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Some programs, scripts and hacks I use ...
If you have any good ideas for improvements, or spot any bugs in the following, let me know and I will try to implement/fix them
Disclaimer
I am not a programmer and this code is certainly not bug proof. It is provided in good faith but with no warranties whatsoever. If, for any reason, you feel that you cannot take responsibility for any damage the use of this code might cause to your hardware, software, data or sanity, then do not install it.
Program/script/hack Installation/usage Description
aline Please read aline A WYSIWYG perl/Tk protein sequence alignment editor for editing and producing marked-up publication-quality sequence alignments
pdb-mode.el Please read pdb-mode A pdb-mode for the Emacs editor. It provides a number of functions of use to people who often manipulate pdb files. Works with with GNU Emacs and Xemacs.
topdraw See TopDraw A WYSIWYG Tcl/Tk application for sketching protein topology diagrams. See TopDraw
plt2mol.pl Save in your path and make executable.
plt2mol.pl < infile.oplot
Converts an oplot object to the molscript external objects interface format. Lets you get electron density into molscript easily.
prodrg-mode.el Please read header of lisp file:prodrg-mode A prodrg-mode for the Emacs editor. It allows one to do ascii sketches of small molecules suitable for submission to the PRODRG server, which will calculate three-dimensional coordinates. Works with XEmacs and GNU Emacs.[pretty much obsolete now - use the molecule drawer on the prodrg page]
aln2als Save in your path and make executable.
aln2als input-file output-prefix
A perl script which will take a Clustal, Multalin or MSF format and produce input for alscript (a .blc file and a .als file). The .als output produces an alignment shaded by similarity. It is designed to provide a starting point for further customisation. Obviously, alscript is required to produce alignment diagrams. [has some issues with misunderstanding clustal format. Use aline instead - see above]
pdbget Save in your path and make executable.
e.g. pdbget 1hh1
A csh script to copy a pdb file to the current directory. It tries 2 local archives first and if they fail, goes online. Requires wget.
3dm2omap.pl Save in your path and make executable.
3dm2omap.pl [-r] [-o] file.3dm
A perl script to convert X-PLOR 3DMATRIX files to OMAP format. Calculates grid parameters and then uses MAPMAN (Gerard Kleywegt; http://xray.bmc.uu.se/usf/mapman_man.html) to convert the files
xpand_cns.pl Save in your path and make executable. Expand non-crystallographic symmetry from CNS ncs.def file. Requires XPAND (Gerard Kleywegt; http://xray.bmc.uu.se/usf/xpand_man.html)
brute.omac Save in your working directory.
In O, make sure your molecules of interest are loaded and type
@brute.omac 
and follow the prompts
An O macro which recruits lsqman (must be in your path) to do a brute force superposition based on the first chain found in both molecules. Saves a lot of retyping lsq_exp commands.
h3.sym,h32.sym Place in your odat/symm directory O-style symmetry operator files for the hexagonal settings of the rhombohedral spacegroups (H3, H32 rather than R3 R32)
grid2xplor Save in your path and make executable.
grid2xplor < infile.kont > outfile.xmap
A little expect script so that one can automate the K2F program supplied with grid, to convert GRID format maps to X-PLOR format.
reicon and retitle Save in your path and make executable.
reicon Cheese
retitle Gorgonzola
Little scripts to change icon name and window title on X-windows systems. No magic, just some control characters