My software notes

May 12, 2007

PyMOL starts to support .MOE file by 1.00beta23

Filed under: pymol/ molmol — kpwu @ 3:18 pm

News from PyMOL mailing list:

This message is for PyMOL users who also use the Molecular Operating
Environment (MOE), a commmercial molecular modeling package published by the
Chemical Computing Group (CCG).

Incentive builds of PyMOL 1.00beta23 include the latest version of what will
hopefully prove to be a broadly useful capacity for reading .MOE files in

The basic idea is that you can do all sorts of fancy molecular calculations
in MOE (an expert package) and then easily share those results with your
non-computational colleagues via PyMOL session files, shows, or rendered
movies simply by reading your .MOE file into PyMOL.

The way it works is that each .MOE file becomes a group object in PyMOL
containing multiple objects with each of the individual chains and graphics
you have defined in MOE. PyMOL then attempts to mimic MOE appearance as
much as practical. Note that multiple .MOE files can be loaded into a
single PyMOL session, enabling you to combine and display results from an
assortment of related calculations.

Current PyMOL sponsors are welcome to download and try this build (1.00b23)
from using the access credentials provided on
their latest invoice receipt.

Please let us know how well it works with your own .MOE files — we
absolutely need more feedback on this feature! If you do experience
problems, please send us your (non-proprietary!) .MOE files for
troubleshooting and test-case development.


PS. Although the PyMOL .MOE reader itself is not open-source, PyMOL session
files and shows containing converted MOE content can be opened by
open-source PyMOL builds.

PPS. If you’re not familiar with MOE,
— though it is proprietary, it has a very open architecture, well-suited
for methods development.

PPPS. Maestro users, stay tuned… dot-MAE is next as soon as .MOE reading
proves stable and complete.

DeLano Scientific LLC
Subscriber Support Services

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