MAKEMS(1U)CSF

NAME

makems - MidasPlus delegate for convenient generation of molecular surfaces

MIDAS COMMAND SYNTAX

Command: delegate start ms makems

DESCRIPTION

Makems is a MidasPlus delegate that takes an atom specification and then generates and displays the corresponding solvent-accessible molecular surface. Makems only works correctly when surfacing a single model; it cannot correctly surface multiple models. If multiple models are present when makems is asked to surface a particular model, the requested model will be surfaced as if the other models did not exist.

     The standard way that makems is invoked is for the user to
     start a MIDAS session, and issue the MIDAS command
          delegate start ms makems
     which runs makems and tells MIDAS to pass commands beginning
     with ms through to makems for further processing.

Any text sent to makems is interpreted as an atom specification to be surfaced. Makems will compute the surface by invoking dms(1) (with default dms settings) and then display the computed surface in MIDAS. Any surface previously computed by makems will be closed first.

EXAMPLES

Some simple examples (the examples assume that makems was invoked as shown in the SYNTAX section above):

ms :CYS

Surface all cysteine residues.

ms

Surface the entire molecule.

ms /color=green

Surface all atoms currently colored green.

BUGS

As mentioned in the DESCRIPTION section, makems only surfaces one model. If the atom specification given to makems spans multiple models, the lowest-numbered one will be surfaced.

AUTHOR

Dr. Sherri Newmyer

The Scripps Research Institute

10550 North Torrey Pines Road

La Jolla, California 92037

newmyer@scripps.edu