[83] in Software_Announce
Rasmol 3d molecule viewer
daemon@ATHENA.MIT.EDU (Alex T Prengel)
Mon Oct 16 12:27:43 1995
To: tidor@MIT.EDU, gerd@lanai.MIT.EDU, rutledge@MIT.EDU, stern@MIT.EDU,
ccummins@MIT.EDU
Cc: facdev@MIT.EDU, nschmidt@MIT.EDU, cfyi@MIT.EDU, software-announce@MIT.EDU
Date: Mon, 16 Oct 1995 12:24:47 EDT
From: Alex T Prengel <alexp@MIT.EDU>
I have installed Rasmol, a 3d molecule viewing utility, on Athena. Rasmol
can read molecule descriptions in a number of standard formats and will
display a 3 dimensional image which the user can rotate and display in
a number of different ways. To run it, do:
add rasmol; rasmol <format> <molecule description file>
at the Athena prompt. The default format is Brookhaven Protein Databank (pdb)
and there are a couple of samples in the data directory in this format. To
run them, do something like rasmol /mit/rasmol/data/1crn.pdb at the Athena
prompt. There are two samples in other formats; to run them, do
rasmol -alchemy /mit/rasmol/data/asprin.alc and
rasmol -mdl /mit/rasmol/data/M27.mol
There is lots of documentation- a man page (man rasmol), a users's guide
in PostScript form (/mit/rasmol/manual.ps), a paper about Rasmol (paper.ps),
a "quick reference" command summary (refcard.ps) and an html version of
the manual with hyperlinks (the latter can be viewed with a Web browser
in local mode - load file /mit/rasmol/doc/rasmol.html).
Rasmol operates in two modes- a "GUI mode" whose commands are accessed
through pull-down menus in the GUI it will pop open, and a
command-line mode (commands entered at the RasMol> prompt in the
background window). Both of these modes are active concurrently.
The instructions state that if a copy of the Brookhaven PDB database exists
locally, setting the environment variable RASMOLPDBPATH to point to its
home directory will allow rasmol to access the molecule description files
in the database. I could not test this since I am not aware of any local
copies. Let me know if there are any and if so, if this feature works.
I have run into a couple of glitches, some of them documented in the
release:
The print command does not work (documented). Work around: output to
PostScript, and print the output using the lpr command.
There are a number of toggle states but the pull down menus do not appear
to show the state of the toggle; some toggles only seem to work once and
cannot be reversed (Options->Hydrogens for displaying Hydrogens or not).
The help pull-down menu selections don't appear to work, but the help
command does work in command-line mode (try "help commands" to get started).
Let me know if you run into other glitches or configuration problems. I
hope this utility will assist you in your teaching! Many thanks to
Professor Larry Stern for pointing me to it.
Alex Prengel, Jr.
Academic Computing Services
Software Acquisition Coordinator
