MidasPlus Description

MidasPlus is capable of displaying molecular structures and surfaces from information in a PDB format file of atomic coordinates. It uses the program DMS to calculate surface parameters. Ancillary programs such as ribbons, neon and conic display very high resolution graphics. The ribbons program requires the HELIX and SHEET records to be present in the PDB file.

Getting Started

Set up for Midas by typing:

setup midas
 or
source /srv/local/bin/midas.set

Then launch Midas by typing:

midas

There is a large user manual available online and in hardcopy format in the Core.

There are four tutorials to help you learn the commands of MidasPlus.

Tutorial One has you attempt to dock an inhibitor into the active site of a protein, while learning basic MidasPlus commands.

Tutorial Two shows you the commands available in the RibbonJr program for generating a ribbon representation of the molecule.

Tutorial Three shows you the command file structure for using neon a program for generating solid stick bonds and shadows.

A short primer on using MidasPlus

Or you can click on one of the small graphics displays on the previous page for a description of how to make a similar model of your protein.

The MidasPlus home page at UCSF contains a FAQ.

A quick list of things, in addition to the general display of molecules, Midas will do is below:

bs: - generate ball-and-stick style diagram in PostScript
conic: - generate CPK-style molecular models with shadows
density: - Midas delegate for displaying XPLOR format elec-tron density data
discern: - Midas delegate for visualizing multi-dimensional data
dms: - calculate a solvent accessible molecular surface
dnacheck: - regenerate DNA files to match Protein Data Bank specifications
esp: - calculate electrostatic potential
expr-smpte: - evaluate SMPTE expressions
fade: - fade from one Iris image to another
fixatname: - correct AMBER pseudo-PDB files so they are in standard PDB format
fixses: - update pre-MidasPlus 2.0 session files
gennuc: - Generate double helical DNA or RNA structures
gentpl: - generate a MIDAS template from a Protein Data Bank coordinate file
ilabel: - label an IRIS image with arbitrary text
itops: - convert an Iris image file to Color PostScript
ksdssp: - generate HELIX and SHEET records from protein coor- dinates
label3d: - Midas delegate for displaying 3-D labels
longbond: - remove long bonds from structure
makems: - MidasPlus delegate for convenient generation of molecular surfaces
midas: - MidasPlus molecular interactive display program
midas.tty: - terminal based version of MidasPlus display program
mrotate: - Midas delegate for interpolating between orientations
ms: - calculate a solvent accessible molecular surface
neon: - generate a molecular model with solid stick bonds and shadows
noeshow: - show MARDIGRAS format NOE constraints ambershow - show AMBER/SANDER Interface format NOE constraints
pdb++: - A C++ class for manipulating Brookhaven Protein DataBank records
pdb2group: - generate Midas group file from Protein Data Bank (PDB) file
pdb2site: - convert a PDB file into a DMS site file
pdbheader: - extract header records from PDB files
pdbopen: - Midas delegate for browsing and opening PDB entries
pdb_read_record, pdb_parse, pdb_write_record: - read and write Brookhaven Protein DataBank records
ms_read_record, ms_parse, ms_write_record: - read and write Molecular Surface (ms) records
ps2illustrator: - convert midas copy file (PostScript) to Adobe Illustrator format
rainbow: - ``rainbow'' color molecule chains
ribbonjr: - generate ribbon representation of proteins
run2ses: - convert a PDBRUN file into a Midas session
scrcopy: - copy a screen image to a color printer
stereoimg: - produce stereo pair of rendered molecule
stereops2illustrator: - convert a stereo midas copy file (PostScript) to Adobe Illustrator format
uncryst: - generate atomic coordinates from crystallographic symmetry
unmtrix: - expand MTRIX records in PDB files
viewdock: - Midas delegate for browsing DOCK output

Please Note: If you publish a figure using this program please cite the following:

Molecular graphics images were produced using the MidasPlus program from the Computer Graphics Laboratory, University of California, San Francisco (supported by NIH RR-01081).

Last Modified: Wednesday, 21-Aug-2002 10:46:05 EDT