Geo Measures Plugin: Difference between revisions
No edit summary |
No edit summary |
||
| Line 7: | Line 7: | ||
The [[Geo Measures Plugin]] can carry out geometric analysis on protein structures.In addition, it makes other trajectory analyzes such as Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors. Altogether there are 14 tools, which can be easily used by the graphical interface. | The [[Geo Measures Plugin]] can carry out geometric analysis on protein structures.In addition, it makes other trajectory analyzes such as Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors. Altogether there are 14 tools, which can be easily used by the graphical interface. | ||
{| | |||
[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]] | [[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]] | ||
| Line 13: | Line 13: | ||
[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]] | [[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]] | ||
|- | |||
[[Image:PDF.png|thumb|300px|left|Probability Density Function]] | [[Image:PDF.png|thumb|300px|left|Probability Density Function]] | ||
| Line 19: | Line 20: | ||
[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]] | [[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]] | ||
|} | |||
Revision as of 09:53, 25 January 2020
| Type | PyMOL Plugin |
|---|---|
| Download | https://github.com/lkagami/geo_measures_pymol/archive/master.zip |
| Author(s) | Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres and Vera Lucia Eifler-Lima |
| License | GNU General Public License v3.0 |
The Geo Measures Plugin can carry out geometric analysis on protein structures.In addition, it makes other trajectory analyzes such as Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors. Altogether there are 14 tools, which can be easily used by the graphical interface.
Installation
Requirements:
PyMOL version higher than 2.0.
It is highly recommended to install PyMOL using the Ananconda3 package [1].
You need to install python packages.
To do this use the command:
pip install pandas matplotlib scipy mdtraj sklearn
Install geo_measures_pymol-master.zip using the PyMOL Plugin Manager
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM