https://pymolwiki.org/api.php?action=feedcontributions&user=LucianoKagami&feedformat=atomPyMOLWiki - User contributions [en]2024-03-29T08:55:05ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13343Geo Measures Plugin2020-12-23T21:58:25Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
{|<br />
|[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
||[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
||[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
|-<br />
|[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
||[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
||[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
|}<br />
<br />
== Video Tutorial ==<br />
----<br />
https://youtu.be/YKmIcU5weI0<br />
----<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
== References ==<br />
<br />
----<br />
<br />
Kagami LP, das Neves GM, Timmers LFSM, Caceres RA,Eifler-Lima VL, Geo-Measures: A PyMOL plugin for protein structure ensembles analysis,Computational Biology and Chemistry(2020)<br />
doi.org/10.1016/j.compbiolchem.2020.107322<br />
<br />
<br />
<br />
----<br />
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13312Geo Measures Plugin2020-06-25T12:08:59Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
{|<br />
|[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
||[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
||[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
|-<br />
|[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
||[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
||[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
|}<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
== References ==<br />
<br />
----<br />
<br />
Kagami LP, das Neves GM, Timmers LFSM, Caceres RA,Eifler-Lima VL, Geo-Measures: A PyMOL plugin for protein structure ensembles analysis,Computational Biology and Chemistry(2020)<br />
doi.org/10.1016/j.compbiolchem.2020.107322<br />
<br />
<br />
<br />
----<br />
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13311Geo Measures Plugin2020-06-25T12:08:11Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
{|<br />
|[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
||[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
||[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
|-<br />
|[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
||[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
||[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
|}<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
== References ==<br />
<br />
----<br />
<br />
Kagami LP, das Neves GM, Timmers LFSM, Caceres RA,Eifler-Lima VL, Geo-Measures: A PyMOL plugin for protein structure ensembles analysis,Computational Biology and Chemistry(2020),doi.org/10.1016/j.compbiolchem.2020.107322<br />
<br />
<br />
<br />
----<br />
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13233Geo Measures Plugin2020-01-25T15:19:10Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
{|<br />
|[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
||[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
||[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
|-<br />
|[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
||[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
||[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
|}<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
<br />
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13232Geo Measures Plugin2020-01-25T15:16:09Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
{|<br />
|[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
||[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
||[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
|-<br />
|[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
||[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
||[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
|}<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
<br />
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13231Geo Measures Plugin2020-01-25T14:53:54Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
{|<br />
[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
<br />
[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
<br />
[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
|-<br />
<br />
[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
<br />
[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
<br />
[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
|}<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
<br />
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13230Geo Measures Plugin2020-01-25T14:50:34Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
<br />
[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
<br />
[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
<br />
[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
<br />
[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
<br />
[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
<br />
'''Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM'''</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13229Geo Measures Plugin2020-01-25T14:50:02Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
<br />
[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
<br />
[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
<br />
[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
<br />
[[Image:Modevector.png|thumb|300px|left|Modevectors]]<br />
<br />
[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13228Geo Measures Plugin2020-01-25T14:48:45Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[Image:Geo measures.png|thumb|300px|left|Geo-Measures Graphical User Interface]]<br />
<br />
[[Image:figure_4.png|thumb|300px|left|Free Energy Landscape]]<br />
<br />
[[Image:Ramachandran.png|thumb|300px|left|Ramachandran Plot]]<br />
<br />
[[Image:PDF.png|thumb|300px|left|Probability Density Function]]<br />
<br />
[[Image:Modevector.jpg|thumb|300px|left|Modevectors]]<br />
<br />
[[Image:Pincer_Angle.png|thumb|300px|left|Pincer Angle]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]<br />
<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13227Geo Measures Plugin2020-01-25T14:35:44Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres and Vera Lucia Eifler-Lima <br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[File:Geo measures.png]]<br />
Geo-Measures Graphical User Interface<br />
<br />
[[File:figure_4.png]]<br />
Free Energy Landscape<br />
<br />
[[File:Ramachandran.png]]<br />
Ramachandran Plot<br />
<br />
[[File:PDF.png]]<br />
Probability Density Function<br />
<br />
[[File:Modevector.jpg]]<br />
Modevectors<br />
<br />
[[File:Pincer_Angle.png]]<br />
Pincer Angle<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=File:Ramachandran.png&diff=13226File:Ramachandran.png2020-01-25T14:28:40Z<p>LucianoKagami: Ramachandran</p>
<hr />
<div>== Summary ==<br />
Ramachandran</div>LucianoKagamihttps://pymolwiki.org/index.php?title=File:PDF.png&diff=13225File:PDF.png2020-01-25T14:27:53Z<p>LucianoKagami: Probability Density Function</p>
<hr />
<div>== Summary ==<br />
Probability Density Function</div>LucianoKagamihttps://pymolwiki.org/index.php?title=File:Pincer_Angle.png&diff=13224File:Pincer Angle.png2020-01-25T14:26:33Z<p>LucianoKagami: Pincer Angle</p>
<hr />
<div>== Summary ==<br />
Pincer Angle</div>LucianoKagamihttps://pymolwiki.org/index.php?title=File:Modevector.png&diff=13223File:Modevector.png2020-01-25T14:25:16Z<p>LucianoKagami: Modevectors</p>
<hr />
<div>== Summary ==<br />
Modevectors</div>LucianoKagamihttps://pymolwiki.org/index.php?title=File:Figure_4.png&diff=13222File:Figure 4.png2020-01-25T14:20:25Z<p>LucianoKagami: Free Energy Landscape</p>
<hr />
<div>== Summary ==<br />
Free Energy Landscape</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13213Geo Measures Plugin2020-01-06T12:43:23Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima and Luís Fernando Saraiva Macedo Timmers<br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13212Geo Measures Plugin2020-01-06T12:42:46Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Rafael Andrade Cáceres, <br />
Vera Lucia Eifler-Lima and Luís Fernando Saraiva Macedo Timmers<br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13211Geo Measures Plugin2020-01-06T12:42:02Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima,Luís Fernando Saraiva Macedo Timmers<br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13210Geo Measures Plugin2020-01-04T13:21:12Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima<br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
----<br />
Requirements:<br />
<br />
PyMOL version higher than 2.0.<br />
<br />
It is highly recommended to install PyMOL using the Ananconda3 package [https://www.anaconda.com/distribution/].<br />
<br />
You need to install python packages. <br />
<br />
To do this use the command:<br />
<br />
pip install pandas matplotlib scipy mdtraj sklearn<br />
<br />
----<br />
<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13209Geo Measures Plugin2019-12-26T15:00:20Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima<br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13208Geo Measures Plugin2019-12-24T17:16:49Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima<br />
|license = GNU General Public License v3.0<br />
}}<br />
<br />
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 15 tools, which can be easily used by the graphical interface.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13207Geo Measures Plugin2019-12-24T17:10:40Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima<br />
}}<br />
<br />
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 15 tools, which can be easily used by the graphical interface.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13206Geo Measures Plugin2019-12-24T17:04:18Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima<br />
}}<br />
<br />
The [[Geo Measures Plugin]] can carry out geometric analysis on protein structures.<br />
<br />
[[File:Geo measures.png]]<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagamihttps://pymolwiki.org/index.php?title=File:Geo_measures.png&diff=13205File:Geo measures.png2019-12-24T17:03:04Z<p>LucianoKagami: </p>
<hr />
<div></div>LucianoKagamihttps://pymolwiki.org/index.php?title=Geo_Measures_Plugin&diff=13204Geo Measures Plugin2019-12-24T17:02:04Z<p>LucianoKagami: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br />
|author = Luciano Porto Kagami, Gustavo Machado das Neves, Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima<br />
}}<br />
<br />
The [[Geo Measures Plugin]] can carry out geometric analysis on protein structures.<br />
<br />
Universidade Federal do Rio Grande do Sul - Laboratório de Síntese Orgânica Medicinal - LaSOM<br />
<br />
== Installation ==<br />
<br />
Install [https://github.com/lkagami/geo_measures_pymol/archive/master.zip geo_measures_pymol-master.zip] using the PyMOL [[Plugin Manager]]<br />
<br />
[[Category:Plugins]]</div>LucianoKagami