Subject: SUMMARY - MOLECULAR GRAPHICS

From: [email-masked] (Ayaz Bakasov, Phys. Chem., ETH Zurich)
Date: Sun, 19 Mar 1995 18:55:51 +0200

Dear Netters,

on March 14, 1995, I posted a question
about molecular graphics packages.

The number of specific responses 
I have received is just 6. However, one
can go ahead with it, it seems.

I thank all who responded with advices
very very much! It's good that good people
are reachable through CCL - so CCL must be
supported!

Some people (seems very 
young people) wrote to me strange things
and I am not posting them.

HOW TO READ SUMMARY:
- the string of ambersands '&&&&&&&&&&&&&'
  serves as a delimiter between two separate
  messages; therefore search please for this
  string (one of messages is very long&useful).

Sincerely,
Ayaz Bakasov.

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The original posting is this:

> Dear Netters,
>
>could someone advise me please on
>a molecular graphics software which:
>
>a) is ftp-able or commercial,
>    for a workstation like IBM/RS or Alpha DEC;
>b) is for not too large molecules (atoms < 20-30);
>c) draws bonds and can mark them (length);
>d) draws bond angles and dihedral angles
>     and can mark them;
>c) draws selected planes for pairs of bonds; 
>e) puts (desirable) different colours
>     on atoms and marks atoms (for slides);
>e) any other useful features on top   
>     of above-specified ones will be welcome
>     (e.g. animation).
>
>
>Tried RASMOL and found that it is for
>VERY large molecules, while I need
>to draw molecules ranging from hydrogen peroxide
>to some first aminoacids. Also, RASMOL doesn't
>take care of small details I am interested in
>(like specification of bond angles and
> dihedral angles on the graph, or drawing
> planes of pairs of bonds)
>
>Perhaps, Mathematica or Maple
>have already some supplementary 
>packages ?!
>
>Thank you.
>It will be my pleasure to summarize
>on the net the suggestions.
>
>Ayaz Bakasov.
>
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The responses follow below in chronological ordering:

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Date:	15-MAR-1995 01:19:29.35
From:	SMTP%"[email-masked]"
Subj:	ISIS Draw can draw 3D features on structures
To:	[email-masked]
It doesnt have any rendering capability, but it is 
designed for generating
queries for 3D pharmacophore searching, so distances, 
angles, dihedrals,
lines, planes, centroids, etc can all be drawn, assigned 
colors, and output
to postscript.  It is sold thru MDL and thru ACS 
software (very low price
for academics - I think $49).

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Date:	15-MAR-1995 09:28:20.39
From:	SMTP%"[email-masked]"
Subj:	Re:  CCL:QUERY - MOLECULAR GRAPHICS
To:	[email-masked] (Ayaz Bakasov, Phys. 
Chem., ETH Zurich)

Dear Ayaz Bakasov

I use SCHAKAL, but I do not think that can
write the bond lenghts and angles on the picture.
You may contact the author and ask him more information

here are some general information

and please let me know if you find something.

Davide

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

thank you for your email. Please find attached to this 
messge some 
information on the SCHAKAL 92 program.

Sincerely
-- 
Egbert Keller                   | Mail: 
[email-masked]
Kristallographisches Institut   | University 
Hebelstrasse 25                 | Phone: +49 761 203 
6438
D-79104 Freiburg i.Br / Germany | FAX:   +49 761 203 
6434

--------------------------------------------------------
-------------------

******************************
Some information on SCHAKAL 92
******************************

SCHAKAL 92 is a computer program for the graphic 
representation of molecular
and crystallographic models. The most important features 
of this program
are specified in the following.

Model types:  simple on-screen rotatable wire model, 
ball-and-stick model
with optionally broken, optionally exaggeratedly tapered 
sticks, space
filling model, intersection trace between space filling 
model and plane.
Automatic generation of bonds and specific drawing 
parameters for the
individual types of atoms. Facility to generate packing 
diagrams and (hkl)
surface models.

Display styles:  outlines; hatching by parallels, 
meridians, or grids;
shading by randomly or regularly dithered dots; 
"realistic" multi-colour
shading. Optional addition of shadows and highlights 
according to a
positionable light source. Optional perspective 
projections; optional
stereo drawings with stereo shading or labelling. 
Optionally depth-dependent
line thickness, darkness, or pseudo-transparency.

Rotations:  on-screen rotations of wire-models. Several 
possibilities to
align the model, e.g. alignment of a least-squares plane 
or a crystallo-
graphic lattice vector. Optional rotations (or 
translations) of parts of the
model, e.g., rotation of substituents about single 
bonds.

Labelling:  facility to label atom circles automatically 
with atom "names",
chemical element symbols, or coordinates, in a manner 
suitable for publica-
tion or documentation (label positions are optimized for 
minimal overlap.
Facility to modify label positions via a graphics 
cursor.

Information: facility to get information on atoms, 
bonds, model statistics,
steric trouble, current switch and parameter settings, 
view direction,
distances, angles, and dihedral angles.

Miscellaneous:  facility to add cursor-defined lines and 
cursor-positioned
text (e.g. chemical formulas) to the drawing (see figure 
captions); facility
to transform crystallographic coordinates; facility to 
generate broken-off
bond sticks in the boundary region of a model. Various 
predefined 3D and 2D
shading patterns.

Data Input:  atom names and coordinates; optional: space 
group symbol or
single symmetry operations; input defining a 
parallelepipedal or polyhedral
section of a crystal structure or a (hkl) "surface 
model".

Program control:  simple unformatted command code, which 
allows to vary all
important drawing variables and to select individual (or 
groups of) atoms/
bonds; facility to pick atoms or bonds via a graphics 
cursor; various "distri-
buted command files" for routine tasks; detailed on-line 
help functions;
printed tutorial manual including 24 figures.

Output devices:  screen;  paper plotter (HP-GL file);  
HP LaserJet III (or
fully compatible), screen image save file (non-standard 
format, described in
the manual [except V16version]);  .PCX file (V256 
version only).

Speed: On a 33 MHz 80486 DOS-PC with extended VGA card 
(1024 x 768), the
following times were required to draw a molecule of 100 
atoms and 100 bonds
on the whole screen (BS = ball+stick model; SP = 
space-filling model):

BS: outlines: 4 sec;  fully shaded model incl. shadows 
and highlights: 22 sec
SP: outlines: 4 sec;  fully shaded model incl. shadows 
and highlights: 64 sec

Examples: see  J. Appl. Crystallography 22, 19-22 (1989) 
(note: high
quality LaserJetIII drawings are not included there)

DOS-PC versions
***************

There are several DOS-PC versions of SCHAKAL 92 
available (none of them is
WINDOWS- or network compatible) having a capacity of 
1200 atoms and 1200 bonds:

a) SCHAKAL 92/V16                 for DOS-PC with 
standard VGA card
b) SCHAKAL 92/V256                for DOS-PC with 
extended VGA card (VESA)
c) SCHAKAL 92/FGA4                for DOS-PC with Spea 
FGA-4 card
d) SCHAKAL 92/XXHR                for DOS-PC with Elsa 
XHR Omega/Gemini card

Requirements:

(1) MS-DOS 5.0 or later; 80386/80387 or 80486 processor 
(the faster the better)

(2) either: a powerful Cache driver (for example MS 
SMARTDRV.EXE)
        or: a RAM-disk of at least 1 MB (2 or - better - 
4 are recommended).

(3) at least 560 kB (573000 Byte) free space within the 
640 kB RAM (memory);
    at least 3 MB free space on your hard disk (much 
more, if you want to
    store various plotter or image files).

(4) a suitable graphics card. For the different 
versions, "suitable" means:

    a) SCHAKAL 92/V16:  a standard or extended VGA card; 
the card will be
       used with a resolution of 640 x 480 and 16 
concurrently displayable
       colours.

    b) SCHAKAL 92/V256: an extended VGA card with 
corresponding colour graphics
       monitor. The VGA card must correspond to the VESA 
standard (or run with
       a VESA driver). SCHAKAL 92/V256  uses VESA modes 
with 256 concurrently
       displayable colours and one of the following 
resolutions:
       640 x 480;  800 x 600;  1024 x 768;  1280 x 1024 
.

       A number of VESA drivers for most extended VGA 
cards will be distributed
       on the SCHAKAL diskette, packed in a .ZIP file. 
You will have to "unzip"
       them with your own PKUNZIP.EXE program.

   c)  SCHAKAL 92/FGA4: A Spea FGA-4 graphics controller 
or a fully compatible
       with a resolution of 1280 x 1024 and 256 
concurrently displayable
       colours.

   d)  SCHAKAL 92/XXHR: An Elsa XXHR 110 or XHR Omega or 
XHR Gemini controller
       with a resolution of 1280 x 1024 and 256 
concurrently displayable colours
       from a palette of 16 millions.

(5) not essential: a plotter which understands HP-GL 
language or stand-alone
    software which is able to translate an HP-GL file 
for your plotter/printer
    (e.g. PRINTGL from Ravitz Software [shareware]).

(6) not essential: an HP LaserJet III or fully 
compatible printer. The printer
    must have at least 2 MB memory.

(7) not essential, and for SCHAKAL 92/V256 only: a 
software which is able to
    copy a .PCX file onto a (colour) printer (e.g. Corel 
Photopaint by Corel
    Corporation or Graphics Workshop for WINDOWS by 
Alchemy Mindworks Inc.
    [shareware]).

Other versions:
***************

These consist of the "general FORTRAN code" plus 
(optionally)
an adaption of this code to a certain system (performed 
by a user of the
program). All versions require compilation with a 
FORTRAN compiler and
(possibly) a C compiler. X-Windows versions are 
comparatively slow; they are,
like all other versions, command driven (not menu 
driven):

e) SCHAKAL 92               general FORTRAN code with 
graphic interface to be
                            adapted to any graphics 
system

f) SCHAKAL 92/AIX-GL        GL-version for IBM-RS/6000; 
requires 3D Adapter
   SCHAKAL 92/AIX-XW        X-Windows version for 
IBM-RS/6000

g) SCHAKAL 92/IRIS-4D       GL-version for Silicon 
Graphics IRIS-4D

h) SCHAKAL 92/SUN           X-Windows version for SUN 
workstations

i) SCHAKAL 92/VAX           X-Windows version for 
VAXstations (limited
                            functionality)

Note: The author (E.K.) is not able to give any direct 
support
with respect to machine-specific problems for versions 
f) to i).

Some Examples for Commands:
***************************

All of SCHAKAL's switches and all parameter settings are 
controlled by
commands, which may be given in arbitrary order. The 
effect of any command
may be altered or cancelled by a command of the same 
type later on
(e.g. after generation of a drawing). Any command begins 
with two label
words which may be followed by parameters, atom codes, 
and/or bond codes.
Note: label words may in any case be abbreviated to one 
letter.
A few examples follow:

Genr Unitcell           [g u]           (add unit cell 
edges to drawing)

Genr Shading            [g s]           (switch for 
shaded drawing)

Use Commandfile         [u c]           (execute 
commands stored on a file)

Help  U  C              [h u c]         (give 
information on the 'U C' command)

Rot X  -12              [etc.]          (rotate -12 deg. 
about X-axis)

Rot Bond  80 C2=C7                      (rotate 
substituent 80 degrees about
                                         the bond 
between C2 and C7)

Kill Bonds  <3.2  Ba=nn (Ba=I           (delete bonds 
between all Ba atoms and
                                         other atoms, if 
dist. <3.2A, but not
                                         between Ba and 
I )
Change Radii *1.15  S1 P (P'2           (increase radii 
by 1.15 for S1 and P
                                         atoms, but not 
for P atoms belonging
                                         to numerical 
group 2)

Xqt Xqt  C1-O12 C1-O12=nn               (draw all atoms 
>from C1 to O12 and all
                                         the bonds in 
which they are parti-
                                         cipating)

Various routine tasks may be accomplished by means of 
"distributed command
files" which contain procedures consisting of large 
numbers of such commands.
An example input to execute such a command file follows 
(generates a shaded
drawing of ball-and-stick plus space-filling model 
including shadows,
highlights, and labelling of non-Hydrogen atoms (see. 
fig.1)):

U C

ca  w

Extent of supply:
*****************

A SCHAKAL 92 supply consists of the following items 
[items a) to i) are
distributed on one or two 3.5" DOS diskette(s)]:

a) the executable program (DOS versions only)

b) the FORTRAN source code of about 35000 lines (all 
versions
   except SCHAKAL 92/V16 and SCHAKAL 92/V256)

c) an interactive hierarchical on-line manual in English 
(about
   300 pages, if printed)

d) a program to make a printout of this manual

e) a space group database

f) some data set examples

g) a number of  "distributed command files" for routine 
tasks

h) installation hints and installation program or 
makefile for
   the distributed version

i) a number of VESA drivers packed into a .ZIP file 
(SCHAKAL 92/V256 only)

j) a printed tutorial manual in English (76 pages, 24 
figures)

k) printed installation hints for the general version 
(all
   versions except DOS versions)

Licencing agreement and licence fees:
*************************************

SCHAKAL 92 is exclusive property of the University of 
Freiburg (represented
by Kristallographisches Institut der Universitaet). 
Legal use of the program
requires undersigning a licencing agreement and the 
following licence fees
to be paid [in Deutschmarks] (PRI = public research 
institute):

version         student      school       univers.       
PRI       commercial
--------------------------------------------------------
---------------------
SCH 92/V16      200.- A)     300.- B)     600.- B)     
800.- B)    1200.- A)
--------------------------------------------------------
---------------------
SCH 92/V256     250.- A)     375.- B)     750.- B)    
1000.- B)    1500.- A)
--------------------------------------------------------
---------------------
All other versions                       1200.- C)    
1600.- C)    2400.- A)
--------------------------------------------------------
---------------------

A) valid for installation on one computer.

B) valid for installation on a group of PCs to which one 
"responsible user"
   has legal and practical access (i.e., all PCs of a 
work group. If the program
   is installed on a large network, each workgroup has 
to pay the licence fee).

C) valid for installation on one computer within one 
unit, where unit is,
   for example, a department of inorganic chemistry, a 
dept. of experimental
   physics, etc. (maximally 2 "Lehrstuehle" = full 
professorships); a corre-
   sponding department within a public research 
institute.

   A discount of 75 %  is offered for installation on a 
second,
   third, etc. computer within the same unit.

   A discount of 60% is offered for a SCHAKAL 92/V16 or 
SCHAKAL
   92/V256 licence within the same unit.

For any registered SCHAKAL 86 / SCHAKAL 88 licence, 
there is an update discount
of 75 % on the corresponding licence fee given in the 
table above (72% for
update from SCHAKAL 88B/V16 to SCHAKAL 92/V256). 
Additional multi-installation
discounts are offered for "All other versions" only (87 
% discount for 2nd,
3rd, etc. installation). The rules given above are 
applied to decide whether an
installation is a 1st, 2nd, or 3rd (etc.) one and 
whether a certain (group of)
computer(s) is covered by an existing SCHAKAL 88 
licence.

There is an additional shipment fee of DM 15.- for 
non-European
countries.

A 50% discount is offered on all licence fees for 
East-European
and for developing countries.

Printing or other kind of multiplication of SCHAKAL 
drawings ...

... in scientific journals, congress invitations, 
letters, internally used
documents or educational scripts: is generally permitted 
(except for a
student's licence).

... in a scientific textbook: requires payment of an 
additional licence fee of
usually DM 50.- to 500.-, depending on the number of 
drawings and the scope
and purpose of the book.

... in other printed or non-printed matter (especially 
advertising material):
requires payment of an additional licence fee of DM 
200.-  to 4000.-, the
latter amount corresponding to an unlimited printing 
licence. For commerical
users of SCHAKAL 88, the difference between the licence 
fee for SCHAKAL 88 and
for SCHAKAL 92 is accounted for, here.

--------------------------------------------------------
-----------
                      Davide M. Proserpio
Dipartimento  di Chimica  Strutturale  e  Stereochimica  
Inorganica
Universita' di Milano,   Via Venezian, 21 -  20133  
Milano,   Italy
phone +39-2-70635120 fax 70635288 - 
[email-masked]
--------------------------------------------------------
-----------

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Date:	15-MAR-1995 17:19:01.12
From:	SMTP%"[email-masked]"
Subj:	RE: CCL:QUERY - MOLECULAR GRAPHICS
To:	"Ayaz Bakasov, Phys. Chem., ETH Zurich" 
<[email-masked]>
Don Boyd has been publishing an updated appendix in 
every volume of Reviews in
Computational Chemistry, published by VCH Publishers. It 
contains information
about many kinds of programs that you might find useful. 
Good luck, Kenny

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Date:	16-MAR-1995 19:26:20.03
From:	SMTP%"[email-masked]"
Subj:	Re: CCL:QUERY - MOLECULAR GRAPHICS
To:	[email-masked] (Ayaz Bakasov, Phys. 
Chem., ETH Zurich)
Dear Ayaz Bakasov 
Do you have tried xmol for RS6000 it print angles etc if 
you want it.
Ask archie for the location.

Yours sincerely
Joerg Heuer

Ask archie for the location.

Joerg Heuer                     e-mail: 
[email-masked] 
Institut fuer Pharmazie, Universitaet Hamburg,
Bundesstraae 45,      
20146 Hamburg,    Germany.

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Date:	16-MAR-1995 20:06:10.80
From:	SMTP%"[email-masked]"
Subj:	Re: CCL:QUERY - MOLECULAR GR
To:	"Ayaz Bakasov, Phys. Chem., ETH" 
<[email-masked]>
Dear Mr. Bakasov,

I am with SoftShell International, we have a program 
called ChemWindow for the
IBM PC or ChemIntosh for the Mac.  This is a chemistry 
drawing program.  I will
gladly send you a free demo of the program if you are 
interested, as well as a
catalog of our other products.  Please let me know, my 
address is
[email-masked]
Thank you.
------------------------------
Date: 3/15/95 6:34 AM
To: Diana Tarasiewicz
From: Ayaz Bakasov, Phys. Chem., ETH

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Date:	17-MAR-1995 17:33:19.03
From:	SMTP%"[email-masked]"
Subj:	Re: CCL:QUERY - MOLECULAR GRAPHICS
To:	[email-masked]
DeskTop Molecular Modeller sounds to be most 
appropriate. It runs on any 
PC, uses Windows, and is available from Oxford 
University Press for about 
250 pounds stirling.  It is part of a suite of programs 
and libraries.  
Contact Mrs Janet Caldwell, Oxford University Press, 
Walton Street, 
Oxford, OX2 6DP (tel: +44 (0)1865 56767 for details.

Yours,
James Crabbe.
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