Linux mol-bio/biochem software - a list. please mail additions

zinc zinc at
Mon Oct 7 00:43:23 EST 1996


here's the current list.  i spent most of today at the console
screwing with damned FORTRAN compilations - not something i enjoy.
anyway, thanks to the following people for their additions:

francis at (B.F. Francis Ouellette)
Ashok Aiyar <aiyar at>
gilbertd at (Don Gilbert)

i will be converting the file to html some point this week.  since i
am having a difficult type focussing at this time, it will have to
wait.  if anyone tests this code and finds my observations to be
mistaken, please mail me (i'm sure you will :) ).

also, the text file is available from my web page, just not in html.
see for a link.

- -patrick finerty
biochem grad student, u of utah


this site seems to have a lot of stuff: 

this web pages lists quite bit of software as well:

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...

if i mention that i compiled or tested any of this stuff you might
want to know my system config.  generally, i keep zifi very
up-to-date, using linux/Documentation/Changes as a guide.  

here is my current config:

		Linux 2.1.1
		libc 5.4.7
		gcc 2.7.2
		g77-0.5.18.bin.tgz installed
something called VMD (Visual Molecular Dynamics) is almost ported: 


Molden	- Molden is a package for displaying Molecular Density from the
	  Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and
	  the Semi-Empirical packages Mopac/Ampac
	- main program is in fortran X-win driver in C

info at

this compiled and ran on my system using the g77-0.5.18.bin.tgz
package from sunsite.  it took a ton of memory to compile - about 25
MB at one point so you should have some serious swap space or if asked
i'll make a binary available (my libc is prob too recent for most
people).  if you install the g77-0.5.18.bin.tgz package be sure to
link g77 to f77 because that's what make tries to use.  pretty cool. 

RasMol	- displays pdb files, writes a variety of output formats.
	- current version is 2.6beta, written in C

i have used the beta version extensively under Linux.  it works like a
charm.  i did not encounter any bugs.  to compile for a 16 bpp
display, you must hack the Makefile produced with xmkmf.  change this
have luck just changing the value in rasmol.h as per the INSTALL

MOLMOL	- MOLMOL is a molecular graphics program for displaying,
	  analyzing, and manipulating the three-dimensional structure
	  of biological macromolecules, with special emphasis on the
	  study of protein or DNA structures determined by NMR
	- version 2.2.0

requires motif to compile and ksh shell to run the script.  a binary
is available on sunsite (or mirrors). the binary works just fine on my
system.  if you use the binary, you also need to get the
molmol-2.2.0-doc.tgz file as well. be sure to move the binary to the
same place the doc files were unpacked.  run the install script and
then run the molmol script.

XtalView- XtalView is a complete package for solving a macromolecular
	  crystal structure by isomorphous replacement, including
	  building the molecular model.
	- version ?, 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
page) but i didn't try to get any.

WhatIf	- WHAT IF is a versatile protein structure analysis program
	  that can be used for mutant prediction, structure
	  verification, molecular graphics, etc. 
	- version ?, in FORTRAN

licensed for a small fee to academics...

Procheck- Checks the stereochemical quality of a protein structure,
	  producing a number of PostScript plots analysing its overall
	  and residue-by-residue geometry.  
	- version 3.4.3, written in FORTRAN

obtain source from: 

this is more fortran fun and games.  this would not compile with g77
as i ran out of memory at about 70 MB...

however, using the f2c package it compiled.  it seems to work ok.

another note, it took a really, really, really, really, long damned
time for 'clean' to compile.  i just went home...

MOPAC	- you have to order this or something.  i couldn't find source
	  or much info.  any WWW search will bring up a ridiculous
	  number of online html manuals though.

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...

US version
GAMESS	- The General Atomic and Molecular Electronic Structure
	  System is a general ab initio quantum chemistry package.
	- version ?, written in ?

site license is free to everyone but must sign a form... 

UK version
GAMESS	- GAMESS--UK is a general purpose ab initio molecular
	  electronic structure program for performing SCF- and
	  MCSCF-gradient calculations, together with a variety of
	  techniques for post Hartree Fock calculations. 
	- version ?, written in ?

stuff from ncbi

database searching tools (for remote database queries)

the ncbi package...

linux binary of the network database search tools:
this includes blastp, blastn, tlbastn, tblastx etc.  works like a
charm under cron control for regular database searching...

this requires the network Entrez program to be configured, get a linux
binary here:

sequin	- ncbi's "new" sequence submission/editing tool
	- version ?, written in C

this compiles and runs just fine on my system.

fasta	- database search tool
	- version ?, written in C

used default makefile but changed THR_CC= to be blank then 'make
RNA folding related software:

Viena RNA package - various calculations of RNA structure
	- version 1.1b, written in C

compiles fine under Linux but Makefile needs tweaking (hell, i managed
to get it to work...)

naview	- An improved algorithm for the display of nucleic acid
	  secondary structures 
	- version ?, written in C

this compiles fine under Linux but i haven't used it.

SeqPup - sequence editor and analysis program.  includes links to
	 network services and external analysis programs.
	- version ?, written in C, binary provided

does not seem completely stable...

tacg	- restriction site analysis program
	- version ?, written in C

works on plain text files with sequence in them...

source code compiled fine.  the provide binary in the bin dist is
a.out (QMAGIC).

SignalScal - scan for transcription factor binding sites
           - version 4.07, written in C, compiles fine

this works great on my system...
it's a good idea to read this file: 

PIMA	- pattern induced multiple sequence alignment
	- version 1.40, written in C, compiles fine

passes builin tests just fine after compilation.

Predator - structural prediction based on multiple alignments
	 - version 1.0, written in C, compiles fine

output on my Linux box was identical to output on an SGI using the
precompiled binary for IRIX and the binary i compiled.

ClustalW - pairwise and multiple alignments
         - version 1.60, written in C, compiles fine

tested it, works fine on my Linux system.

Seqsee - protein sequence analysis package
       - version 1.2, written in C, compiles fine
       - available upon request from
	 seqsee at

Pratt	- pattern discovery in sets of unaligned sequences
	- version 2.0, written in C, minor changes

this segfaults but only apparently after a run has finished.
otherwise appears ok...


Primer3 - PCR primer design
        - release 0.1, written in C, compiles fine

all tests passed just fine on my system.

GDE	- genetic data environment
	- release ?, written in ?
	- gopher:// 

binaries are a.out (ZMAGIC), requires (a.out) xview libraries. 
i tried to compile this myself but not very hard - it wouldn't work.


- -- 
"Those that give up essential liberty to obtain a little temporary
 safety deserve neither liberty nor safety." -- Benjamin Franklin (1773)
			  finger for PGP key
zifi runs LINUX 2.1.1  -=-=-=WEB=-=-=->

Version: 2.6.2
Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface


More information about the Bio-soft mailing list