| 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 |
