Subject: SGI Z-buffer

From: [email-masked]
Date: Tue, 24 Aug 1993 13:40:17 -0500 (EST)

I am planning to purchase an entry level Silicon Graphics Indigo.
I have no illusions about memory requirements and plan to specify 32MB
RAM and at least a 1GB disk, so I can run G92 efficiently.

	However, I am uncertain about graphics program requirements for
chemistry software.  Specifically, can I run commonly available graphics
programs on the entry level machine, or is a Z-buffer necessary?  I just
want the graphics program to run, not necessarily at top speed.  Graphics
upgrades on the Indigo seem quite expensive.

	Thank you for your help.

Don Williams
Chemistry Dept.
University of Louisville
Louisville, KY 40292
[email-masked]

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From: [email-masked] (Peter Shenkin)
Date: Tue, 24 Aug 93 18:45:29 -0400

Entry-level graphics is fast enough to rotate small molecules 
interactively, even in a CPK representation.  Trouble is, it looks 
ugly, due to low-resolution graphics, few bit planes and dithering.  
Entry-level graphics does Z buffering in software.

The next step up is XS graphics.  This has no Z buffer, even in
software.  In answer to your question:  Yes, this makes it a poor
choice for an application that tries to rotate molecules and give 
a "nice" 3D representation.  The next step up beyond this is XS-24.  
This also has no Z buffer, even in software, and is therefore also 
a poor choice.

The first step beyond entry-level that gives you a Z buffer at all
is XS-24Z.  This provides a hardware Z buffer and very nice graphics, 
indeed.  More expensive models than this offer greater speed, and in 
some cases bells and whistles, such as "fog", "texture mapping", and 
other things which molecular visualization programs could, in principle, 
use to good effect, but, for the most part, do not bother to implement;
for one thing, they wouldn't work on the lower models that lots
of people have.  This is YATTMCWTAOOGL (Yet Another Thing That May
Change With The Advent Of OpenGL).

Bottom line:  get at least XS-24Z if you can.  If you can't, get
entry-level graphics.  If you're going to want to do a lot of 
visualization of large molecules, such as proteins, try to get
even a faster graphics engine, such as XZ or Elan.  SGI sells
a special package that includes an Indigo R4000 XZ with 32 Mb RAM
and 1.2 Gb disk.  It's imaginable that the special pricing of the
package might make this not much more expensive than the same
machine with XS-24Z, but I don't really know.

By the way, your choice of 32 Mb and 1.2 Gb is a reasonable minimum 
configuration for molecular modeling.  For ab-initio quantum 
calculations you'd probably want to increase main memory considerably.
For molecular modeling of large molecules, e.g. proteins, you'd
probably want to increase swap space to 100 Mb from the default 
40 Mb once you receive the machine.

	Hope this helps,
	-P.
************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************
Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ.,
New York, NY  10027;  [email-masked];  (212) 854-5143
********************** Wagner, Beame, Screvane in '93! **********************