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QM and QM/MM calculations setup for UCSF Chimera

Home Page: http://tangram-suite.readthedocs.io/en/latest/tangram_qmsetup.html

Python 100.00%

quantum-chemistry graphical-interface ucsf-chimera

tangram_qmsetup's Introduction

Tangram QMSetup

A Chimera GUI extension to create Gaussian input files.

License

A fork of ebsel is distributed with QMSetup, which in turn uses data from BSE.

The Role of Databases in Support of Computational Chemistry Calculations
--Feller, D.; J. Comp. Chem., 17(13), 1571-1586, 1996.

Basis Set Exchange: A Community Database for Computational Sciences
--Schuchardt, K.L., Didier, B.T., Elsethagen, T., Sun, L., Gurumoorthi, V., Chase, J., Li, J., and Windus ; T.L. J. Chem. Inf. Model., 47(3), 1045-1052, 2007, doi:10.1021/ci600510j.

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tangram_qmsetup's Issues

"molecule changed" triggers get stuck after GUI closing

Default spin value

Spin value in the entry Spin is the multiplicity (2S+1 where S is the spin).
So, minimal value is 1.

ONIOM layers selection preview

Use different depictions for H, M and L layers when the Layers & Flex dialog is open with ONIOM method enabled.

H: repr bs
M: repr stick
L: repr wire, with thin ribbons (or none)

This could be toggled on or off with a dedicated checkbox.

JSON exports do not consider layers

Layers/freeze state dict use chimera.Atom objects as keys, which cannot be serialized to JSON. We can either change the key o modify the JSON dumper.

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