When you start Moilin outside Oscail it always
starts up with the screen blank and the jobname set to ptest and
the path set to c:\moilin\scratch.
To build molecules click Bu on the toolbar
and click the centre of the screen.
Clicking OK will build methane and clicking a H atom will allow the structure to be extended..
You can also load molecules from the
library.
Short Description of overall strategy.
Móilín Stand-alone When Moilin is started outside Oscail it
always starts up in the Moilin scratch folder with the jobname set to ptest and
all atoms purged. This scratch folder is initally set to \moilin\scratch but may be
altered in Moilin. The simplest strategy is to build into (or load existing
molecules into) the ptest job and then to use the Save Current Job As option to
save any molecule created.
Móilín Under Oscail Under Oscail
the same approach is possible if the Ptest Moilin Scratch option is
selected in Oscail before Moilin is started.
General Operating Principles
Moilin starts in Display mode in which the model may be rotated using left click
and drag or the cursor keys (shift left-right cursor = Xrot).
When the program is idle in Tinker, Build, Mopac, Firefly or Iconc modes a
right click will return to Display mode.
It is also possible to rotate the molecule(s) in most modes by left clicking a clear area of the screen and then clicking and dragging the mouse. An exception here is the geometry function in build mode. While this is active (the stop sign is red) the molecule will not rotate.
The best way to learn how to use Moilin
is to look at some of the tutorials and then try to emulate one of the examples
which is close to what you would like to do.
More Details
Móilín is a molecule builder and viewer which acts a front end for Tinker,
Mopac, Orca, Firefly (Formerly PC-GAMESS) and Iconc.
Tinker provides Molecular mechanics modelling. Tinker 7.1 can be obtained
from http://dasher.wustl.edu/tinker/.
or from here.
Mopac provides semi-empirical M.O. calculations (AM1,
PM3 etc.) and MO plots.
Orca is a very powerful free quantum chemistry package and it is strongly
recommended it should be installed in C:\orca.
Iconc provides extended Huckel calculations and permits modelling of some
transition metal compounds.
Firefly provides semi-empirical M.O. calculations (AM1,
PM3 etc.) and high-level HF and dft orbital plots are provided for B3LYP 3-21G
and B3LYP 6-31G. Firefly 8.0.1 can be obtained from
http://classic.chem.msu.su/gran/gamess/.
Mopac and Iconc are supplied in the Moilin download.
It is possible to build and optimize molecules using mouse clicks.
Moilin is very easy to use.
There are two versions of Móilín version X and version 9.
Version X may be started stand alone or using the M button on the Oscail
toolbar. Version 9 is started from within Moilin-X Version X is easy to use, has rendered graphics, high
quality hard copy, automatic dihedral angle scan and connections to Tinker,
Mopac, Orca, Firefly and Iconc. Version 9 has
simpler faster graphics, optimisation using Tinker and more advanced molecule handling features e.g. it can move
molecules relative to one another do molecular fitting, origin shift and axes display. It is important that crystallographic operations are kept separate from Moilin operations.
The software makes an effort to avoid problems. Moilin will examine the current directory contents on startup and will refuse to start if
(a) the Library directory is in the path or
(b) the directory contains only crystallography files.
Moilin will overwrite INS files in the current directory by default. If you use Oscail and FORMATS to generate
an input file for Moilin from an INS file a new directory is requested to try to prevent problems.