Dear Lloyd,
We also use Molecular Dynamics Image Space--and have recently upgraded on an Indigo II SGI-based IRIX 6.5 operating system.
It was a highly complex upgrade process--I required a lot of help from the IT people here and at MD.
What are the specific problems you are encountering?
some things to keep in mind (although you probably have already checked this out):
Are you using a GPIB-SCSI-A box (with NI-488M software for IRIX 5.3 and 6.2) to connect the the INDY? 
Which INDY are you using? do you even need a GPIB-SCSI-A box at all?
Which OS version are you using?
Who have you spoken to at molecular dynamics?
I have worked extensively with Deb Timberlakes with the scanning division at Molecular Dynamics. She has been very helpful--try her at (800)743-7782.
Feel free to contact me directly if you have any questions, but try Deb first (she may just remember my name if you mention it!).
Good luck,
Laura

Laura M. Patrone, Ph.D.
Wyeth-Ayerst Research
Investigative Pathology
641 Ridge Road
Chazy, NY 12921
(518) 846-6318
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>>> Lloyd Donaldson <[log in to unmask]> 06/11 4:19 PM >>>
Dear List Members

Are there any Molecular Dynamics Image Space users out there who may be able to
help us. We recently upgraded the operating system on our INDY but were unable
to reinstall Image Space. The Setup module refuses to run. MD seem to no longer
offer support on this software other than to tell us it should work under the
new OS. If you can help please contact me off the list. Thanks

Lloyd Donaldson
Forest Research, Rotorua, New Zealand