THE Cascade FAQ                                          October 1995
(forboded asked questions about Cascade V2)

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1.  What is Cascade?
2.  Who dunnit?
3.  What do these programs do?
4.  How can I get Cascade running on my system?
5.  How about some examples?
6.  What about the Copyright?
7.  Where can I get the calculation programs and informations about them?
8.  Where can I get the graphic programs and informations about them?
9.  How can I customize Cascade for my needs?
10. How do I handle the Cascade shell?
11. Where is the Unix version?
12. I know a good display program. How can I contribute to Cascade?
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

1. What is Cascade?
===================

Cascade means:

Cascade Aids Semi-empiric Calculators Access
Displays Eventually :-)

Cascade is a shell and a selection of scripts which convert semi-
empirical data (from programs like MOPAC, AMPAC and VAMP) into
data used by some three-dimensional display programs.
It thus enables the user to visualize the calculated molecule geometry.

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2. Who dunnit?
==============

The authors of this package are:
(in alphabetical order)

Andreas Dosche          (dosche@mi.uni-erlangen.de)
Pf"alzer Wald-Str. 112
90469 N"urnberg

Ralph Puchta            (puchta@anorganik.chemie.uni-erlangen.de)
Eifelweg 22
90469 N"urnberg

Michael Reichenb"acher  (reichenb@mi.uni-erlangen.de)
Pachelbelstr. 126
90469 N"urnberg

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3. What do these programs do?
=============================

If you have access to one of the following programs
(DOS Versions or Unix versions)

MOPAC or AMPAC or VAMP
and
RASWIN or 3DV or JMR or CHEMVIEW or POVRAY or MV or PCMODEL or PLUTON

and you would like to SEE the molecule
(as opposed to a confusing mass of numbers and coordinates)

then the following tools should be of interest to you:

pac2mol  converts outputs from AMPAC, MOPAC (more specifically,
	 .out- or .lis-files) to VAMP .mol-files

vamp2mol converts VAMP .out-files to VAMP .mol-files
	 Note that some VAMP versions directly create a .mol-file.


mol2coo  converts .mol-files to .coo-files, that can be shown by JMR 
	 (Jim's Molecule Renderer)

mol2dat  converts .mol-files to .dat-files, that can be shown by CHEMVIEW

mol2pdb  converts .mol-files to .pdb-files, that can be shown by 
	 RASWIN (though it is far from using all features of 
	 the pdb format, as it has only the necessary parts for displaying 
	 the molecule, and there are no semi-empiric calculations 
	 of encymes - yet) or MOLWIN and many others

mol2spf  converts .mol-files to .spf-files, that can be shown by Pluton

mol23dv  converts .mol-files to .3dv-files, that can be shown by 3DV

mol2str  converts .mol-files to .str-files, that can be shown or converted
	 to Postscript using MV.

mol2xyz  converts .mol-files to .xyz-files, that can be shown by MOLWIN, e.g.

mol2dt3  converts .mol-files to .dt3-files, that can be shown by PCMODEL


cascade.exe is a shell for those scripts. Furthermore you can start JMR,
Povray, Chemview, MV (needs 570000 byte free RAM!) and 3dv from it.
It also contains two routines to convert mol-files to pov-files.

At last, there are two tools pdb2mol and xyz2mol, that are still in a
testing phase. We have included them nevertheless to enable the users of
cascade to play around with them. Please report your opinions and your
suggestions to the authors.
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4. How do I get Cascade running on my system?
=============================================

First of all, use install to copy the files to your hard disk.
Then you have to insert the following line in your autoexec.bat:
SET CASCADE=<path to cascade>
If you don't set the environment variable, cascade will not find 
its ini-file.

If you want to use the shell, you have to set the paths to 
MV, JMR, 3DV, POVRAY, etc., to your command.com 
(you won't be able to start the awk-scripts without command.com)
and to an editor (edit.com, for example). 
All these paths must end with the program-file and its extension. 
The paths for awk.exe and 3dv.exe and the awk-scripts will be set 
automatically.
You also must set the paths to Povray (povray.exe and the path to your 
colors.inc, an include-file for povray).
Example:
c:\pov\povray.exe (for povray.exe)
c:\pov\include\   (for colors.inc)
You can change these options in SET PATHS and SET PARAMETERS FOR POVRAY

Alternatively, you can use the batch-files in the awk subdirectory, 
In order to do that, you also have to insert this line in your autoexec.bat:
SET AWKDIR=<path to the awk-scripts>
Finally, the batch-files and the awk executable should be copied onto the
PATH.

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5. How about some examples?
===========================

There are some examples of input files, some output files and
some files generated in intermediate states. They can be found
in the subdirectory daten of the installation directory.

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6. What about the Copyright?
============================

Our scripts are object to the GNU public license. See the file COPYING,
which you should have received with this package.

This license also applies to GAWK.

As for the copyright 3DV, we assume that it is freely redistributable (at
least). Read the appropriate documentation for further info.

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7. Where can I get the calculation programs and informations about them?
========================================================================

Try your local ftp-side or the nearest of the below listed sides:

 A M P A C
-----------
Author: M.J.S. Dewar, E.S. Healy, D.A. Liotard, J.M. Ruiz
FTP:
ftp://kekule.osc.edu/pub/chemistry/software
ftp://ftp.uni-koeln.de/chemie/ampac2.1
ftp://nic.funet.fi/pub/sci/chem/qcpe/ampac2.1
ftp://ftp.ibp.fr/pub9/TeX/CTAN/support/translit/pub/chemistry/
		 software/SOURCES/FORTRAN/mopac6_sources/ampac21
ftp://ftp.jate.u-szeged.hu/pub/netlib/incoming/ampac216.tar.Z
ftp://cs.dal.ca/comp.archives/sci.chem/ampac-cray-unix-chemistry-program

M O P A C 
-----------
Author: James Stewart, F.J. Seiler
FTP:
ftp://kekule.osc.edu/pub/chemistry/software/MSDOS/mopac_for_dos
ftp://kekule.osc.edu/pub/chemistry/software/OS-2/mopac6
ftp://kekule.osc.edu/pub/chemistry/software/SOURCES/FORTRAN/mopac7_sources

 V A M P
---------
Author: Tim Clark et al. (from the Department of Organic Chemistry, 
	University of Erlangen-Nrnberg)
EMail:   clark@organik.uni-erlangen.de
Comment: VAMP is a commercial program, I (Ralph) know the program from
	 my local university, where it runs on a Unix workstation, and
	 I had to work with the output.

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8. Where can I get the graphic programs and informations about them?
====================================================================

Again, try your local ftp-side :-) or the nearest of the below listed
sites:

 3 D V 
-------
Author: Oscar Garcia
EMail:  WANTED! See below.
Comment: Tool, designed for another purpose but very, very fast. Great!
FTP:
ftp://ftp.clarkson.edu/pub/simtel20-cdrom/msdos/graphics/3dv25.zip
ftp://bunsen.hrz.uni-marburg.de/mirror1/simtel/graphics/3dv25.zip
ftp://faui43.informatik.uni-erlangen.de/mounts/epix/public/pub/pc/
      msdos/graphics/misc/3dv25.zip
ftp://ftp.bhp.com.au ASCII/pc/garbo/pc/graphics/3dv25.zoo
ftp://ftp.comp.vuw.ac.nz/ITS/ms-dos/Graphics/3dv25.zip

 C h e m v i e w 
-----------------
Author: unknown
Comment: Chemview is a part of Chemical, but sometimes you can get it
	 separatedly, too. (though that might be an older version), 
	 so look out for Chemview, too.
FTP:
ftp://bunsen.hrz.uni-marburg.de/mirror1/simtel/chemstry/chemical.zip 
ftp://ftp.sunet.se/pub/pc/mirror/SimTel/msdos/chemstry/chemical.zip
ftp://ftp.technion.ac.il/pub/unsupported/simtel/msdos/chemstry/chemical.zip

J M R (Jim's Molecule Renderer)
---------------------------------
Author:  Jim Javito
EMail:   javito@netcom.com
Comment: An easy to use molecular renderer
FTP:
ftp://kekule.osc.edu/pub/chemistry/software/MS-DOS/Raytraced-Molecules-for-DOS
ftp://bunsen.hrz.uni-marburg.de/mirror1/simtel/chemstry
ftp://wrzx02.rz.uni-wuerzburg.de/pub/pc/simtel/msdos/chemstry
ftp://plaza.aarnet.edu.au/micros/pc/SimTel/msdos/chemstry
ftp://rcs1.urz.tu-dresden.de/pub/soft/msdos/simtel.mirror/chemstry

 M o l W i n
-------------
Author: Pavel V. Ganelin        
EMail:  48ganelin@cua.edu
Comment: Nice visualization tool for Windows
FTP: Simtel areas
ftp://ftp.sunet.se/pub/pc/mirror/SimTel/win3/chem/molwin23.zip
ftp://ftp.switch.ch/mirror/simtel/win3/chem/molwin23.zip
ftp://ftp.th-darmstadt.de/pub/machines/ms-dos/SimTel/win3/chem/molwin23.zip
ftp://micros.hensa.ac.uk/mirrors/simtel/win3/chem/molwin23.zip
ftp://nic.uakom.sk/pub/dos/win3/chem/molwin23.zip
ftp://ftp.univie.ac.at/systems/dos/simtel/win3/chem/molwin23.zip

 M V
-----
Author:  Pawel Wzietek
EMail:   wzietek@.l-psud.fr
Comment: MV is a shareware program, which allows you to view your molecule
	 from different point of views, and to create a postscript file of
	 your molecule.
	 To run MV from cascade, you need a co-processor and free RAM
	 of at least 570000 bytes!
FTP:
Simtel areas

 P C M O D E L
---------------
Author: ???
EMail: ???
Comment: PCModel is a widely used DOS program to display molecules.
FTP: ???

 P l u t o n
-------------
Author:  A.L. Spek
EMail:   spea@xray.chem.ruu.nl
WWW:     http://www.cryst.chem.ruu.nl
Comment: Good visualization program, if you want to use molecule pictures
	 in a publication.
FTP:
ftp://xraysoft.chem.ruu.nl

 P O V R A Y
-------------
Author: Chris Young (Team Coordinator)
EMail:  76702.1655@compuserve.com
Comment: PovRay is a widely known raytracing program. There exist versions 
for DOS, Unices, Amiga, etc. Mighty, but difficult, if you do not use our 
Cascade.
FTP: 
ftp://alfred.ccs.carleton.ca

 R a s M o l / R a s W i n
---------------------------
Author:  Roger Sayle
EMail:   rasmol@ggr.co.uk
Comment: The best display program for molecules. Actually, it's
	 a program to display biochemical molecules.
FTP:
ftp://ftp.uni-stuttgart.de/pub/scivi/chemie/rasmol
ftp://pascal.zedat.fu-berlin.de/science/chemistry/rasmol
ftp://felix.embl-heidelberg.de/pub/software/dos
ftp://plaza.aarnet.edu.au/graphics/graphics/packages/rasmol
ftp://sunsite.doc.ic.ac.uk/biology/biocomputing/moleculear/rasml
ftp://colonsay.dcs.ed.ac.uk/export/rasmol
ftp://bioinformatics.weizmann.ac.il/pub/databases/pdb/pub/other_sw/rasmol

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9. How can I customize Cascade for my needs?
============================================

To change the attributes of the atoms, simply edit the
atom declaration file: atoms.dec

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10. How do I handle the Cascade shell?   
======================================

In CONVERT you can find the routines to convert your molecule-files.
Before you can start mol2pov, you have to adjust your parameters in 
SET PARAMETERS FOR POVRAY and EDIT INCLUDE-FILE FOR POVRAY.
In OPTIONS you can adjust the paths to your display-programs.
In RENDER you can start the display- and render-programs.
You can change the include file for povray (position of camera, lightsource)
in EDIT INCLUDE-FILE...
With EDIT ATOMDECLARATION-FILE, you can change the attributes of the atoms,
which are used in cascade. Examine the header of this file to recognize
the function of the columns.
With EDIT FILES, you can edit any text-file (if you have set the path to
an editor).
In EDIT you can also start a picture-viewer.

10.1. How to render a space-filling model with povray
----------------------------------------------------
First, you have to set the scaling-factor for the radius of the atoms (in
SET PARAMETERS FOR POVRAY), the position of the camera, the light_source, ...
The scaling-factor must be bigger than 1!
Then start CONVERT MOL2POV.
When you are asked for the radius of the sticks, click on CANCEL.
Then you can render the created pov-file (RENDER POVRAY).

10.2. How to render a ball-and-stick model with povray
-----------------------------------------------------
Same as space-filling model.
The scaling-factor must be smaller than 1 and you have to enter the radius 
of the sticks.

10.3. How to use PREVIEW effectively
------------------------------------
When you started PREVIEW, type 'h' the see the descriptions of this program.
With the keys 'd' and 'c', you can calibrate the rotation-speed for different
computers.
If you type 's', the program will create a new mol-file. Render this file
with Povray with the following position of the camera:
x = 0, y = 0, z = distance to (0, 0, 0).
The molecule will have the same position in the rendered image as you saw it
in PREVIEW.
The atoms in Preview will have the same color as defined in atoms.dec for MV!

10.4. How to render a movie with Povray
---------------------------------------
Adjust the parameters for Povray. The x- and z-coordinates of the camera and
the lightsource will be ignored (You can only adjust the distance to the 
molecule with these parameters).
The molecule will be rotated round an axis through the point look_at.
These axis is always parallel to the y-axis.
Start RENDER MOVIE.
Swap the x- and y-coordinates is used to tilt the molecule.
The routine will create the files MOVIE???.pov and RENDER.BAT.
To render the images, you have to leave Cascade and start RENDER.BAT.
This batch-file renders each single image. If you splitt RENDER.BAT, you can
render the images by stages.
Then you have to join the images to a movie (with Video for Dos,
Dave's Targa Animator, ...).

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 

11. Where is the Unix version?
==============================

Most display programs are MSDOS programs.
The following programs have Unix equivalents (that we know of):
AMPAC, MOPAC, VAMP (not free), RASWIN(=rasmol), POVRAY. Only those
are supported by the Unix version of this package, which can be found
at the same place where you got this package.

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12. I know a good display program. How can I get it into Cascade?
=================================================================

No problem, contact us and tell us where to get the program. If it has
an ASCII file as input, there are good chances that we will write an 
awk-script for it. (If we like it as much as you, that is.) 
Alternatively, you might want to write an awk-script yourself and send 
it to us, we will gladly include it in Cascade then. 
(Mind that it has to be freely redistributable)

**************************************************************************

WHERE IN THE WORLD IS OSCAR GARCIA?
===================================

If you know of the whereabouts of Oscar Garcia,
the man who programmed the wonderful 3dv program,
we'd like to hear about it.

His last known (i.e., that we know of) EMail-address was

garciao@mof.govt.nz

That was May 1992.

Thank you to everybody who helps to find him.

**************************************************************************
Also available from the authors: plot3d, an awk-script to view functions
of two variables using 3dv.
**************************************************************************
