https://wiki.pymol.org/index.php?action=history&feed=atom&title=Geo_Measures_Plugin 2026-07-10T06:36:29Z Revision history for this page on the wiki MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Geo_Measures_Plugin&diff=14860&oldid=prev 2021-03-01T03:06:23Z

<p>1 revision</p> <p><b>New page</b></p><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>

Cchem https://wiki.pymol.org/index.php?title=Geo_Measures_Plugin&diff=14767&oldid=prev 2020-07-20T16:19:41Z

<p>2 revisions</p> <p><b>New page</b></p><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>

Cchem https://wiki.pymol.org/index.php?title=Geo_Measures_Plugin&diff=14674&oldid=prev 2020-02-03T03:40:42Z

<p>10 revisions</p> <p><b>New page</b></p><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>

Cchem https://wiki.pymol.org/index.php?title=Geo_Measures_Plugin&diff=14661&oldid=prev 2020-01-06T03:02:03Z

<p>6 revisions</p> <p><b>New page</b></p><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>

Cchem https://wiki.pymol.org/index.php?title=Geo_Measures_Plugin&diff=14631&oldid=prev 2019-10-14T18:49:22Z

<p>1 revision</p> <table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface"> <tr class="diff-title" lang="en"> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:49, 14 October 2019</td> </tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

Cchem https://wiki.pymol.org/index.php?title=Geo_Measures_Plugin&diff=14630&oldid=prev 2019-10-14T12:40:09Z

<p>created</p> <p><b>New page</b></p><div>{{Infobox script-repo<br /> |type = plugin<br /> |download = https://github.com/lkagami/geo_measures_pymol/archive/master.zip<br /> |author = Luciano Porto Kagami et al.<br /> }}<br /> <br /> The [[Geo Measures Plugin]] can carry out geometric analysis on protein structures.<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>

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