science software (mol biol/biochem/biology) under Linux
zinc at zifi.genetics.utah.edu
Fri Oct 4 17:41:22 EST 1996
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i'm attempting to compile a list of software that either people have
claimed runs under Linux or that is known to run under Linux for the
people at Caldera (Caldera is Ray Noorda's ( of Novell fame ) new
here is my list so far. if people have additions i'd love to have
them. it would be nice if you could include a brief description or a
URL pointing to a web page with a description. also, a URL for the
source or binary executable would be super..
- -patrick finerty
biochem grad student, u of utah
a lot of these are in FORTRAN so how well they compile is probably due
to how good the fortran support on a system is...
something called VMD (Visual Molecular Dynamics) is almost ported:
fortran source, got it from
available on sunsite, also available here:
it _is_ possible to compile this for 16 bpp display, i've done it and
used it a lot myself. you just have to change the Makefile to use
- -DSIXTEENBIT instead of -DEIGHTBIT or -DTHIRTYTWOBIT
also in fortran (crystallographers love fortran). have to sign a
license to get source but not for binaries...
it looks like binaries are avail for Linux...(according to the above
licensed for a small fee to academics...
obtain source from:
this is more fortran fun and games. it seems to compile almost but i
haven't tried to use it yet...
i searched all over for this - couldn't find the source! only a ton
of damned html manuals. a post to bionet.software is in order...
i heard the GAMESS programs compile under Linux but i did not try them
as you have to go through a little effort to get them...
site license is free to everyone but must sign a form...
Entrez/Cn3D from ncbi
database searching tools (for remote database queries)
the ncbi package...
linux binary of the network database search tools:
this requires the network Entrez program to be configured, get a linux
binary here: ftp://ncbi.nlm.nih.gov/entrez/network/linux.tar.Z
used default makefile but changed THR_CC= to be blank.
then make sall
RNA folding related software:
Viena RNA package:
compiles fine under Linux but Makefile needs tweaking (hell, i managed
to get it to work...)
this compiles fine under Linux
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