The Datafile PD-CD 5/DATAFILE_PDCD5.iso/rasmol/scipts/dna3/!DNA3/DNA3_TXT

Text File | 1996-04-12 | 8KB | 185 lines

This document has the following sections:

INSTALLATION OF RASMOL SCRIPT
OPERATION OF SCRIPT
SCRIPT SPEED/PACING/TIMING
SCRIPT REVISION HISTORY

This script is distributed from the RasMol Home Page,
http://www.umass.edu/microbio/rasmol.
Look there for updates and other scripts.

Most scripts are available in two versions.  One runs
unattended, continuously.  The other contains pauses
('press any key to continue') and is intended to
illustrate a lecture.

Installing and running a script is really quite simple.
However, the first time you do it, there are a few
details which might not be obvious.  This document will
help to make your first script-running experience
smooth and easy.  Once you have run a script, you'll
be able to re-run it or run other scripts quite easily.

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INSTALLATION OF RASMOL SCRIPT

MACINTOSH, UNIX

Detailed, optimized installation instructions for these
operating systems are not available at this time.  If
you can provide such instructions, please send them to
[e-mail].

For the MacIntosh, you can either download the
self-extracting archive DNA3.SEA.HQX (if
available), or use ftp to 'mget *' all the files of the
script.  (Precede the ftp command 'mget *' with
'prompt' to toggle off interactive prompting; that is,
so ftp won't ask you to confirm the transfer of each
and every script file.)  If the script files are put in
the same folder as the RasMac program, the script will
run.  This works, but may not be ideal because multiple
scripts will mix hundreds of files on one folder.  If
you know how to get RasMac to run a script in a different
folder, please email details to [e-mail].

WINDOWS/DOS

Each script consists of a top level script plus many
subscripts and some PDB files.  It is therefore
advisable to install each script in a separate
subdirectory. For example, assuming you have installed
the RasWin program files in C:\RASWIN, the script DNA3
could be installed in C:\RASWIN\DNA3.

To do this, copy the packed file DNA3ZIP.EXE into the
desired subdirectory, and then run it as a DOS program
at the DOS prompt (which will unpack it).

Now, in Windows, with the RasWin icon selected, select
File, Preferences, and change the Working Directory to
the one containing the unpacked script files.  (If you
want access to RasWin's built-in help, you must also
copy RASWIN.HLP into the working directory.)

If you have several scripts, you may wish to create a
separate RasWin icon for each.  This would enable you
to change scripts smoothly during a lecture, without
repeatedly reconfiguring one icon's working directory.
With the RasWin icon highlighted, select File, Copy.
Now use File, Properties to change the working
directory to the one for the script, and the
Description (which will appear under the icon) to the
script name.  Thus you will end up with a
script-name-labeled RasWin icon for each script.

If you wish, you can even configure the Properties to
run the script automatically when the icon is
double-clicked.  To do this, put '-script dna3.top'
after RASWIN.EXE in the Command Line slot of the
Properties box.  [WARNING: there is a bug in RasWin
beta 2.6. Scripts started in this way terminate at the
first pause, returning the RasMol> prompt.  Therefore,
scripts will have to be run manually, with a 'script
dna3.top' command in the command window, until this is
fixed.]

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OPERATION OF SCRIPT

If you can provide details for Macintosh or Unix, please
send them to [e-mail].  However, the
principles are very similar in all operating systems.

Run RasMol.  (Under Windows, double-click on the RasWin
icon.)  If the black RasMol graphics window extends to
the bottom of the screen, move and reshape it so that
it fills the top 5/6 of the screen, leaving the bottom
1/6 uncovered.

The major problem beginners have is not being able to
find the RasMol Command Line window.  When you run
RasMol, a black window will open entitled "RasMol
Version N.N", with pull-down menus named File, Edit,
Display, Colours, Options, Export, Help.  This is the
graphics window.  (For a tutorial on how to use RasMol,
see the web site http://www.umass.edu/microbio/rasmol,
and look under classroom/education.)

A separate, second window, the Command Line Window, is
also opened when you run RasMol.  Under Windows, the
Command Line Window starts out minimized to an icon
near the bottom of the screen. If you can see the icon,
click on it to open it.  If you cannot see it, under
Windows, use Alt-Tab to cycle through all the windows
until you find one titled "RasMol Command Line" --
then release the Alt key to open the window.  The
Command Line Window is white.

Once you have the Command Line Window open, move it so
that its bottom lines up with the bottom of the screen.
Press Enter until the 'RasMol>' prompt is repeated all
the way to the bottom of the Command Line Window.
Arrange the two RasMol windows so that when the black
graphics window is in the foreground, exactly seven lines
of 'RasMol>' prompt are visible in the portion of the
white Command Line Window which shows below the black
graphics window.  These 7 lines will display the script
captions when the script is running. (The 7th line will
always be blank, so there are actually a maximum of
6 lines of caption text.)

DNA3.TOP is the top-level script. Start it by typing
'script dna3.top' in the RasWin command line window,
then pressing Enter.

This script pauses frequently, waiting for the lecturer
(or student) to press the space bar to proceed.  It is
designed to permit rotation of images with the mouse
during pauses.  In many cases, it restores the
orientation of the molecule after pressing the space
key to continue.

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SCRIPT SPEED/PACING/TIMING

Script execution speed is affected by the speed of your
computer, the speed of your graphics card, the screen
resolution, and the size of the RasWin graphics window.
Starting with a full-screen graphics window, you can
speed up execution by reducing the resolution from 1024
x 768 to 800 x 600 to 640 x 480 pixels.  Under Windows,
this is usually done with a SetRes (or related) icon in
the Windows Control Panel.  Further increases in speed
can be obtained by reducing the size of the graphics
window (to less than full-screen).  Quick previewing of
scripts can be done very quickly in a tiny graphics
window.

Windows: RasWin32 beta 2.6 (the 32 bit program) is
several times faster than RasWin 2.6 (the 16 bit
program).  To run RASWIN32 you may need a Windows
accessory package which is provided free by MicroSoft.
For details see:

http://www.umass.edu/microbio/rasmol/getras.htm

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SCRIPT REVISION HISTORY

Revised 4/12/96.  One cytosine in the 19-base-pair
segment in this crystal was rotated 180 degrees from
the normal position.  (If anybody knows why, please let
me know.)  Naturally, this is the one I picked
originally to show hydrogen bonding! A GC pair at a
different position is enlarged in this revision so that
the hydrogen bonding is normal.  Also, the dATP was
inadvertantly shown as ATP (ribose instead of
deoxyribose); this is now fixed (thanks to Jose
Fernandez Fernandez).

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-Eric Martz
[e-mail]