Subject: Summary: Visualization of molecules and arbitrary geometric objects

From: Jonathan Greene <[email-masked]>
Date: Tue, 07 Jul 1998 19:40:21 -0700

Below is the original posting, followed by (lightly edited) responses
grouped by program.

=== Original posting ==================================

We (and probably others!) are interested in a visualization tool as
described below:

1. 3D graphics of quality similar to RasMol  with interactive rotation,
zoom, pan, etc.
2. Import and display multiple small molecules in various styles (tube,
wireframe, etc.).
3. Import and display multiple geometric objects, such as triangulated
meshes, iso-surfaces of a field, spheres of arbitrary radius, lines.
These should be arbitrary data specified by the user, not something
computed from the molecule by the tool itself.
4. Interactive selection of objects to control their color and turn
their visibility on or off.
5. Interactive measurements, e.g. select two atoms and report distance
between them.
6. Runs on PC under Windows.
7. Could be a stand-alone program that gets its input via files, or
better yet a toolkit with an API to which we could pass the data.

If you know of anything like this, please e-mail me. I will summarize
responses for the list.

Some of the things we've considered:
WebLab, Rasmol: don't import arbitrary geometry.
Chime 2.0: doesn't support interactive measurements, limited ability to
import geometry.
Insight, Midas, C2-SDK: limited to UNIX.
Catalyst: cannot maintain alignment of multiple molecules when imported,

geometry limited to spheres in hypotheses.

Jonathan Greene, CombiChem, Inc.
[email-masked]

=== CAChe ===================================================

Date: Thu, 28 May 1998 15:14:38 -0800
From: Daniel Poole <[email-masked]>

In response to your recent email, the product that fits your 3-D
molecular
visualation needs is a software package entitled CAChe:

>1. 3D graphics of quality similar to RasMol  with interactive rotation,

>zoom, pan, etc.

After building or importing a molecule, end-users can select, zoom in or

out, rotate, translate, and scale any organic or inorganic chemical
structure imagineable, containing any element.

>2. Import and display multiple small molecules in various styles (tube,

>wireframe, etc.).

CAChe supports viewing and editing of structures from experimental
crystallographic data or from standard databases such as MDL, Brookhaven

Protein Databank, Cambridge Crystallographic, as well as SD and MOL
files.

CAChe has the ability to display molecules as simple line drawing, space

filling CPK (Corey-Pauling-Kolton model), wire frame, ball & stick, ball
&
cylinder, and as partial charge and calculated bond order (atoms
displayed
as dotted or shaded spheres) in addition to choices for atom labeling,
atom
shape, atome color, etc.

>3. Import and display multiple geometric objects, such as triangulated
>meshes, iso-surfaces of a field, spheres of arbitrary radius, lines.
>These should be arbitrary data specified by the user, not something
>computed from the molecule by the tool itself.

Choices such as size, shape, shading, ability to hide or show atoms,
bonds
& electrons of a cetain type, color palettes, labeling, isplay to text,
lines, etc are just a sampling of  the settings that can be adjusted and

defined by the end-user.

>4. Interactive selection of objects to control their color and turn
>their visibility on or off.

Yes, absolutely a feature.

>5. Interactive measurements, e.g. select two atoms and report distance
>between them.

Yes, absolutely.

>6. Runs on PC under Windows.

Yes, Windows 95 or NT versions are available.
Specs:
486-66 but Pentium recommended
Windows 95 or NT 4.0
16 MB RAM but 32 MB recommended
100 MB HD space
SVGA monitor
WinSock compliant TCP/IP stack

>7. Could be a stand-alone program that gets its input via files, or
>better yet a toolkit with an API to which we could pass the data.

CAChe is available as stand-alone, desktop tool, but can also be
configured
as a client-server, able to send out experimental calcuations to a
server.

Additional information,  demo CDs, or a trial-use are all available to
get
a closer look at the CAChe software.

>> We wish to display arbitrary geometry that we can specify
superimposed on
>> the molecules.

You can draw "dummy" atoms, not part of your molecule, and set these
up as specific shapes like squares or triangles etc. of defined sizes
and
shapes using geometry labels, to see if your molecule fits inside it.
But
I get the nagging feeling this is not what you're asking me.

Dan Poole
Oxford Molecular

=== ChemSymphony ===============================================

Date: Fri, 22 May 1998 11:13:31 +0100
From: Adam Hodgkin <[email-masked]>

ChemSymphony can do pretty much all that you are asking for and
ChemSymphony Beans gives you access to the toolkit and the API's. Using
the
Beans you can do a LOT MORE than you are asking for. Check out our www
site:

http://www.cherwell.com/chemsymphony/index.html

Note that we offer both (1) a free LITE applet; (2) a suite of applets
--
ChemSymphony Pro (JDK 1.0); and (3) ChemSymphony Beans which will be of
primary interest if you are willing to do your own software development
for
an intranet etc (requires JDK 1.1).

Below I give some url's which take you straight to examples of the
functions you seek. Our support of geometric objects is via the
chemistry
file formats which ChemSymphony takes as input (Sneddon edited some PDB
files); but we note the suggestion that direct support of geometric
objects
would be a nice feature.

>1. 3D graphics of quality similar to RasMol  with interactive rotation,

>zoom, pan, etc.

lots of examples eg

http://www.cherwell.com/chemsymphony/example8.html

>2. Import and display multiple small molecules in various styles (tube,

>wireframe, etc.).

http://www.cherwell.com/chemsymphony/example3.html

>3. Import and display multiple geometric objects, such as triangulated
>meshes, iso-surfaces of a field, spheres of arbitrary radius, lines.
>These should be arbitrary data specified by the user, not something
>computed from the molecule by the tool itself.

http://www.sas.upenn.edu/~carrollp/sneddon.html

>4. Interactive selection of objects to control their color and turn
>their visibility on or off.

This is more customisable with ChemSymphony Beans

>5. Interactive measurements, e.g. select two atoms and report distance
>between them.

See (select angles, bond lengths etc and collect a list):

http://www.sas.upenn.edu/~carrollp/jo.html  or
http://www.cherwell.com/chemsymphony/sulfanil2.html

>6. Runs on PC under Windows.

And Unix and Mac and any system with suitable Java.

>7. Could be a stand-alone program that gets its input via files, or
>better yet a toolkit with an API to which we could pass the data.

http://www.cherwell.com/chemsymphony/ChemSymphonyBeans/CSBeansUse/CSBeansIntro.html

Our white paper gives explanations and examples of how the Beans can be
used to construct intranet solutions

     Adam Hodgkin                    |  e-mail:  [email-masked]
     Chairman                        |  Phone:   +44 (0)1865 784810
     Cherwell Scientific Publishing  |  Fax:     +44 (0)1865 784801
     Oxford OX4 4GA, UK              |  URL:     http://www.cherwell.com

=== DataExplorer ================================================

Date: Thu, 21 May 1998 17:07:16 -0500 (CDT)
From: "Fred P. Arnold" <[email-masked]>

If you're willing to massage your data a bit (such as recast it into HDF

format), the obvious answer would seem to be DataExplorer from IBM.
www.almaden.ibm.com/dx.  I used it in conjunction with a solid-state
band
code to visualize unit-cells, atoms, and electron densities in a variety

of formats.

                                                        -fred

                                        Frederick P. Arnold, Jr.
 "...But if you give theorists enough   Advanced Research Systems
  time, they can predict anything."     5640 S. Ellis Ave
        Dr. M. S. Turner, U. Chicago.   Chicago, IL 60637

=== ICM =====================================================

Date: Fri, 22 May 1998 10:43:51 -0500
From: Info <[email-masked]>

   We have a program which satisfies to all your criteria and is
used in pharmaceutical companies and academia now for 6 years.
The program is ICM and is distributed by Molsoft, LLC.

>1. 3D graphics of quality similar to RasMol  with interactive rotation,

>zoom, pan, etc.

   High quality, representations include wire (+chemical
representations),
ball, stick, surface, molecular surface (both solid and mesh), cpk,
depth queing, side by side and hardware stereo, clipping planes.

>2. Import and display multiple small molecules in various styles (tube,

>wireframe, etc.).

   Import of pdb, mol, mol2, csd

>3. Import and display multiple geometric objects, such as triangulated
>meshes, iso-surfaces of a field, spheres of arbitrary radius, lines.
>These should be arbitrary data specified by the user, not something
>computed from the molecule by the tool itself.

   Import any geometrical object of dots and/or lines and/or triangles
   in the wavefront format or the ICM easy text format
   Functions in ICM to create such objects, interactive editing of
   these objects

>4. Interactive selection of objects to control their color and turn
>their visibility on or off.

   Flexible selections, display, undisplay, color etc. command
   Interactive selections.

>5. Interactive measurements, e.g. select two atoms and report distance
>between them.

   Yes

>6. Runs on PC under Windows.

   Runs on PC under Windows (as well as under LINUX, DEC, SGI)

>7. Could be a stand-alone program that gets its input via files, or
>better yet a toolkit with an API to which we could pass the data.

   Can be a stand alone program or read from a pipe and quit

Molsoft L.L.C.
P.O.Box 113
Metuchen NJ 08840
fax 732-321-4180
tel  732-321-8690
e-mail [email-masked]

http://www.molsoft.com

=== MacroModel =================================================

Date: Thu, 21 May 1998 16:40:33 -0400
From: "Peter Shenkin" <[email-masked]>

Our new MacroModel interface will do all these things, I think, but
won't
be ready for some months.

Date: Fri, 22 May 1998 13:46:22 -0400
From: "Peter Shenkin" <[email-masked]>

I spoke too soon.  Arbitrary geometric objects will be included in
a later revision, not in our first release, sorry.  Also, it will
run on NT, but probably not vanilla Windows.

* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code
3153 *
** NY, NY  10027;  [email-masked];  (212)854-5143;  FAX: 678-9039
***
*MacroModel WWW page:
http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

=== Sculpt =======================================================

Date: Thu, 21 May 1998 14:25:22 -0700
From: Dan Haun <[email-masked]>

Allow me to add one more variability. You're interested in an
interactive
visualization tool and you had tried Chime 2.0 with limitations on not
having the capabilities to measure between atoms as well as limitations
in
geometries.   I'd like to introduce you to SCULPT which has the
capabilities of hot linking with Chime 2.0 and does allow you to measure

distances and torsion angles.  It won't however pass the test for all of

the geometry requirements; it does allow you exhibit mutiple small
molecules, it does allow you to have rendering options such as tubes,
wire
frames, and CPK spheres; it does not allow one to alter colors of atoms
o
nor does it highlight.  It also runs on the PC for Windows95/NT,
PowermAcs
and SGIs', and allows one to copy and paste from ISIS draw,
ChemBuilder3D,
Chem3D and ChemWindows.    It also allows one to overlay mutiple
structures
for confirmational analyses.

If you are interested or know others who are working with organic
structures, I would invite you to try SCULPT http://www.intsim.com.

Daniel P. Haun                                Tel:       (619) 658-9462
Interactive Simulations Inc.             Toll Free: (888) 272-8578
5330 Carroll Canyon Rd.                Email:     [email-masked]
San Diego, CA 92121                    Fax:       (619) 658-9463
Web site http://www.intsim.com

=== Tinker ======================================================

Date: Thu, 21 May 1998 14:59:54 -0700
From: guo <[email-masked]>

here it is: http://dasher.wustl.edu/tinker/

=== VMD =======================================================
Date: Fri, 22 May 1998 17:59:00 +0400 (MSD)
From: Eugene Leitl <[email-masked]>

 > 1. 3D graphics of quality similar to RasMol  with interactive
rotation,
 > zoom, pan, etc.

VMD does nicely.

 > 2. Import and display multiple small molecules in various styles
(tube,
 > wireframe, etc.).

VMD does that also.

 > 3. Import and display multiple geometric objects, such as
triangulated
 > meshes, iso-surfaces of a field, spheres of arbitrary radius, lines.
 > These should be arbitrary data specified by the user, not something
 > computed from the molecule by the tool itself.

Err, you would have to tweak the sources to do that. Tcl scripts may
suffice, but I doubt that.

 > 4. Interactive selection of objects to control their color and turn
 > their visibility on or off.

Tcl scripts.

 > 5. Interactive measurements, e.g. select two atoms and report
distance
 > between them.

Should do.

 > 6. Runs on PC under Windows.

Why would one cripple himself deliberately? Windows as a
computational/viz platform is doomed anyway. Have you considered
installing Linux/Win95 as a dual-boot on that PC?

Date: Thu, 21 May 1998 19:45:18 -0500
From: "Sergei Izrailev" <[email-masked]>

I guess, running on Windows is one of your main requirements,
and it is not met yet. The Windows port is under way, but it'll
take several months to complete. VMD thus falls into the same category
as Insight, Midas, C2-SDK: limited to UNIX.  I would like to emphasize
that
VMD is a free program distributed with the source code written in C++,
so you can adapt it for your needs. Please take a look at VMD web page
http://www.ks.uiuic.edu/Research/vmd/

I'll go through the rest of the list.

> 1. 3D graphics of quality similar to RasMol  with interactive
rotation,
> zoom, pan, etc.

Yes.

> 2. Import and display multiple small molecules in various styles
(tube,
> wireframe, etc.).

Yes. Actually, VMD can also display large molecules (such as proteins
and DNA).

> 3. Import and display multiple geometric objects, such as triangulated

> meshes, iso-surfaces of a field, spheres of arbitrary radius, lines.
> These should be arbitrary data specified by the user, not something
> computed from the molecule by the tool itself.

First of all, yes, VMD can draw user-provided geometrical objects
through
its powerful and easy to learn Tcl based scripting language. Importing
of
triangulated meshes and iso-surfaces can be added with relatively little

effort through the Tcl interface. For the import to be fast, of course,
some source code modifications may be needed.

> 4. Interactive selection of objects to control their color and turn
> their visibility on or off.

Yes, through very easy to use interface.

> 5. Interactive measurements, e.g. select two atoms and report distance

> between them.

Yes.

> 6. Runs on PC under Windows.

As I mentioned earlier, we are working on porting VMD to Windows,
but it'll take some time.

> 7. Could be a stand-alone program that gets its input via files, or
> better yet a toolkit with an API to which we could pass the data.

It's a stand-alone program, which uses several external programs
for various purposes, including import/export of files and calculation
of surfaces. Adding another interface should not be a problem with the
source code provided.

Please write to [email-masked] if you have further questions.

Sincerely,

Sergei Izrailev

=== gOpenMol ===================================================

Date: Sat, 23 May 1998 18:39:08 +0300 (EET DST)
From: Leif Laaksonen <[email-masked]>

Please have a look at gOpenMol (http://laaksonen.csc.fi/gopenmol/).
It's a very flexible program you can extend by writing more Tcl/Tk
code or you can write extensions using the dynamic loading feature.

Yes you can import arbitrary spheres and you can tilt them (like eggs),
lines, cylinders, arrows. However, you can not import triangulated
meshes
or iso-surfaces. I'm currently implementing that. Later there will be
a Tcl command to save or load the triangulated meshes.

If you mean by interactive the possibility to "pick" atoms the answer is

no. However, you can measure lenghts, angles, torsions by writing in
the atom name or number. You can also follow the variation of the
property
through a trajectory.

The picking is a bit tricky because the GUI is pure Tcl/Tk that talks to

gOpenMol and not the other way around.

Center for Scientific Computing    | Phone:      358 9 4572378
P.O. Box 405                       | Mobile:     358 400425203
FIN-02101 Espoo                    | Telefax:    358 9 4572302
FINLAND                            | Mail:  [email-masked]
URL: http://laaksonen.csc.fi/leif.laaksonen.html