MROTATE(1U)CSF

NAME

mrotate - MidasPlus delegate for interpolating between orientations

MIDAS COMMAND SYNTAX

Command: delegate start mr mrotate

DESCRIPTION

     Mrotate is a MidasPlus delegate that generates MIDAS
     commands that transform models from one orientation to
     another.  The standard way that mrotate is invoked is for
     the user to start a MIDAS session, and issue the MIDAS
     command
          delegate start mr mrotate
     which runs mrotate and tells MIDAS to pass commands
     beginning with mr through to mrotate for further processing.
     The complete set of commands that mrotate can handle are
     described in the COMMANDS section of this manual page.

EXAMPLE

A few typical uses of mrotate are demonstrated in this section. It is assumed throughout this section that the standard PDB file 1alc (A-lactalbumin) has been opened for display in MIDAS as model 0 and is the molecule of interest for transformation purposes.

Setting up

     The first thing is to start the mrotate delegate with the
     command:
          delegate start mr mrotate
     You should receive a reply indicating the delegate started
     normally.  After issuing the above command, all commands
     prefaced with mr will be handled by the mrotate delegate,
     while other commands will be processed by MIDAS.

Taking snapshots of orientations

     To save an orientation as a potential endpoint of
     interpolation later, use the command:
          mr snapshot s1
     The s1 in the above command is the name that is assigned to
     the orientation; the name will be used in interpolation
     commands later.  To save another orientation, move the model
     around using the mouse and issue the command:
          mr snapshot s2

Interpolating between orientations

To interpolate from orientation s1

to s2, use the commands: reset s1 mr interp s1 s2 0 The reset command puts the model back into orientation s1. The interp command makes mrotate generate a series of MIDAS commands which will transform model 0 from orientation s1 to orientation s2. Note that model 0 must be the only model selected, and that it must already be in orientation s1 when the command is given. To save the generated MIDAS commands in file com, use the command: mr store com s1 s2 0

Finishing up

     To terminate the mrotate delegate, use the command:
          mr stop
     All saved snapshots will, of course, be lost.

COMMANDS

     When mrotate is acting as a delegate for MIDAS (as shown in
     the DESCRIPTION section), the user can give it commands by
     typing
          mr mrotate_command
     in the MIDAS command window.  The list of commands is given
     below in alphabetical order.

interp from to n

Generate the command to interpolate model n from orientation from to orientation to. This command assumes that model n is already in orientation from. If models other than n are selected, they will also be affected by the rotations and translations that mrotate generates.

snapshot name

Take a snapshot of the current orientation, and associate name with it. The standard MIDAS command: savepos name is also executed automatically so the orientation may be recovered later in MIDAS using the command: reset name Note that only the orientation (i.e., the atomic positions) are saved; other attributes, such as colors and whether atoms are displayed are ignored. Name may be used in later interp and store commands as either the from or to orientation.

stop Terminate the delegate.

store filename from to n

This command does exactly the same thing as interp except the MIDAS commands are appended to file filename instead of being sent to MIDAS.

BUGS

Makes too many assumptions about where models are in MIDAS.

SEE ALSO

MidasPlus User's Manual