From ccl@www.ccl.net Tue Jan 28 10:19:26 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA22041; Tue, 28 Jan 1997 09:45:16 -0500 (EST) Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by bedrock.ccl.net (8.8.3/950822.1) id JAA09144; Tue, 28 Jan 1997 09:45:15 -0500 (EST) From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #16365) id <01IEQPWVEW7K90MZEW@vms.cis.pitt.edu>; Tue, 28 Jan 1997 09:45:11 -0400 (EDT) Date: Tue, 28 Jan 1997 09:45:11 -0400 (EDT) Subject: Which Softwares exists to help Chiral Synthesis ? To: chemistry@ccl.net Message-id: <01IEQPWVGHNM90MZEW@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters We are interested in finding which softwares exists for help in (1) Research and (2) Teaching about Chiral Synthesis. We know one "CHIRON" from Professor Hanessian. Has anybody used this package either for research or teaching ? Any help will be useful. Please send response (satyam+@pitt.edu) Satyam From chrirena@techunix.technion.ac.il Tue Jan 28 10:26:50 1997 Received: from techunix.technion.ac.il for chrirena@techunix.technion.ac.il by www.ccl.net (8.8.3/950822.1) id KAA22227; Tue, 28 Jan 1997 10:08:19 -0500 (EST) Received: from localhost (chrirena@localhost) by techunix.technion.ac.il (8.8.5/8.6.10) with SMTP id RAA07531 for ; Tue, 28 Jan 1997 17:07:43 +0200 (IST) Date: Tue, 28 Jan 1997 17:07:38 +0200 (IST) From: Irena Efremenko To: CHEMISTRY@www.ccl.net Subject: MolDraw manual Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="=====================_854473616==_" Content-ID: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --=====================_854473616==_ Content-Type: TEXT/PLAIN; CHARSET=us-ascii Content-ID: Thanks to Dr. Luca Pedocchi and Prof. Piero Ugliengo answering my question conserning MolDraw manual. Here are their messages: ----------------------Message 1---------------- From luca@lcfs.chim.unifi.it Tue Jan 28 15:53:05 1997 Date: Mon, 27 Jan 1997 08:38:14 +0100 From: "Dr. Luca Pedocchi" Dear Irena, if you are speaking of MolDraw from University of Turin, there is a www page at http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html Regards Luca -- Dr. Luca Pedocchi Laboratorio di Chimica Fisica delle Interfasi via Cavour, 82 - 50129 Firenze - ITALY http://lcfs.chim.unifi.it/solid/pedocchi e-mail luca@lcfs.chim.unifi.it phone +39-55-2757793 fax +39-55-219802 Non esistono uomini cattivi, se sono cucinati bene (Stefano Benni) -----------------------Message 2------------------------ From ugliengo@ch.unito.it Tue Jan 28 15:53:41 1997 Date: Mon, 27 Jan 1997 11:20:16 +0200 (IST) From: Piero Ugliengo 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: ugliengo@ch.unito.it 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 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: Content-Description: =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 =B3 =B3 M O L D R A W User Manual =B3 =B3 =B3 =B3 Release 4.5 (20/12/1991) =B3 =B3 =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 =20 =20 =20 =20 =20 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) =20 and G. Chiari - Dipartimento di Scienze Mineralogiche e Petrolo- giche, Universit=85, Via Valperga Caluso 37, I-10125 Torino, Italy. =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 Reference: P. Ugliengo, G. Borzani & D. Viterbo - J. Appl. = =20 Cryst. 21, 75, (1988). =20 =20 =20 =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 INSTALLATION INSTRUCTIONS =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 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 =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 CONFIGURING MOLDRAW =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 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 =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 MOLDRAW INPUT FILE DESCRIPTION =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 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. =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 MOL FILES KEYWORDS =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 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: 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: ugliengo@ch.unito.it MOLDRAW program at: http://www.ch.unito.it/ch/DipIFM/Software/MOLDRAW/moldraw.html --=====================_854473616==_-- From jstewart@iti2.net Tue Jan 28 11:19:45 1997 Received: from cougar.iti2.net for jstewart@iti2.net by www.ccl.net (8.8.3/950822.1) id KAA22302; Tue, 28 Jan 1997 10:24:25 -0500 (EST) Received: from 171-29-106.ipt.aol.com (171-29-106.ipt.aol.com [152.171.29.106]) by cougar.iti2.net (8.7.6/8.7.3) with SMTP id IAA06896 for ; Tue, 28 Jan 1997 08:25:10 -0700 Message-Id: <3.0.16.19691231170000.3bef1628@iti2.net> X-Sender: jstewart@iti2.net (Unverified) X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Tue, 28 Jan 1997 08:24:05 -0700 To: CHEMISTRY@www.ccl.net From: "James J. P. Stewart" Subject: Putting New Parameters into MOPAC Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" When new parameters are added to the BLOCK DATA file in MOPAC, the source of the parameters should be supplied as well. MOPAC uses the presence of the reference as evidence for the parameters - specifically, the blank space at the start of the line. MOPAC93 is NOT designed to handle 'd' orbitals for any method. There is a single 'd' orbital element - Ti - but it is intended for use in demonstrating Russel-Saunders coupling only. That is, it is qualitative, not quantitative. Jimmy Stewart James J. P. Stewart ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | Jimmy Stewart | E-mail | | Stewart Computational Chemistry | jstewart@fai.com (preferred) | | 15210 Paddington Circle | jstewart@iti2.net (local address) | | Colorado Springs CO 80921-2512 | MrMopac@aol.com (for fun) | | USA .ooo0 | Phone: (719) 488-9416 | | ( ) Oooo. | Fax: (719) 488-9758 | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ From mn1@helix.nih.gov Tue Jan 28 13:23:19 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id NAA24304; Tue, 28 Jan 1997 13:01:14 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.4/8.8.4) id NAA09282; Tue, 28 Jan 1997 13:01:12 -0500 (EST) Date: Tue, 28 Jan 1997 13:01:12 -0500 (EST) From: "M. Nicklaus" Message-Id: <199701281801.NAA09282@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: G94: Problem with PES Scan in DFT Cc: mn1@helix.nih.gov Dear CCL'ers, I seem to be having a problem with a Potential Energy Surface (PES) scan in G94. I am running a relaxed PES scan on a nucleoside analog, trying to rotate the base. I am running this job at the DFT method/basis set B3LYP/6-31G(d). I'm using cartesian coordinates (a newzmat-generated input file with a Z-matrix didn't work previously), pre-optimized at the same level of theory from X-ray coordinates. For the first few conformations, everything seems to have proceeded nicely; i.e., the energy started out some 20 kcal/mol or so above the (presumed) global energy minimum, and then came down, during the partial optimization, to a reasonable value a few kcal/mol above the global min. With the current conformation, however, the job seems to be stuck, since for nearly 20 steps now, the energy has only been oscillating in a narrow band. Here's a grep of the output file (slightly modified through a filter --don't worry about the origin of the kcal/mol scale): SCF Done: E(RB+HF-LYP) = 6.587 kcal/mol ( -877.288353458 A.U.) after 12 cycles SCF Done: E(RB+HF-LYP) = 6.501 kcal/mol ( -877.288490683 A.U.) after 12 cycles SCF Done: E(RB+HF-LYP) = 6.470 kcal/mol ( -877.288539921 A.U.) after 11 cycles SCF Done: E(RB+HF-LYP) = 6.443 kcal/mol ( -877.288582731 A.U.) after 12 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591742 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288590115 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591793 A.U.) after 9 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591832 A.U.) after 8 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588866 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591957 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288590211 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288592040 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588983 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591984 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588800 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591901 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288589705 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288592037 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588677 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591887 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288589980 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288592074 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588420 A.U.) after 10 cycles I'd hate to kill this job--which has already taken up ca. 20 CPU-days--if there'e any chance that it's going to converge at some reasonable time. So here are my questions: (a) Can anyone give me a hint as to what's going on here? Has anyone seen a similar behavior before? (b) Should I kill this job now, or wait a bit longer? How much longer? (c) If this is a known effect, is there anything I can do to avoid it? Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ From ccl@www.ccl.net Tue Jan 28 19:19:29 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA29979; Tue, 28 Jan 1997 18:26:41 -0500 (EST) Received: from hub.ucsb.edu for zheng@bioorganic.ucsb.edu by bedrock.ccl.net (8.8.3/950822.1) id SAA28708; Tue, 28 Jan 1997 18:26:40 -0500 (EST) Received: from bioorganic ([128.111.114.116]) by hub.ucsb.edu; id AA25844 sendmail 4.1/UCSB-2.1-sun Tue, 28 Jan 97 15:26:41 PST for chemistry@ccl.net Received: by bioorganic (931110.SGI/930416.SGI) for @hub.ucsb.edu:chemistry@ccl.net id AA21779; Tue, 28 Jan 97 15:27:03 -0800 Date: Tue, 28 Jan 97 15:27:03 -0800 From: zheng@bioorganic.mechanisms.ucsb.edu (Yajun Zheng) Message-Id: <9701282327.AA21779@bioorganic> Apparently-To: chemistry@ccl.net Hi, I am looking for the pKa of catechol (o-hydroxyphenol). Any info will be appreciated. Thanks. Yajun