to delete more than one atom or atomic sequence=20
     at a time. A deleted atom is deleted from the main memory.  Label-
     ing  is available by entering a "*". A -1 is entered to  exit  the=20
     sequence of deleting command and save the final fragment.
     Syntax:   frag
     %
    =20
     -HCOP   :  to have graphic output on the supported  printers.  The=20
     time  taken to complete the printout is about 6 minutes on an  IBM=20
     PC  AT  running  at  6  Mhz.  Five  different  possibilities   are=20
     available.
     Syntax:=20
              hcop0 : with EGA gives hard-copy of current drawing.
                      Image is printed using 960 bits per inch.=20
                      With  CGA  gives reduced  hard-copy  using  PLUTO=20
                      representation of the structure and 1920 bpi's.
              hcop0s : with EGA hard-copy using labelled PLUTO  repre-
                       sentation of the structure with 960 bpi's.
              hcop0p : with  EGA hard-copy  using  unlabelled  PLUTO=20
                       representation of the structure with 960 bpi's.
              hcop1s : with CGA hard-copy using labelled PLUTO  repre-
                       sentation of the structure with 960 bpi's.
              hcop1p : with  CGA hard-copy  using  unlabelled  PLUTO=20
                       representation of the structure with 960 bpi's.
     ***Important  note**** - When using hcop1s/1p options the  drawing=20
     is  split  in  two halves. After completion of each  half  on  the=20
     screen,  to  obtain the hard-copy the user must digit  a  "h".  By=20
     digiting  any other character one gets out of the command  without=20
     hard-copy.
     %

     -HELP   :   to obtain on screen help. The choice of  a  particular=20
     command is menu driven using the arrow keys. To exit choose "EXIT"=20
     from the menu.
     Syntax:  help
     %
    =20
     -HKL   :   to  obtain a view of the current  structure  along  the=20
     direction  perpendicular to the crystallographic plane  of  Miller=20
     indices  h,k,l. After issuing the hkl command the program  propmts=20
     for  the  indeces. A subsequent use of the SLAB  command  cut  the=20
     structure in slices perpendicular to that direction. For hexagonal=20
     systems the user should simply drop the third index i (k h i l, in=20
     which i=3D-(h+k)).
     Syntax:  hkl
     %
    =20
     -HYD  :  to  restore display of  hydrogen  atoms.  All  subsequent=20
     commands will show hydrogen atoms.
     Related command:  NOHYD
     Syntax:  hyd
     %      =20
    =20
     -KILL  :  to remove an atom from the current structure.  The  user=20
     can  specify one atom at the time and terminate with a void  line.=20
     The deleted atom will be marked by an X. The marked atoms will  be=20
     purged from the main memory and connectivity recomputed. The atoms=20
     connected via LINK command may become unlinked after execution  of=20
     the KILL command.
     Syntax:  kill
     %=20
    =20
     -INERZ  : to compute the three principal moments of inertia.  They=20
     are displayed and written into the LOG file.
     Syntax:   inerz
     %      =20
    =20
     -INFO : to display a summary of the features of the current struc-
     ture.  Molecular weights, brutto formula, total number  of  atoms,=20
     bonds  and fragments as well as cell parameters will be  reported.=20
     Other  data  can be reported depending on the current  release  of=20
     MOLDRAW.
     Syntax:   info
     %
    =20
     -LABE   : to label either selected or all atoms of  the  molecule.=20
     The  labels  have the color of the last element  in  the  periodic=20
     table,  whereas  the hydrogen labels have the color  normally  at-
     tributed to the Boron atom. The labels are rotable with the struc-
     ture.  The  NOLABEL command  unlabels the  structure.  The  LABExx=20
     command in which xx is the element symbol only labels the atoms of=20
     that  selected  element. LABEnn in which nn is a  sequence  number=20
     only labels the atom with that particular number.
     Syntax: labec    to label only carbon  atoms
             labeo    "  "     "    oxygen    "
             labeh    "  "     "    hydrogen  "
             laben    "  "     "    nitrogen  "
             labef    "  "     "    fluorine  "
             labesi   "  "     "    silicon   "
             labex    to label only heavy atoms (S, Cl, Br, ..)
             labe13   "  "     "    the atom number 13
             labe*    to label all the atoms
             label    to interactively select and label atom(s)
                      using the arrow keys.  =20
     %
    =20
     -LINK   :  to link with a bond two atoms which are not  bonded  by=20
     the  standard connectivity algorithm. The program prompts for  the=20
     numbers of the two atoms to be linked. One or more pairs of  atoms=20
     may  be  indicated; a void enter will terminate this  input.  This=20
     option  is useful when managing unusual  structures,  particularly=20
     metallorganic  molecules. See UNLINK for the reverse  action.  See=20
     the WRITE command to save the modified structure permanently.
     Syntax: link
     %
    =20
     -MATZ  :  to generate a Z-matrix starting from the current  atomic=20
     coordinates. The program displays the atoms one at a time and  for=20
     each atom prompts for the three atoms which define a row of the  Z=20
     matrix.  The three sequence numbers are separated by  commas.  The=20
     internal coordinate representation is set-up and written into  the=20
     LOG  file using the AMPAC format. To end this command three  nega-
     tive  numbers  are required. The sequence  numbers  following  the=20
     first three atoms must always be
         atom 1    0,0,0
         atom 2    1,0,0
         atom 3    2,1,0
     Syntax:   matz
     %

     -MATZG  :  to automatically generate the Z-matrix of  the  current=20
     structure  and  store it into a user specified MOL file.  No  user=20
     input is required. This could be useful to built a Z-matrix of the=20
     displayed molecule to be used with the SCAN command. The algorithm=20
     is  capable of adding dummy atoms when three atoms result  collin-
     ear, but the atoms which are chemically bounds are not necessarely=20
     used to define the bonds in the Z-matrix.
     Syntax:  matzg
     %
    =20
     -MOV  : to translate the molecule in steps. The user  is  prompted=20
     for  input  of  the step value ( in =8F units).  The  movements  are=20
     carried out using the arrow keys of the numerical keypad.
     Syntax:  mov
     %
    =20
     -NAME : to display the name of the MOL file currently displayed.
     Syntax:  name
     %
    =20
     -NBOND  :  to compute the non-bonded energy using Buckingham model=20
     potentials.  Only the atoms included in the MOLDPAR file  are  pa-
     rametrized. All other atomic species are treated as carbon  atoms.=20
     The values of the energy are written into the LOG file.
     Syntax:   nbond
     %
    =20
     -NEIGH : this command offers two options: 1) generate and draw all=20
     molecules surrounding a  central molecule or fragment(s) within  a=20
     given  intermolecular  distance (default 4.5 =8F); 2)  generate  the=20
     polyhedron formed by all atoms surrounding a target atom within  a=20
     given  distance  (default  4.5=8F).  The  cell  is  first  generated=20
     according to the specifications described under CELLG.
     Related commands: NONEIGH, CELLG, SETCENT.
     Syntax: neigh
     %
    =20
     -NEXT  :  to  generate a sequence of unit  cells  in  a  specified=20
     direction.  After  this command the user is asked  for  the  three=20
     indices  of the required direction and for the number of cells  to=20
     be repeated in that direction. This command acts on the unit  cell=20
     only and not on the result of a previous NEXT command.
     Related commands: NONEXT, CELLG.
     Syntax: next
     % =20
    =20
     -NEWDIR   :   several directories or subdirectories of  MOL  files=20
     each  with  the corresponding DIREC.TXT file may be  present.  The=20
     default  directory  is  that initially specified  by  the  MCONFIG=20
     procedure. In order to access a new list of MOL files located in a=20
     different  directory,  the user must select the new  directory  by=20
     means  of the DOS shell and then inform MOLDRAW of this change  by=20
     the NEWDIR command. Related commands: REWDIR, READ.
     Syntax:  newdir =20
     %
    =20
     -NFRAG   :   to  search  and  label  all  the  unlinked  molecular=20
     fragments.  The  labeling of the fragments may be cleared  by  the=20
     ENFRAG command. A maximum of 200 fragments is allowed.
     Syntax  :  nfrag
     %
    =20
     -NOCELL  :   to  delete  from  memory  all  the  symmetry  related=20
     molecules and restore the initial situation after a CELLG command.
     Syntax:    nocell
     %
    =20
     -NOHYD  : to hidden all hydrogen atoms, without erasing them  from=20
     main memory.
     Related command: HYD.
     Syntax:  nohyd
     %
    =20
     -NOLABEL : to unlabel the structure. No selection of any  particu-
     lar atom type is allowed.
     Related command: LABE.
     Syntax:  nolabel
     %
    =20
     -NONEIGH  : to delete from memory all molecules  surrounding   the=20
     central  molecule   and to restore the initial situation  after  a=20
     NEIGH command.
     Syntax: noneigh=20
     %
    =20
     -NOPERSP  :  to display the  molecule  without  any  perspective=20
     correction of the view.
     Related command: PERSP.
     Syntax:  nopersp
     %
    =20
     -NOSLAB : to restore the display of all atoms currently present in=20
     memory, after they have been clipped off by a SLAB command.
     Syntax: noslab.
     %

     -PARAM : to change the default values  (stored in the  MOLDPAR.DTA=20
     file) of the following parameters:
         Covalent radii used in computing connectivity,=20
         Tolerance for the covalent radii used in computing
         connectivity,
         Graphic radii used for the displayed balls,
         Van der Waals radii used for the WAALS and VDW commands,
         Scale factor to scale the value of the van der Waals radii.
     Related command: RESPAR.
     Syntax:  param
     %               =20
    =20
     -PGEOM  :  to write into the LOG file a list of all bond  lengths,=20
     bond  angles and torsion angles for the current  molecular  struc-
     ture.=20
     Syntax:   pgeom
     %
    =20
     -PERSP : to obtain perspective projection based on the relations:
                X =3D D * X /(D-X)    Y =3D D * Y /(D-Y)
     where  D  is the given distance of the observer from  the  nearest=20
     point  of  the molecule. Perspective view is the default  mode  of=20
     display with D=3D10. Related command: NOPERSP.=20
     Syntax:  persp 30  to decrease the perspective effects
              persp 10  to increase the   "  "       "  "
     %
    =20
     -PLANE   :   to  obtain a view of the whole  structure  along  the=20
     normal  to the plane defined by three atoms. The  program  prompts=20
     for  the three atoms. Commas are required as a separators  between=20
     the atom sequential numbers.
     Syntax:   plane
     %
    =20
     -PLOT :  to plot the molecule on the display. Stick representation=20
     with different colors for different atoms is normally used. Atomic=20
     coordinates must be present in memory (input by a READ command).
     Syntax: plot
     %
    =20
     -PLUTO   :   to represent the molecules in a pseudo  three  dimen-
     sional  way. Atoms are displayed as sphere and bonds are drawn  as=20
     cones  or  cylinders.  A fast hidden line  removal  algorithm   is=20
     implemented.
     Syntax:  pluto
     %
    =20
     -POLY  :   to  generate a spherical fragment with  all  the  atoms=20
     surrounding  a given target atom at a selected  distance  (default=20
     4.5=8F). All atoms outside the search radius will be purged from the=20
     main memory and cannot be recovered.=20
     Syntax:  poly
     %
    =20
     -READ : to read a particular coordinate file. The selection of the=20
     file is menu driven using the arrow keys. The main results of  the=20
     run  are written on a LOG file and the user may specify  any  name=20
     for  this file. If  no name is entered, a file named SPOOL.LOG  is=20
     automatically created after pressing carriage return. At least one=20
     MOL  file must be present on the disk. Normally MOLDRAW  recognize=20
     all the unlinked fragments present in the input structure, but for=20
     large  and highly connected systems (such as several cells  of  an=20
     inorganic crystal) this may cause some trouble; to avoid  problems=20
     MOLDRAW  always set to one the total number of fragment as  a  de-
     fault action. The user can issue the NFRAG command at any time, to=20
     search for unlinked fragments during a MOLDRAW session.=20
     Syntax:  read
     %
    =20
     -RECON  :  to recompute the connectivity of the molecule in  memo-
     ry.  This is useful when new interatomic connections are  revealed=20
     by  a  NEIGH command (e.g.  start with the  asymmetric  unit  then=20
     generate the neighbors within a selected radius and then recompute=20
     the connectivity with RECON). The CLEAN command may be used before=20
     RECON  in order to delete atoms in coincident  spatial  positions.=20
     See the CLEAN syntax for full details.
     Syntax  :  recon
     %
    =20
     -RESPAR  :  to read the MOLDPAR.DTA file and restore  the  default=20
     values of the parameters changed by the PARAM command.
     Syntax : respar
     %  =20
    =20
     -REWDIR   :  to rewrite the contents of the file  DIREC.TXT  where=20
     the  list  of  the  available MOL files  is  stored.  Useful  when=20
     accessing a new directory in which no DIREC.TXT file exist or  new=20
     MOL  files  have been added and/or old files deleted,  or  when  a=20
     fragment has been generated.
     Related commands: NEWDIR, READ.
     Syntax  :  rewdir
     %
    =20
     -ROT? : to rotate, of a given angle, the whole molecule around the=20
     ?  reference  axis,  where ? stands for X,Y or Z. The  Z  axis  is=20
     assumed to be perpendicular to the display plane.
     Syntax: rotx  5 for    clockwise    rotation of  5 deg. around X=20
             roty -5  "  anti-clockwise     "     "   "   "     "   Y
             rotz 10  "     clockwise       "     "  10   "     "   Z
     %

     -SAVE   :   to save the coordinates of the displayed view  of  the=20
     molecule. The program ask for a file name (default:  NEWCONN.MOL).=20
     No  connectivity  information are stored in the  file.  See  WRITE=20
     command to store complete information.
     Syntax:  save
     %
    =20
     -SAVEP   :   to save the coordinates of the current  view  of  the=20
     molecule  in the standard PLUTO-78 format. The program ask  for  a=20
     file name (default: PLUTO.PLI). The file PLI is used by the  PLU90=20
     series of program. See the above section on plotting and  printing=20
     on Laser for more details.=20
     Syntax:  savep
     %
    =20
     -SAVES   :   to save the coordinates of the current  view  of  the=20
     molecule  in  the  standard SCHACKAL  88B/V16  format  (E.  Keller=20
     Kristallographisches  Institut der Universitaet, Hebelstr. 25,  D-
     7800  Freiburg,  FRG). The program ask for a file  name  (default:=20
     SHACK.DAT). Once created the program SCHACKAL can be run using the=20
     following  minimal series of commands to read and get a very  nice=20
     picture:
          l d           ---> load data
          shack         ---> file name
          g b           ---> set a ball & stick representation
          x             ---> display the structure
          o             ---> orient the molecule via arrows
          g c           ---> set a van der Waals representation
          x             ---> display the structure
     Syntax:  saves
     %
    =20
     -SCAN   :   to  make a series of  scans  of  selected  geometrical=20
     degrees of freedom relative to the current structure as  specified=20
     in the MOL file under the SCAN keyword. The geometry must be given=20
     using MATZ keyword in the MOl file.  This option is useful to move=20
     monomers  defining an hydrogen bond complex to look for  the  best=20
     conformation.  Refer to the detailed description of the SCAN  key-
     word in the MOL FILE KEYWORDS.
     Syntax:  scan
     %
    =20
     -SCONT   :  to display  non-bonded contacts less than a  specified=20
     threshold  (default: sum of van der Waals radii). All results  are=20
     written  into  the LOG file. Selection of a given pair  of  atomic=20
     types  is also possible. A minimum and a maximum  distance  within=20
     which contacts will be searched is also definable.
     Syntax:   scont
     %

     -SETCENT : After a NEIGH command the central initial fragment  may=20
     be  highlighted by a different color. The SETCENT command is  used=20
     to   eliminate/restore  the identification color  of  the  central=20
     initial fragment after a NEIGH command       =20
     Syntax:  setcent
     %
    =20
     -SLAB  :  to clip off atoms above/below (in the Z  direction)  the=20
     specified  top/bottom  atom of the structure. The  specified  atom=20
     remains always visible.=20
     Related command: NOSLAB.
     Syntax: slab
     %
    =20
     -SOLID    :  to generate a picture as close as possible to the kit=20
     molecular models. Any bond assumes a cilindric shape, depending on=20
     the  FATS and FATB parameters, and different colors are  used  for=20
     different atoms. The hydrogen size is scaled.
     Syntax:  solid
     %
    =20
     -SQUARE    :  to clip off the current structure in the X-Y  plane,=20
     by  defining a rectangular window around a given target atom.  The=20
     user  can  specify  the left-lower,  right-lower,  left-upper  and=20
     left-lower  limits of the window centered on the chosen atom.  All=20
     the  outside  atoms will be definitively purged off.  The  default=20
     window is -4.5,4.5,-4.5,4.5 Angstroms.
     %=20
    =20
     -STEREO   :  to display a stereo plot of the structure. Red  (left=20
     eye)  and green (right eye) glass are required to feel the  tridi-
     mensional view. The title of the structure currently displayed  is=20
     also  displayed. This option is not allowed when the CGA board  is=20
     used. Pressing any key will quit the command.
     Syntax: stereo
     %
    =20
     -STICK  :  to display the molecule using stick  representation  of=20
     bonds. Different colors are used for different atoms.
     Syntax:  stick
     %
    =20
     -SURF    : to generate a van der Waals molecular surface by  means=20
     of  colored  dots, to allow better visibility  of  the  underneath=20
     structure. With release 4.5, a special connettivity file is  writ-
     ten  to  the disk and will be used for the current  structure  any=20
     time  the  SURF command is issued. The Z-axis is  divided  into  a=20
     series  of slabs of thickness provided by the user. The number  of=20
     dots per atom is also a variable which can be entered by the user.=20
     The present algorithm is not perfect, so that it is recomended  to=20
     experience with various combination of parameters.
     Syntax: surf
     %
    =20
     -TITLE   :   to display the title record of the MOL  file  in  the=20
     command line. This option may be useful when taking photographs of=20
     the display. Pressing any key will quit this command.
     Syntax: title
     %
     -TORS  : to compute the torsion angle defined by four  atoms.  The=20
     program  automatically prompts for the four atoms. The  input  se-
     quential  numbers  must be separated by commas.  Entering  a  void=20
     record will quit this option. Angles greater than 180 degrees  are=20
     transformed according to the formula : A =3D A - 360. The  resulting=20
     angle is also written into the LOG file.
     Syntax:  tors
    =20
           1,6,8,15 to compute torsion angle formed by atoms 1,6,8,15
           ..........................................................
     %
    =20
     -UNLINK : to disconnect two linked atoms. The program ask for  the=20
     sequential  numbers  of the atoms to unlink. Pressing  enter  will=20
     terminate  the  command. Checking is made to ensure that  the  two=20
     atoms were really linked.
     Syntax: unlink =20
     %
    =20
     -UVW  : to obtain a view of the current structure along the  crys-
     tallographic   direction of component u,v,w the  program  prompts.=20
     See also the HKL command.
     Syntax:  uvw
     %
    =20
     -VDW   :  to display the current structure as a series  of  inter-
     capsed  van der Waals spheres associated with each  atom. =20
     Syntax: vdw
     %
    =20
     -VDWS   :   to  display  the current  structure  as  a  series  of=20
     intercapsed  van  der  Waals spheres associated  with  each  atom.=20
     Furthermore, a stick representation is also superposed. =20
     Syntax: vdws
     %
    =20
     -VIEW : to display a view of the molecule along the normal to  the=20
     best  molecular  least  square plane. Each  atomic  coordinate  is=20
     weighted using the corresponding atomic weight.
     Syntax: view=20
     %

     -VOLUME : to calculate the molecular volume as defined by a series=20
     of  interlinked  van der Waals spheres centered on  each  atom.  A=20
     Monte  Carlo algorithm is used to calculate the volume using  5000=20
     integration  points. The user may specify the number of points  on=20
     the same line. The computed value is within 1 per cent of the true=20
     analytical value.
     Syntax: volume
             volume 2000      calculate the volume using 2000 points=20
     %
    =20
     -WAAL  :  to display the current structure as a series of van  der=20
     Waals  spheres  associated  to each atom.  This  option,  although=20
     inaccurate  in reproducing the correct sphere intercaps,  is  very=20
     fast. The picture can not be rotate but this is possible by  means=20
     of the following sequence of commands: fats 1; fatb 1.6.=20
     Syntax:  waal
     %
    =20
     -WAALS :  to display the current structure as a series of van  der=20
     Waals spheres associated to each atom with superimposed the  stick=20
     representation of the structure. This option, although  inaccurate=20
     in reproducing the correct sphere intercaps, is very fast.=20
     Syntax:  waals
     %
    =20
     -WCELL   :  to restore the drawing of the cell box after an  ECELL=20
     command.
     Related commands: CELLG, ECELL, NOCELL.=20
     Syntax: wcell.
     %
    =20
     -WRITE   :  to save the current structure in a file including  the=20
     connectivity  information. The program  ask for a file  name  (de-
     fault:  FRAGM.MOL). Useful to store permanently a structure  after=20
     many link and/or unlink commands.
     Syntax: write=20
     %
    =20
     -ZOOM  :   to  scale the drawing of the  molecule  by  a  specific=20
     factor. The zooming factor can be less than one. A blank space  is=20
     requested  as  a  separator between the keyword  and  the  zooming=20
     factor. Automatic cutting is performed if the drawing is too large=20
     to be contained on the screen.
     Syntax: zoom 2 / zoom 4 / zoom .2
     %
    =20

                                   INDEX
    =20
     INSTALLATION   INSTRUCTIONS                            2       =20
        MOLDRAW.MAN
        MOLDXR.EXE
        MOLDCRY.EXE
        Installing MOLDRAW onto hard-disk
        Running MOLDRAW from floppies
     CONFIGURING MOLDRAW                                    3
        General MOLDRAW functionality
     MOL  INPUT   FILE    DESCRIPTION                       4
        Important note about release 4.5 MOL format=20
        Molecular plots on plotter and Laser-printer
     MOL  FILE  KEYWORDS                                    6
        TITLE                                               6
        CELL                                                6
     Molecular Geometry Specification                     =20
        COORD                                               6
        COORDAU                                             7
        COSYMB                                              7
        MATZ                                                7
        GROUP                                               8
        SYMNUM                                              8
        SYMSIM                                              9
        CHARGE                                              9
        SCAN                                                9
     DESCRIPTION  OF  OTHER  FILES                          10
        MOLDPAR.DTA                                         10
        MCONFIG.DTA                                         11
        SPOOL.LOG                                           11
        PLUTO.PLI                                           11
        FRAGM.MOL                                           11=20
     DESCRIPTION  OF  INTERACTIVE  COMMANDS                 12
         *                                        12
        ADD                                       12
        ANG                                       12  =20
        ASPE                                      12  =20
        BALL                                      13  =20
        BARICE                                    13
        BROT                                      13  =20
        CELLG                                     13  =20
        CLEAN                                     14  =20
        CLS                                       14  =20
        COL                                       14  =20
        CROT                                      14  =20
        DIST                                      14  =20
        DOS                                       14  =20
        DRAW                                      15  =20
        ECELL                                     15  =20
        ELETT                                     15  =20
        ENANT                                     15  =20
        END                                       15  =20
        ENERG                                     15  =20
        ENERI                                     15  =20
        ENFRAG                                    15  =20
        FATB                                      15  =20
        FATS                                      16  =20
        FRAG                                      16  =20
        HCOP                                      16  =20
        HELP                                      17  =20
        HKL                                       17
        HYD                                       17  =20
        KILL                                      17
        INERZ                                     17  =20
        INFO                                      17  =20
        LABE                                      17  =20
        LINK                                      18
        MATZ                                      18  =20
        MATZG                                     19
        MOV                                       19  =20
        NAME                                      19  =20
        NBOND                                     19  =20
        NEIGH                                     19  =20
        NEXT                                      19  =20
        NEWDIR                                    19  =20
        NFRAG                                     20  =20
        NOCELL                                    20  =20
        NOHYD                                     20  =20
        NOLABEL                                   20  =20
        NONEIGH                                   20  =20
        NOPERSP                                   20  =20
        NOSLAB                                    20  =20
        PARAM                                     21  =20
        PGEOM                                     21  =20
        PERSP                                     21  =20
        PLANE                                     21  =20
        PLOT                                      21  =20
        PLUTO                                     21  =20
        POLY                                      21  =20
        READ                                      22  =20
        RECON                                     22  =20
        RESPAR                                    22  =20
        REWDIR                                    22  =20
        ROT?                                      22  =20
        SAVE                                      23  =20
        SAVEP                                     23  =20
        SAVES                                     23  =20
        SCAN                                      23
        SCONT                                     23  =20
        SETCENT                                   24  =20
        SLAB                                      24  =20
        SOLID                                     24
        SQUARE                                    24
        STEREO                                    24  =20
        STICK                                     24  =20
        SURF                                      24
        TITLE                                     24  =20
        TORS                                      25  =20
        UNLINK                                    25
        UVW                                       25
        VDW                                       25  =20
        VDWS                                      25  =20
        VIEW                                      25  =20
        VOLUME                                    26
        WAAL                                      26  =20
        WAALS                                     26  =20
        WCELL                                     26  =20
        WRITE                                     26
        ZOOM                                      26  =20
=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=
=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=
=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A=1A

--=====================_854473616==_
Content-Type: TEXT/PLAIN; CHARSET=us-ascii
Content-ID: <[email-masked]>
Content-Description: 

----------------------------------------------------------------------------
Prof. Piero Ugliengo
Dip. Chimica Inorganica, Chimica Fisica
e Chimica dei Materiali
Via P. Giuria, 7
I-10125 Torino

Voice: +39-11-6707515
FAX:    +39-11-6707855
E-mail: [email-masked]
MOLDRAW program at:
http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html

--=====================_854473616==_--