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MAID
 
MAID
MAID builds protein structure into electron-density maps. It does it in a series of sequential steps. The first step is the fitting of the secondary alpha-helix and beta-sheet structures. These `fits' are then used to determine the local amino-acid sequence assignment. These assigned fits are then extended through the loop regions and fused with the neighboring sheet or helix. The program was developed on the unaveraged 2.5 Å selenomethionine MAD electron-density map of a 291-residue protein. A major advantage of the MAID fitting procedure is that it maintains ideal bond lengths and angles and constrains [varphi]/[psi] angles to the appropriate Ramachandran regions. 
Features

    * Works on medium resolution (2.8-2.5A) data.
    * More accurate than textal
    * More complete than resolve
    * Builds polyalanine structure 
    * Builds side chains
    * Detects NCS and expands the model by NCS symmetry
    * Might require 2-24 hours to complete.

MAID runs on Linux and DecAlpha machines s; the executable is in:
/joule2/programs/lx_bin/maidbatch or just type "maidbatch"

The documentation is in /joule2/programs/maid/glmaid_linux/glmaid_linux/MANUAL5_word.txt :

The program is available from: http://www.msi.umn.edu/~levitt/

Reference:
"A New Software Routine that Automates the Fitting of Protein X-Ray Crystallographic Electron Density Maps" D. G. Levitt; Acta Cryst. D57: 1013-1019

Instructions outlined:
1) Make an x-plor format electron density map.
2) Extend the map to just cover the molecule boundaries.
3) If available, make a mask the covers the molecule boundaries and use this mask to cut out electron density from symmetry related molecules. The cookie cutout can be performed using mapman and the 'oper m1 * m2' option.
4) Think of a rootname to describe your molecule.
5) Type: "maidbatch rootname setup", then answer questions.
6) Copy the pdb sequence to rootname.maidpdbsequence
7) Type: "maidbatch rootname complete"
8) Maid will run to completion. You will get 3 pdb files. 1) a mainchain trace (maidfit_trace.pdb 2) mainchain with sidechains ddocked (maidfit_extend.pdb) . 3) ncs expanded model. (maidfit_expand.pdb)