[comp.sys.sgi] Molecular Modeling

BUG@campus.swarthmore.EDU (06/02/89)

We are starting to model small molecules and pieces of crystalline solid,
and would like to draw atoms and bonds and manipulate the images in 3D as
quickly and efficiently as possible.  Has anyone out there ordered the
"Release Tape #1 for the 4D; and if so, was it worth it"?  In particular
we would like to
 - use "sliders" to translate and rotate
 - use our 56 bitplanes to the max for quick manipulation of images
 - store frames for quick replay

Also, if anyone has information about vendors for output devices (photographic
or videotape), or has encountered a version of Clark Still's MACROMODEL
which has been ported to SG workstations,  I would very much appreciate
hearing from you.  Thanks very much!!!
    Amy Bug,  Physics Dept.  Swarthmore College (BUG@SWARTHMR)

uh311ae@sun7.lrz-muenchen.de (Henrik Klagges) (10/08/90)

Hello !

I do some molecular modeling on a 4D/210GTX, mainly using the insightII
program from Biosym. I get, however, various bugs. It starts with annoying
procedures while creating CPK surfaces and ends up with:

"A serious internal error has occured. The program cannot continue."
"caught core_trap() in sys_await_event.c"

This happens especially often when I use medium-sized assemblies. and start
a Discover run to minimize the structures. Who knows about these errors or 
has any experience to share about the insight or quanta programs ? 

I really would like insight as a tool, if it wouldn't beam my work into
cores all day long.

Thanks !

Henrik Klagges

Disclaimer: These are *my* opinions. They can be attributed to 
			"human error" :-).
   

Scanning tunnel microscope group at 
Ludwig-Maximilians-Universitaet Munich (IBM Research group)
EMail: Try uh311ae@sun7.lrz-muenchen.de OR @DM0LRZ01.BITNET
SMail: Moorbachweg 7, D8210 Prien, FRG

doelz@urz.unibas.ch (10/10/90)

In article <4778@tuminfo1.lan.informatik.tu-muenchen.dbp.de>, uh311ae@sun7.lrz-muenchen.de (Henrik Klagges) writes:
> program from Biosym. I get, however, various bugs. It starts with annoying
> procedures while creating CPK surfaces and ends up with:
> 
> "A serious internal error has occured. The program cannot continue."
> "caught core_trap() in sys_await_event.c"
> 
> This happens especially often when I use medium-sized assemblies. and start

I am working with the software mentioned for over two years now. The 
problem is patience. Some procedures are time-consuming, and BIOSYM's 
surfaces in CPK are special in order to permit depth-cueing effects. The 
calculation takes long and the input queue is open. Once this queue 
recognizes overflow, core_trap() prevents a segmentation violation error 
and, therefore, exits. You should contact the BIOSYM office in Munich 
if you need more detailed information. 

The easiest workaround is to wait for completion of the steps and hit the 
mouse button afterwards. 

Regards 
Reinhard