https://github.com/insilichem/tangram
:black_square_button::atom_symbol: A collection of molecular modelling tools for UCSF Chimera
https://github.com/insilichem/tangram
bioinformatics cheminformatics graphical-interface ucsf-chimera
Last synced: 10 months ago
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:black_square_button::atom_symbol: A collection of molecular modelling tools for UCSF Chimera
- Host: GitHub
- URL: https://github.com/insilichem/tangram
- Owner: insilichem
- License: other
- Created: 2017-11-03T17:08:03.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2019-03-26T16:41:42.000Z (almost 7 years ago)
- Last Synced: 2023-10-20T20:24:08.323Z (over 2 years ago)
- Topics: bioinformatics, cheminformatics, graphical-interface, ucsf-chimera
- Language: Shell
- Homepage: http://tangram-suite.readthedocs.io
- Size: 685 KB
- Stars: 16
- Watchers: 5
- Forks: 3
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Tangram Suite
=============
[](http://tangram-suite.readthedocs.io/en/latest/?badge=latest) [](https://github.com/insilichem/tangram/releases)
It\'s composed of several independent graphical interfaces and commands
for UCSF Chimera. Each extension or *tan* has its own separate
repository, as detailed in the list below. The project name is (almost)
always prefixed with *tangram\_* for easy identification.
As installing extensions in UCSF Chimera can be tricky, specially if
external dependencies are required, in this repository we provide [Linux
and MacOS installers](https://github.com/insilichem/tangram/releases) to
handle that for you. More details are provided below. The documentation
will be collected here, as well.
Tangram extensions
------------------
After the installation, a new menu will be available under *Tools*,
called *InsiliChem*.
- **Calculation setup**
> - [MMSetup](https://github.com/insilichem/tangram_mmsetup):
> Setup MD calculations with OpenMM and ommprotocol \[WIP\]
> - [QMSetup](https://github.com/insilichem/tangram_qmsetup): QM
> and QM/MM calculations setup
- **Visualization**
> - [3D-SNFG](https://github.com/insilichem/tangram_snfg): Enable
> easy visualization of saccharydic residues
> - [BondOrder](https://github.com/insilichem/tangram_bondorder):
> Automatic bond order perception for UCSF Chimera \[WIP\]
> - [GAUDIView](https://github.com/insilichem/gaudiview):
> Lighweight visualization of results coming from docking,
> conformational search or multiobjective optimization
> - [TalaDraw](https://github.com/insilichem/tangram_taladraw):
> Build 3D structures out of two-dimensional sketches
- **Analysis**
> - [NCIPlotGUI](https://github.com/insilichem/tangram_nciplot):
> Straightforward interface to setup calculations for NCIPlot
> and visualize them
> - [NormalModes](https://github.com/insilichem/tangram_normalmodes):
> Perform Normal Modes Analysis and view them directly on-screen
> - [PLIPGUI](https://github.com/insilichem/tangram_plipgui):
> Depict protein-ligand interactions, as calculated with PLIP
> - [PoPMuSiCGUI](https://github.com/insilichem/tangram_popmusicgui):
> Depict and apply the predictions made by PoPMuSiC calculations
> - [PropKaGUI](https://github.com/insilichem/tangram_propkagui):
> Analyze and depict the expected pKa values of protein residues
> with PropKa 3.1
> - [SubAlign](https://github.com/insilichem/tangram_subalign):
> Align two, potentially different, molecules based on partial
> matches of substructures
- **Utilities & Patches**
> - [OrbiTraj](https://github.com/insilichem/tangram_orbitraj): A
> subtle modification to UCSF Chimera\'s MD Movie extension to
> allow the visualization of volumetric data along a molecular
> trajectory
> - [ReVina](https://github.com/insilichem/tangram_vinarelaunch):
> Resubmit failed AutoDock Vina jobs without reconfiguring the
> GUI
Installation and usage
----------------------
Check the [docs](http://tangram-suite.readthedocs.io/en/latest/)!
Help and support
----------------
Feel free to [submit an issue in this repository](https://github.com/insilichem/tangram/issues) if you have
any problems with the installation process. However, if the issue is
extension-specific, please use the Issues section of the corresponding
repository (links are provided in the list above).