MAID: an automated map-fitting
routine. Copyright David G. Levitt, 2000.
MAID by David Levitt at the
University of Minnesota uses torsion angle molecular
dynamics for automated building of the amino acid sequence
of a protein into an electron density map and is described
new software routine that automates the fitting of protein
X-ray crystallographic electron density maps." D. G. Levitt.
(2001). Acta Crystallogr. D57, 1013-1019.
research now focusses on pharmacokinetics, with David's
permission MAID can be obtained below.
- MAID runs best on a 64 bit computer and, although you can run it on a 32 bit machine, it tends to stop prematurely and may not complete all three stages of the model-building process, namely "trace", "extend" and "expand". Therefore it is recommended that you run it on a 64 bit machine with a 64 bit operating system, although you may still get a useful starting model of the structure if you do run it on a 32 bit system. Anyhow, I am confident that the 64 bit version on a 64 bit machine will work as well as MAID used to on an SGI, a long time ago and its a lot quicker!
- There is a simple GUI for running MAID in batch- or background-mode without having to read the manual and this is called MAIDaid. If you run the MAIDaid GUI, you can now ignore the rest of this
paragraph. MAID itself requires the electron density
map to be in X-PLOR/CNS ASCII format and it should be
normalised, i.e. the mean density should be zero and the
RMS density should be 1.0. Maps not already in this format
can be converted using MAPMAN (in the Uppsala suite) or
re-calculated using the PHENIX gui as follows: in the
PHENIX 'Maps' tab, use the 'FFT map coefficients' option
and set 'Map scaling' to 'sigma' and 'Format' to 'XPLOR'.
However, this normalisation is now done automatically
by MAIDaid, whenever needed. MAIDaid will also read
CCP4 maps, convert them to X-PLOR format and normalise
them, as required.
- By default, PHENIX produces a map covering the unit cell
and CCP4 produces a map which covers just the asymmetric
unit. This may or may not give MAID some problems! It may
be better to build a dummy water molecule roughly in the
middle of the protein density and save it as PDB file.
Subsequently using PHENIX or CCP4 to calculate the map
around this water molecule with say a 35 - 40 Angstrom
border may give better results.
This version of MAID can be compiled using most UNIX and Linux
compilers. Follow the compiler directions in the MANUAL to
choose your compiler. (Special thanks to Ralf Grosse-Kunstleve
(email@example.com) for allowing me (DGL) to use the "compiler
Click on the underlined file - and direct it to the directory
Download MAID code, manual and makefile (tar and zipped) by
clicking on: maid_unix_12nov01.tar.gz
In the directory where the
.tar.gz file is located:
Unzip the file: gunzip filename.tar.gz
untar the file: tar xvf file.tar
This will create a new subdirectory glmaid_unix containing
all the files you need to compile MAID.
Read either MANUAL5_word.doc or MANUAL5_word.txt for
instructions for compiling and running MAID.
Newer linux version
A newer linux version which includes the maidaid GUI for starting
the batch version of MAID can be obtained here:
64 bit or here 32 bit (Sep 2015).
Note that the only difference between these two files is that maid and maidaid have been compiled on 64 and 32 bit linux. If it turns out that you need to compile everything from source, either will be fine because the programs themselves are identical in each. Remember that MAID will nearly always work better on a 64 bit system.
To run the program, unzip the files with your linux file manager or as described above, then
go to the linux_maid folder and double-click on the maidaid file icon or
use a terminal window to enter the following command in the
linux_maid folder: ./maidaid
In case of problems, first ensure that both maidbatch and
maidaid are executable i.e. type: chmod u+x maidbatch maidaid
If maidbatch does not work, you can compile it from source by opening a terminal window in
the folder where the program files are and typing "make" noting that you will, of course, need to have 'make' and g++ installed first. It is also fairly easy to compile maidaid by installing the latest FLTK library from the website (www.fltk.org) in the usual unix way (i.e. "./configure", "make", "sudo make install"). It seems to work better if you install FLTK from source in this way rather than getting it via your linux package manager. In the maid folder, open a terminal window and type: "fltk-config --compile maidaid.cxx" to compile maidaid itself. Finally, if the maidaid font size turns out to be too small, installing the X freetype font library (libxft-dev) with your package manager and repeating the FLTK build will help.
Note that this linux version is based on the tweaked one I made
for Windows, so please read the paragraphs below since they give
the general idea of what to do.
David's original code
for the batch version of MAID has been tweaked by myself (J.
Cooper) so that it can be compiled by MinGW and run on Windows.
There is also a basic GUI, which I have called MAIDaid, for
launching MAID without having to read the manual, although there
is an on-screen help button, if needed. The Windows version can
be obtained as a zip file here:
64 bit or here 32 bit (Sep 2015).
The files are within a folder called 'maid' which contains the
original program manual (MANUAL5_WORD.txt and .doc). The easiest
option should be to run MAID using the MAIDaid GUI which you can
start by just double-clicking MAIDaid.exe. You can even make a
neat short-cut to this program on the Windows desktop! However,
please remember that the MAIDaid.exe file must be in the same
folder as maidbatch.exe, which is the batch version of the MAID
program. In the unlikely event that MAIDaid starts OK but stops when you click on
'Prepare files', right-click on the executable and select
'Troubleshoot compatibility' to sort it out. Note, the 'screen'
i.e. interactive version of MAID hasn't (yet) been compiled for
Windows (or Linux).
A folder (test_maps) with a few sample maps in the right format
and the corresponding amino acid sequences is provided for
If necessary, maidbatch can be compiled using g++ in MinGW or MinGW-w64 (as appropriate) and MSYS which provides a
Windows 'make' program (note that GNU make.exe and the 'makefile' are
provided). MAIDaid can be compiled with MinGW or MinGW-w64 (as appropriate) using MSYS, firstly to install FLTK and then to run the
I'm afraid all the people with MACs round here
have left, so I haven't been able to prepare anything, but it
shouldn't be too hard to compile the program using the source
code for the Linux version.
Note that for some reason Coot may not manage to read in PDB files produced by MAID so you may need to renumber all of the residues with a PDB file utility, such as PDBSET, and insert the right the CRYST and SCALE cards. Just type the following in a command shell:
pdbset xyzin input.pdb xyzout output.pdb
cell 55 66 77 90 90 90
with appropriate filenames and values for your crystal symmetry. The residue numbering, etc, can be corrected in Coot later.
As of Aug 2015 I have been able to iron-out a couple of annoying bugs in maidaid so it is a lot more stable on Windows and linux but please let me know how it goes.