AMBER Archive (2005)

Subject: Re: AMBER: stereo

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Wed Feb 09 2005 - 14:02:13 CST

Quoting Filip Lankas <filip.lankas_at_epfl.ch>:

>
> Hello Amber users,
>
> this is not directly about Amber, but about visualization. We would like
> to buy a good machine and software for stereo visualization of
> biomolecules - what would be your preferred choice? Any comments are
> welcome.
>
> Thank you,
>
> Filip

Be sure to closely check all your software providers information. The good news
is that stereo support in applications is getting easier all the time - so, with
mddisplay (http://www.structbio.vanderbilt.com/~cmoth/mddisplay) , we were able
to generically support stereo on Windows, Linux, and newer SGI hardware with no
source code changes whatsoever.

My current workstation is a dual Xeon DELL workstation, running Linux, with a
high end NVIDIA Quadro card that supports hardware stereo. Compared to an older
SGI (which is not fair at all to SGI), the stereo is stunning.

But, we still use an older program "psshow" for a lot of work in the lab - and
that requires a trip to the SGI to run.

Choice of CRT monitor is very important too. I happen to use an SGI monitor
with my DELL workstation. It has a refresh rate sufficient to keep each eye
properly updated. That's important. Other workstations in our lab use higher
end flat screen SONY CRTs. Again, do your homework. Specs are changing all the
time.. Go with a monitor tested by your stereoglasses/emitter vendor - it will
cost you a few hundred $ more than an off-the-shelf monitor - but is a requisite
expense.

MOE runs in stereo very well on my Linux workstation. Chimera is OK... but at
least in the version I have you have to tell it about stereo at startup - which
is a bit clunky. Dino displays stereo fine on my workstation.

Hope that helps.

Chris

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