C643: Introduction to the Molecular Visualization Facility


StereoView Room


The Role of a Molecular Modeling Specialist

Molecular Modeling is an experimental technique, similar to "wet lab" techniques.

Unlike other experiments, molecular modeling will always generate a result. In fact, the generation of a result has become very easy with modern molecular modeling software. Yet theories and strategies have also become more complex, requiring the expertise of a molecular modeling specialist to judge the result:

  • Have proper techniques been used (is the result accurate?)
  • Have proper controls and control experiments been used (is the result reliable or significant?)
  • Are there limitations:
    • If not all possibilities are calculated, has the modeler searched enough of parameter space?
    • If the results depend on a basis set, has the modeler limited the modeling to a parameter space that is too small?
Therefore, the result depends as much on the quality of the modeler as the quality of the technique. This course is designed as an introduction to more specialized molecular modeling techniques for those who want to investigate particular molecular modeling methods in greater detail.


Molecular Visualization is the process of interpreting molecular models.

Four Types of Visualization Models:
  1. simplification
  2. didactical illustration
  3. analgization
  4. mathematical description


Computing

Molecular Modeling has been paced by three developments:

Why use UNIX workstations?

  1. UNIX workstations are easier to program and support
    Workstation Relative Cost (time & resources)
    Programming Support
    UNIX 1 1
    WINTEL 3-5 2
    Mac 6-10 10

  2. UNIX workstations have historically been used for scientific computing. Many molecular modeling applications run only on UNIX workstations.

  3. WINTEL workstations now meet or exceed many of the specifications & benchmarks for particular parts of a desktop UNIX workstation. One exception is graphics performance---SGI workstations are still faster (although the gap between WINTEL and SGI workstations continues to decrease).

  4. The INTERACTION of the parts of a workstation is still MUCH faster with UNIX workstations than with WINTEL workstations.

  5. In my opinion, server-client computing will continue to be dominated by UNIX servers and WINTEL clients. The middle ground of high-end clients and low-end servers will continue to be a mixture of UNIX and WINTEL workstations.


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Last updated: 01/23/2001