https://pymolwiki.org/api.php?action=feedcontributions&user=MarkoJukic&feedformat=atomPyMOLWiki - User contributions [en]2024-03-28T09:12:43ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=ProBiS_H2O&diff=12759ProBiS H2O2018-05-08T10:20:27Z<p>MarkoJukic: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = insilab.org<br />
|author = Marko Jukic<br />
|license = <br />
}}<br />
<br />
== Update & Download ==<br />
<br />
The most recent version can be obtained at the [http://insilab.org/probis-h2o/ Insilab web page].<br />
<br />
== Description == <br />
<br />
In order to help in identification of '''conserved water sites''', we developed '''ProBiS H2O''' workflow that supports the complete<br />
process of data collection, extraction, identification of conserved water locations and result visualisation. '''ProBiS H2O'''<br />
workflow adopts the available experimental pdb data deposited in online databases or local user experimental data<br />
collections, collects similar macromolecular systems, performs local/specific binding site superimposition with the<br />
computational speed and accuracy of ProBiS algorithm, collects the experimental water location data reported in the<br />
parent macromolecule systems and transposes gathered data to the examined system, its specific chain, binding site or<br />
individual water. Water location data is then clustered to identify discrete spaces with high conservation of water<br />
molecules and visualised in the context of studied system. '''ProBiS H2O''' workflow is a robust, transparent and fast<br />
methodology with emphasis on experimental data that can identify trends in water localization intra/inter macromolecule<br />
or macromolecule-small molecule interfaces. For further info please refer to the relevant articles by the authors of ProBiS<br />
H2O.<br />
<br />
<br />
<br />
<br />
ProBiS H2O Plugin is '''free for Academic (NON-COMMERCIAL) use'''.<br />
For '''COMMERCIAL use the potential users have to write to [mailto:marko.jukic@ffa.uni-lj.si Marko Jukic]'''.<br />
<br />
<br />
== ProBiS H2O Plugin Features == <br />
<br />
<br />
# Graphical User Interface<br />
# lean and fast workflow<br />
# fast iteration<br />
# data logging and export<br />
# usage of custom datasets<br />
<br />
<br />
== Requirements & Dependencies == <br />
<br />
Python 2.7, NumPy (>= 1.6.1), SciPy (>= 0.9), scikit-learn (>= 1.18), PyMOL software, ProBiS (installed during ProBiS H2O setup).<br />
<br />
The plugin works in Unix like systems. Testing environment was Ubuntu 16.04. <br />
<br />
== Installation == <br />
<br />
ProBiS H2O is installed as a PyMOL plugin:<br />
<br />
# Run PyMOL<br />
# Install the plugin in PyMOL by following the path: Plugin > Plugin Manager > Install New Plugin<br />
# Restart PyMOL!<br />
<br />
<br />
After plugin is installed, it can be run from PyMOL by following Plugin>ProBiS H2O and used through PyMOL Tcl-Tk<br />
GUI where plugin window supplements PyMOL default control and display windows.<br />
<br />
'''Important note''': Before first time usage use SETUP DB button to set up th working environment.<br />
<br />
<br />
== First Time Usage == <br />
<br />
In the lower left corner of the ProBiS H2O main window resides SETUP DB button. Before usage ProBiS H2O plugin<br />
requires up-to-date information on RCSB sequence clustering and ProBiS algorithm binary file. When SETUP DB button<br />
is pressed ProBiS H2O plugin creates /Probis_H2O/ folder in default working directory of PyMOL (default is user home<br />
directory) and downloads recent sequence clustering data from RCSB PDB Database. ProBiS H2O plugin also creates<br />
/Probis_H2O/.pro/ folder where ProBiS algorithm binary file is downloaded to achieve a final workspace:<br />
<br />
~/Probis_H2O/.pro/probis<br />
~/Probis_H2O/clusters50.txt<br />
~/Probis_H2O/clusters70.txt<br />
~/Probis_H2O/clusters90.txt<br />
~/Probis_H2O/clusters95.txt<br />
~/Probis_H2O/bc-30.out<br />
~/Probis_H2O/bc-40.out<br />
~/Probis_H2O/bc-50.out<br />
~/Probis_H2O/bc-70.out<br />
~/Probis_H2O/bc-90.out<br />
~/Probis_H2O/bc-95.out<br />
~/Probis_H2O/bc-100.out<br />
<br />
Final step is to grant probis binary executable rights:<br />
<br />
$sudo chmod +x ~/Probis_H2O/.pro/probis<br />
<br />
== Usage == <br />
<br />
Plugin is composed of three respective tabs:<br />
<br />
<br />
==== Define System Tab ==== <br />
<br />
Default workflow proceeds in following steps (all the data manipulation is performed in /Probis_H2O/ working directory<br />
that was configured using SETUP DB button):<br />
<br />
[[File: Define_system_tab.PNG|390 px]]<br />
<br />
<br />
# User inputs a desired PDB ID as examined system<br />
# User presses “Find” button to display identified structures in cluster<br />
# User downloads all relevant structures by pressing “Download” button (this step is in parentheses because this step is optional if the user already analysed a particular protein cluster and has the structures already downloaded. If it is a first time experiment, the “Download” button downloads the set from the PDB website)<br />
# User identifies binding sites or chains of the examined system (1.)<br />
# User selects desired binding site or chain from a list<br />
# User proceeds with conserved water identification by pressing GO button<br />
<br />
<br />
==== Cluster Analysis Tab ==== <br />
<br />
After the calculation is finished ProBiS H2O switches to the cluster analysis tab and displays the results<br />
<br />
[[File: Cluster_analysis_tab.PNG|390 px]]<br />
<br />
# User displays the studied system in PyMOL display window by clicking “fetch/reset” button. This button can be used for resetting the display for alternative clustering representation<br />
# User selects the cluster from calculated clusters window<br />
# User displays the relevant cluster with display button<br />
<br />
[[File: Feature 4duh.PNG|500 px]]<br />
<br />
==== About/Help Tab ==== <br />
<br />
The users can get reference information on the About/Help tab. <br />
<br />
<br />
== Reference == <br />
<br />
'''If you are using ProBiS H2O in your work, please cite:'''<br />
<br />
Jukič, Marko, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, doi: 10.1021/acs.jcim.7b00443<br />
[https://pubs.acs.org/doi/10.1021/acs.jcim.7b00443]<br />
<br />
== Licensing == <br />
<br />
ProBiS H2O software is copyrighted by : <br />
<br />
:'''Marko Jukic''' <br />
:Fakulteta za farmacijo <br />
:Univerza v Ljubljani <br />
:Askerceva 7<br />
:SI-1000 Ljubljana <br />
:Slovenia.<br />
<br />
The terms stated in the following agreement apply to all files associated with the software <br />
unless explicitly disclaimed in individual files.<br />
<br />
# Copyright Notice<br />
# ================<br />
#<br />
# The PyMOL Plugin source code in this file is copyrighted, but you can<br />
# freely use and copy it as long as you don't change or remove any of<br />
# the copyright notices.<br />
#<br />
# ----------------------------------------------------------------------<br />
# This PyMOL Plugin is Copyright (C) 2017 by Marko Jukic <marko.jukic@ffa.uni-lj.si><br />
#<br />
# All Rights Reserved<br />
#<br />
# Permission to use, copy and distribute<br />
# versions of this software and its documentation for any purpose and<br />
# without fee is hereby granted, provided that the above copyright<br />
# notice appear in all copies and that both the copyright notice and<br />
# this permission notice appear in supporting documentation, and that<br />
# the name(s) of the author(s) not be used in advertising or publicity<br />
# pertaining to distribution of the software without specific, written<br />
# prior permission.<br />
#<br />
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,<br />
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN<br />
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR<br />
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF<br />
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR<br />
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR<br />
# PERFORMANCE OF THIS SOFTWARE.<br />
# ----------------------------------------------------------------------<br />
<br />
<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>MarkoJukichttps://pymolwiki.org/index.php?title=ProBiS_H2O&diff=12758ProBiS H2O2018-05-08T10:17:41Z<p>MarkoJukic: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = insilab.org<br />
|author = Marko Jukic<br />
|license = <br />
}}<br />
<br />
== Update & Download ==<br />
<br />
The most recent version can be obtained at the [http://insilab.org/probis-h2o/ Insilab web page].<br />
<br />
== Description == <br />
<br />
In order to help in identification of '''conserved water sites''', we developed '''ProBiS H2O''' workflow that supports the complete<br />
process of data collection, extraction, identification of conserved water locations and result visualisation. '''ProBiS H2O'''<br />
workflow adopts the available experimental pdb data deposited in online databases or local user experimental data<br />
collections, collects similar macromolecular systems, performs local/specific binding site superimposition with the<br />
computational speed and accuracy of ProBiS algorithm, collects the experimental water location data reported in the<br />
parent macromolecule systems and transposes gathered data to the examined system, its specific chain, binding site or<br />
individual water. Water location data is then clustered to identify discrete spaces with high conservation of water<br />
molecules and visualised in the context of studied system. '''ProBiS H2O''' workflow is a robust, transparent and fast<br />
methodology with emphasis on experimental data that can identify trends in water localization intra/inter macromolecule<br />
or macromolecule-small molecule interfaces. For further info please refer to the relevant articles by the authors of ProBiS<br />
H2O.<br />
<br />
[[File: Feature 4duh.PNG|500 px]]<br />
<br />
<br />
ProBiS H2O Plugin is '''free for Academic (NON-COMMERCIAL) use'''.<br />
For '''COMMERCIAL use the potential users have to write to [mailto:marko.jukic@ffa.uni-lj.si Marko Jukic]'''.<br />
<br />
<br />
== ProBiS H2O Plugin Features == <br />
<br />
<br />
# Graphical User Interface<br />
# lean and fast workflow<br />
# fast iteration<br />
# data logging and export<br />
# usage of custom datasets<br />
<br />
<br />
== Requirements & Dependencies == <br />
<br />
Python 2.7, NumPy (>= 1.6.1), SciPy (>= 0.9), scikit-learn (>= 1.18), PyMOL software, ProBiS (installed during ProBiS H2O setup).<br />
<br />
The plugin works in Unix like systems. Testing environment was Ubuntu 16.04. <br />
<br />
== Installation == <br />
<br />
ProBiS H2O is installed as a PyMOL plugin:<br />
<br />
# Run PyMOL<br />
# Install the plugin in PyMOL by following the path: Plugin > Plugin Manager > Install New Plugin<br />
# Restart PyMOL!<br />
<br />
<br />
After plugin is installed, it can be run from PyMOL by following Plugin>ProBiS H2O and used through PyMOL Tcl-Tk<br />
GUI where plugin window supplements PyMOL default control and display windows.<br />
<br />
'''Important note''': Before first time usage use SETUP DB button to set up th working environment.<br />
<br />
<br />
== First Time Usage == <br />
<br />
In the lower left corner of the ProBiS H2O main window resides SETUP DB button. Before usage ProBiS H2O plugin<br />
requires up-to-date information on RCSB sequence clustering and ProBiS algorithm binary file. When SETUP DB button<br />
is pressed ProBiS H2O plugin creates /Probis_H2O/ folder in default working directory of PyMOL (default is user home<br />
directory) and downloads recent sequence clustering data from RCSB PDB Database. ProBiS H2O plugin also creates<br />
/Probis_H2O/.pro/ folder where ProBiS algorithm binary file is downloaded to achieve a final workspace:<br />
<br />
~/Probis_H2O/.pro/probis<br />
~/Probis_H2O/clusters50.txt<br />
~/Probis_H2O/clusters70.txt<br />
~/Probis_H2O/clusters90.txt<br />
~/Probis_H2O/clusters95.txt<br />
~/Probis_H2O/bc-30.out<br />
~/Probis_H2O/bc-40.out<br />
~/Probis_H2O/bc-50.out<br />
~/Probis_H2O/bc-70.out<br />
~/Probis_H2O/bc-90.out<br />
~/Probis_H2O/bc-95.out<br />
~/Probis_H2O/bc-100.out<br />
<br />
Final step is to grant probis binary executable rights:<br />
<br />
$sudo chmod +x ~/Probis_H2O/.pro/probis<br />
<br />
== Usage == <br />
<br />
Plugin is composed of three respective tabs:<br />
<br />
<br />
==== Define System Tab ==== <br />
<br />
Default workflow proceeds in following steps (all the data manipulation is performed in /Probis_H2O/ working directory<br />
that was configured using SETUP DB button):<br />
<br />
[[File: Define_system_tab.PNG|390 px]]<br />
<br />
<br />
# User inputs a desired PDB ID as examined system<br />
# User presses “Find” button to display identified structures in cluster<br />
# User downloads all relevant structures by pressing “Download” button (this step is in parentheses because this step is optional if the user already analysed a particular protein cluster and has the structures already downloaded. If it is a first time experiment, the “Download” button downloads the set from the PDB website)<br />
# User identifies binding sites or chains of the examined system (1.)<br />
# User selects desired binding site or chain from a list<br />
# User proceeds with conserved water identification by pressing GO button<br />
<br />
<br />
==== Cluster Analysis Tab ==== <br />
<br />
After the calculation is finished ProBiS H2O switches to the cluster analysis tab and displays the results<br />
<br />
[[File: Cluster_analysis_tab.PNG|390 px]]<br />
<br />
# User displays the studied system in PyMOL display window by clicking “fetch/reset” button. This button can be used for resetting the display for alternative clustering representation<br />
# User selects the cluster from calculated clusters window<br />
# User displays the relevant cluster with display button<br />
<br />
==== About/Help Tab ==== <br />
<br />
The users can get reference information on the About/Help tab. <br />
<br />
<br />
== Reference == <br />
<br />
'''If you are using ProBiS H2O in your work, please cite:'''<br />
<br />
Jukič, Marko, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, doi: 10.1021/acs.jcim.7b00443<br />
[https://pubs.acs.org/doi/10.1021/acs.jcim.7b00443]<br />
<br />
== Licensing == <br />
<br />
ProBiS H2O software is copyrighted by : <br />
<br />
:'''Marko Jukic''' <br />
:Fakulteta za farmacijo <br />
:Univerza v Ljubljani <br />
:Askerceva 7<br />
:SI-1000 Ljubljana <br />
:Slovenia.<br />
<br />
The terms stated in the following agreement apply to all files associated with the software <br />
unless explicitly disclaimed in individual files.<br />
<br />
# Copyright Notice<br />
# ================<br />
#<br />
# The PyMOL Plugin source code in this file is copyrighted, but you can<br />
# freely use and copy it as long as you don't change or remove any of<br />
# the copyright notices.<br />
#<br />
# ----------------------------------------------------------------------<br />
# This PyMOL Plugin is Copyright (C) 2017 by Marko Jukic <marko.jukic@ffa.uni-lj.si><br />
#<br />
# All Rights Reserved<br />
#<br />
# Permission to use, copy and distribute<br />
# versions of this software and its documentation for any purpose and<br />
# without fee is hereby granted, provided that the above copyright<br />
# notice appear in all copies and that both the copyright notice and<br />
# this permission notice appear in supporting documentation, and that<br />
# the name(s) of the author(s) not be used in advertising or publicity<br />
# pertaining to distribution of the software without specific, written<br />
# prior permission.<br />
#<br />
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,<br />
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN<br />
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR<br />
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF<br />
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR<br />
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR<br />
# PERFORMANCE OF THIS SOFTWARE.<br />
# ----------------------------------------------------------------------<br />
<br />
<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>MarkoJukichttps://pymolwiki.org/index.php?title=Main_Page&diff=12757Main Page2018-05-08T09:12:56Z<p>MarkoJukic: added new plugin news</p>
<hr />
<div>__NOTOC__<br />
{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"<br />
|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]<br />
|}<br />
{| align="center" style="padding-bottom: 3em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"<br />
| To request a new account, email SBGrid at: accounts (@) sbgrid dot org<br />
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"<br />
|}<br />
<br />
{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"<br />
|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''<br />
|-<br />
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[PyMOL_mailing_list|Getting Help]]'''<br />
|}<br />
<br />
{| width="100%"<br />
| style="vertical-align: top; width: 40%" |<br />
{| class="jtable" style="float: left; width: 90%;"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates<br />
|-<br />
! New Plugin<br />
| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.<br />
|-<br />
! Official Release<br />
| [https://pymol.org PyMOL v2.1 has been released] on March 13, 2018.<br />
|-<br />
! Selection keywords<br />
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!<br />
|-<br />
! Plugin Update<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL<br />
|-<br />
! New Script<br />
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons<br />
|-<br />
! New Plugin<br />
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.<br />
|-<br />
! New Plugin<br />
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.<br />
|-<br />
! New Plugin<br />
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.<br />
|-<br />
! New Plugin<br />
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.<br />
|-<br />
! 3D using Geforce<br />
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.<br />
|-<br />
! Older News<br />
| See [[Older_News|Older News]].<br />
|}<br />
|style="vertical-align: top; width: 40%"|<br />
{| class="jtable" style="float: right; width: 90%"<br />
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...<br />
|-<br />
|<div class="didyouknow" ><br />
<DynamicPageList><br />
randomcount=1<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
escapelinks=false<br />
allowcachedresults=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DynamicPageList><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DynamicPageList><br />
imagecontainer=Covers<br />
randomcount=1<br />
escapelinks=false<br />
openreferences=true<br />
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n<br />
ordermethod=none<br />
allowcachedresults=false<br />
</DynamicPageList><br />
<br />
|}</div>MarkoJukichttps://pymolwiki.org/index.php?title=ProBiS_H2O&diff=12756ProBiS H2O2018-05-08T09:07:33Z<p>MarkoJukic: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = insilab.org<br />
|author = Marko Jukic<br />
|license = <br />
}}<br />
<br />
== Update & Download ==<br />
<br />
The most recent version can be obtained at the [http://insilab.org/lisica-plugin Insilab web page].<br />
<br />
== Description == <br />
<br />
In order to help in identification of '''conserved water sites''', we developed '''ProBiS H2O''' workflow that supports the complete<br />
process of data collection, extraction, identification of conserved water locations and result visualisation. '''ProBiS H2O'''<br />
workflow adopts the available experimental pdb data deposited in online databases or local user experimental data<br />
collections, collects similar macromolecular systems, performs local/specific binding site superimposition with the<br />
computational speed and accuracy of ProBiS algorithm, collects the experimental water location data reported in the<br />
parent macromolecule systems and transposes gathered data to the examined system, its specific chain, binding site or<br />
individual water. Water location data is then clustered to identify discrete spaces with high conservation of water<br />
molecules and visualised in the context of studied system. '''ProBiS H2O''' workflow is a robust, transparent and fast<br />
methodology with emphasis on experimental data that can identify trends in water localization intra/inter macromolecule<br />
or macromolecule-small molecule interfaces. For further info please refer to the relevant articles by the authors of ProBiS<br />
H2O.<br />
<br />
[[File: Feature 4duh.PNG|500 px]]<br />
<br />
<br />
ProBiS H2O Plugin is '''free for Academic (NON-COMMERCIAL) use'''.<br />
For '''COMMERCIAL use the potential users have to write to [mailto:marko.jukic@ffa.uni-lj.si Marko Jukic]'''.<br />
<br />
<br />
== ProBiS H2O Plugin Features == <br />
<br />
<br />
# Graphical User Interface<br />
# lean and fast workflow<br />
# fast iteration<br />
# data logging and export<br />
# usage of custom datasets<br />
<br />
<br />
== Requirements & Dependencies == <br />
<br />
Python 2.7, NumPy (>= 1.6.1), SciPy (>= 0.9), scikit-learn (>= 1.18), PyMOL software, ProBiS (installed during ProBiS H2O setup).<br />
<br />
The plugin works in Unix like systems. Testing environment was Ubuntu 16.04. <br />
<br />
== Installation == <br />
<br />
ProBiS H2O is installed as a PyMOL plugin:<br />
<br />
# Run PyMOL<br />
# Install the plugin in PyMOL by following the path: Plugin > Plugin Manager > Install New Plugin<br />
# Restart PyMOL!<br />
<br />
<br />
After plugin is installed, it can be run from PyMOL by following Plugin>ProBiS H2O and used through PyMOL Tcl-Tk<br />
GUI where plugin window supplements PyMOL default control and display windows.<br />
<br />
'''Important note''': Before first time usage use SETUP DB button to set up th working environment.<br />
<br />
<br />
== First Time Usage == <br />
<br />
In the lower left corner of the ProBiS H2O main window resides SETUP DB button. Before usage ProBiS H2O plugin<br />
requires up-to-date information on RCSB sequence clustering and ProBiS algorithm binary file. When SETUP DB button<br />
is pressed ProBiS H2O plugin creates /Probis_H2O/ folder in default working directory of PyMOL (default is user home<br />
directory) and downloads recent sequence clustering data from RCSB PDB Database. ProBiS H2O plugin also creates<br />
/Probis_H2O/.pro/ folder where ProBiS algorithm binary file is downloaded to achieve a final workspace:<br />
<br />
~/Probis_H2O/.pro/probis<br />
~/Probis_H2O/clusters50.txt<br />
~/Probis_H2O/clusters70.txt<br />
~/Probis_H2O/clusters90.txt<br />
~/Probis_H2O/clusters95.txt<br />
~/Probis_H2O/bc-30.out<br />
~/Probis_H2O/bc-40.out<br />
~/Probis_H2O/bc-50.out<br />
~/Probis_H2O/bc-70.out<br />
~/Probis_H2O/bc-90.out<br />
~/Probis_H2O/bc-95.out<br />
~/Probis_H2O/bc-100.out<br />
<br />
Final step is to grant probis binary executable rights:<br />
<br />
$sudo chmod +x ~/Probis_H2O/.pro/probis<br />
<br />
== Usage == <br />
<br />
Plugin is composed of three respective tabs:<br />
<br />
<br />
==== Define System Tab ==== <br />
<br />
Default workflow proceeds in following steps (all the data manipulation is performed in /Probis_H2O/ working directory<br />
that was configured using SETUP DB button):<br />
<br />
[[File: Define_system_tab.PNG|390 px]]<br />
<br />
<br />
# User inputs a desired PDB ID as examined system<br />
# User presses “Find” button to display identified structures in cluster<br />
# User downloads all relevant structures by pressing “Download” button (this step is in parentheses because this step is optional if the user already analysed a particular protein cluster and has the structures already downloaded. If it is a first time experiment, the “Download” button downloads the set from the PDB website)<br />
# User identifies binding sites or chains of the examined system (1.)<br />
# User selects desired binding site or chain from a list<br />
# User proceeds with conserved water identification by pressing GO button<br />
<br />
<br />
==== Cluster Analysis Tab ==== <br />
<br />
After the calculation is finished ProBiS H2O switches to the cluster analysis tab and displays the results<br />
<br />
[[File: Cluster_analysis_tab.PNG|390 px]]<br />
<br />
# User displays the studied system in PyMOL display window by clicking “fetch/reset” button. This button can be used for resetting the display for alternative clustering representation<br />
# User selects the cluster from calculated clusters window<br />
# User displays the relevant cluster with display button<br />
<br />
==== About/Help Tab ==== <br />
<br />
The users can get reference information on the About/Help tab. <br />
<br />
<br />
== Reference == <br />
<br />
'''If you are using ProBiS H2O in your work, please cite:'''<br />
<br />
Jukič, Marko, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, doi: 10.1021/acs.jcim.7b00443<br />
[https://pubs.acs.org/doi/10.1021/acs.jcim.7b00443]<br />
<br />
== Licensing == <br />
<br />
ProBiS H2O software is copyrighted by : <br />
<br />
:'''Marko Jukic''' <br />
:Fakulteta za farmacijo <br />
:Univerza v Ljubljani <br />
:Askerceva 7<br />
:SI-1000 Ljubljana <br />
:Slovenia.<br />
<br />
The terms stated in the following agreement apply to all files associated with the software <br />
unless explicitly disclaimed in individual files.<br />
<br />
# Copyright Notice<br />
# ================<br />
#<br />
# The PyMOL Plugin source code in this file is copyrighted, but you can<br />
# freely use and copy it as long as you don't change or remove any of<br />
# the copyright notices.<br />
#<br />
# ----------------------------------------------------------------------<br />
# This PyMOL Plugin is Copyright (C) 2017 by Marko Jukic <marko.jukic@ffa.uni-lj.si><br />
#<br />
# All Rights Reserved<br />
#<br />
# Permission to use, copy and distribute<br />
# versions of this software and its documentation for any purpose and<br />
# without fee is hereby granted, provided that the above copyright<br />
# notice appear in all copies and that both the copyright notice and<br />
# this permission notice appear in supporting documentation, and that<br />
# the name(s) of the author(s) not be used in advertising or publicity<br />
# pertaining to distribution of the software without specific, written<br />
# prior permission.<br />
#<br />
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,<br />
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN<br />
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR<br />
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF<br />
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR<br />
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR<br />
# PERFORMANCE OF THIS SOFTWARE.<br />
# ----------------------------------------------------------------------<br />
<br />
<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>MarkoJukichttps://pymolwiki.org/index.php?title=ProBiS_H2O&diff=12755ProBiS H2O2018-05-08T09:05:54Z<p>MarkoJukic: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = insilab.org<br />
|author = Marko Jukic<br />
|license = <br />
}}<br />
<br />
== Update & Download ==<br />
<br />
The most recent version can be obtained at the [http://insilab.org/lisica-plugin Insilab web page].<br />
<br />
== Description == <br />
<br />
In order to help in identification of '''conserved water sites''', we developed '''ProBiS H2O''' workflow that supports the complete<br />
process of data collection, extraction, identification of conserved water locations and result visualisation. '''ProBiS H2O'''<br />
workflow adopts the available experimental pdb data deposited in online databases or local user experimental data<br />
collections, collects similar macromolecular systems, performs local/specific binding site superimposition with the<br />
computational speed and accuracy of ProBiS algorithm, collects the experimental water location data reported in the<br />
parent macromolecule systems and transposes gathered data to the examined system, its specific chain, binding site or<br />
individual water. Water location data is then clustered to identify discrete spaces with high conservation of water<br />
molecules and visualised in the context of studied system. '''ProBiS H2O''' workflow is a robust, transparent and fast<br />
methodology with emphasis on experimental data that can identify trends in water localization intra/inter macromolecule<br />
or macromolecule-small molecule interfaces. For further info please refer to the relevant articles by the authors of ProBiS<br />
H2O.<br />
<br />
[[File: Feature_4duh.PNG.PNG|500 px]]<br />
<br />
<br />
ProBiS H2O Plugin is '''free for Academic (NON-COMMERCIAL) use'''.<br />
For '''COMMERCIAL use the potential users have to write to [mailto:marko.jukic@ffa.uni-lj.si Marko Jukic]'''.<br />
<br />
<br />
== ProBiS H2O Plugin Features == <br />
<br />
<br />
# Graphical User Interface<br />
# lean and fast workflow<br />
# fast iteration<br />
# data logging and export<br />
# usage of custom datasets<br />
<br />
<br />
== Requirements & Dependencies == <br />
<br />
Python 2.7, NumPy (>= 1.6.1), SciPy (>= 0.9), scikit-learn (>= 1.18), PyMOL software, ProBiS (installed during ProBiS H2O setup).<br />
<br />
The plugin works in Unix like systems. Testing environment was Ubuntu 16.04. <br />
<br />
== Installation == <br />
<br />
ProBiS H2O is installed as a PyMOL plugin:<br />
<br />
# Run PyMOL<br />
# Install the plugin in PyMOL by following the path: Plugin > Plugin Manager > Install New Plugin<br />
# Restart PyMOL!<br />
<br />
<br />
After plugin is installed, it can be run from PyMOL by following Plugin>ProBiS H2O and used through PyMOL Tcl-Tk<br />
GUI where plugin window supplements PyMOL default control and display windows.<br />
<br />
'''Important note''': Before first time usage use SETUP DB button to set up th working environment.<br />
<br />
<br />
== First Time Usage == <br />
<br />
In the lower left corner of the ProBiS H2O main window resides SETUP DB button. Before usage ProBiS H2O plugin<br />
requires up-to-date information on RCSB sequence clustering and ProBiS algorithm binary file. When SETUP DB button<br />
is pressed ProBiS H2O plugin creates /Probis_H2O/ folder in default working directory of PyMOL (default is user home<br />
directory) and downloads recent sequence clustering data from RCSB PDB Database. ProBiS H2O plugin also creates<br />
/Probis_H2O/.pro/ folder where ProBiS algorithm binary file is downloaded to achieve a final workspace:<br />
<br />
~/Probis_H2O/.pro/probis<br />
~/Probis_H2O/clusters50.txt<br />
~/Probis_H2O/clusters70.txt<br />
~/Probis_H2O/clusters90.txt<br />
~/Probis_H2O/clusters95.txt<br />
~/Probis_H2O/bc-30.out<br />
~/Probis_H2O/bc-40.out<br />
~/Probis_H2O/bc-50.out<br />
~/Probis_H2O/bc-70.out<br />
~/Probis_H2O/bc-90.out<br />
~/Probis_H2O/bc-95.out<br />
~/Probis_H2O/bc-100.out<br />
<br />
Final step is to grant probis binary executable rights:<br />
<br />
$sudo chmod +x ~/Probis_H2O/.pro/probis<br />
<br />
== Usage == <br />
<br />
Plugin is composed of three respective tabs:<br />
<br />
<br />
==== Define System Tab ==== <br />
<br />
Default workflow proceeds in following steps (all the data manipulation is performed in /Probis_H2O/ working directory<br />
that was configured using SETUP DB button):<br />
<br />
[[File: Define_system_tab.PNG|390 px]]<br />
<br />
<br />
# User inputs a desired PDB ID as examined system<br />
# User presses “Find” button to display identified structures in cluster<br />
# User downloads all relevant structures by pressing “Download” button (this step is in parentheses because this step is optional if the user already analysed a particular protein cluster and has the structures already downloaded. If it is a first time experiment, the “Download” button downloads the set from the PDB website)<br />
# User identifies binding sites or chains of the examined system (1.)<br />
# User selects desired binding site or chain from a list<br />
# User proceeds with conserved water identification by pressing GO button<br />
<br />
<br />
==== Cluster Analysis Tab ==== <br />
<br />
After the calculation is finished ProBiS H2O switches to the cluster analysis tab and displays the results<br />
<br />
[[File: Cluster_analysis_tab.PNG|390 px]]<br />
<br />
# User displays the studied system in PyMOL display window by clicking “fetch/reset” button. This button can be used for resetting the display for alternative clustering representation<br />
# User selects the cluster from calculated clusters window<br />
# User displays the relevant cluster with display button<br />
<br />
==== About/Help Tab ==== <br />
<br />
The users can get reference information on the About/Help tab. <br />
<br />
<br />
== Reference == <br />
<br />
'''If you are using ProBiS H2O in your work, please cite:'''<br />
<br />
Jukič, Marko, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, doi: 10.1021/acs.jcim.7b00443<br />
[https://pubs.acs.org/doi/10.1021/acs.jcim.7b00443]<br />
<br />
== Licensing == <br />
<br />
ProBiS H2O software is copyrighted by : <br />
<br />
:'''Marko Jukic''' <br />
:Fakulteta za farmacijo <br />
:Univerza v Ljubljani <br />
:Askerceva 7<br />
:SI-1000 Ljubljana <br />
:Slovenia.<br />
<br />
The terms stated in the following agreement apply to all files associated with the software <br />
unless explicitly disclaimed in individual files.<br />
<br />
# Copyright Notice<br />
# ================<br />
#<br />
# The PyMOL Plugin source code in this file is copyrighted, but you can<br />
# freely use and copy it as long as you don't change or remove any of<br />
# the copyright notices.<br />
#<br />
# ----------------------------------------------------------------------<br />
# This PyMOL Plugin is Copyright (C) 2017 by Marko Jukic <marko.jukic@ffa.uni-lj.si><br />
#<br />
# All Rights Reserved<br />
#<br />
# Permission to use, copy and distribute<br />
# versions of this software and its documentation for any purpose and<br />
# without fee is hereby granted, provided that the above copyright<br />
# notice appear in all copies and that both the copyright notice and<br />
# this permission notice appear in supporting documentation, and that<br />
# the name(s) of the author(s) not be used in advertising or publicity<br />
# pertaining to distribution of the software without specific, written<br />
# prior permission.<br />
#<br />
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,<br />
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN<br />
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR<br />
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF<br />
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR<br />
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR<br />
# PERFORMANCE OF THIS SOFTWARE.<br />
# ----------------------------------------------------------------------<br />
<br />
<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>MarkoJukichttps://pymolwiki.org/index.php?title=File:Feature_4duh.PNG&diff=12754File:Feature 4duh.PNG2018-05-08T08:58:20Z<p>MarkoJukic: </p>
<hr />
<div></div>MarkoJukichttps://pymolwiki.org/index.php?title=File:Cluster_analysis_tab.PNG&diff=12753File:Cluster analysis tab.PNG2018-05-08T08:57:40Z<p>MarkoJukic: cluster analysis tab of ProBiS H2O plugin.</p>
<hr />
<div>cluster analysis tab of ProBiS H2O plugin.</div>MarkoJukichttps://pymolwiki.org/index.php?title=File:Define_system_tab.PNG&diff=12752File:Define system tab.PNG2018-05-08T08:54:04Z<p>MarkoJukic: define system tab of ProBiS H2O plugin</p>
<hr />
<div>define system tab of ProBiS H2O plugin</div>MarkoJukichttps://pymolwiki.org/index.php?title=ProBiS_H2O&diff=12751ProBiS H2O2018-05-08T08:52:26Z<p>MarkoJukic: init commit</p>
<hr />
<div>{{Infobox script-repo<br />
|type = plugin<br />
|filename = insilab.org<br />
|author = Marko Jukic<br />
|license = <br />
}}<br />
<br />
== Update & Download ==<br />
<br />
The most recent version can be obtained at the [http://insilab.org/lisica-plugin Insilab web page].<br />
<br />
== Description == <br />
<br />
In order to help in identification of '''conserved water sites''', we developed '''ProBiS H2O''' workflow that supports the complete<br />
process of data collection, extraction, identification of conserved water locations and result visualisation. '''ProBiS H2O'''<br />
workflow adopts the available experimental pdb data deposited in online databases or local user experimental data<br />
collections, collects similar macromolecular systems, performs local/specific binding site superimposition with the<br />
computational speed and accuracy of ProBiS algorithm, collects the experimental water location data reported in the<br />
parent macromolecule systems and transposes gathered data to the examined system, its specific chain, binding site or<br />
individual water. Water location data is then clustered to identify discrete spaces with high conservation of water<br />
molecules and visualised in the context of studied system. '''ProBiS H2O''' workflow is a robust, transparent and fast<br />
methodology with emphasis on experimental data that can identify trends in water localization intra/inter macromolecule<br />
or macromolecule-small molecule interfaces. For further info please refer to the relevant articles by the authors of ProBiS<br />
H2O.<br />
<br />
<br />
ProBiS H2O Plugin is '''free for Academic (NON-COMMERCIAL) use'''.<br />
For '''COMMERCIAL use the potential users have to write to [mailto:marko.jukic@ffa.uni-lj.si Marko Jukic]'''.<br />
<br />
<br />
== ProBiS H2O Plugin Features == <br />
<br />
<br />
# Graphical User Interface<br />
# lean and fast workflow<br />
# fast iteration<br />
# data logging and export<br />
# usage of custom datasets<br />
<br />
<br />
== Requirements & Dependencies == <br />
<br />
Python 2.7, NumPy (>= 1.6.1), SciPy (>= 0.9), scikit-learn (>= 1.18), PyMOL software, ProBiS (installed during ProBiS H2O setup).<br />
<br />
The plugin works in Unix like systems. Testing environment was Ubuntu 16.04. <br />
<br />
== Installation == <br />
<br />
ProBiS H2O is installed as a PyMOL plugin:<br />
<br />
# Run PyMOL<br />
# Install the plugin in PyMOL by following the path: Plugin > Plugin Manager > Install New Plugin<br />
# Restart PyMOL!<br />
<br />
<br />
After plugin is installed, it can be run from PyMOL by following Plugin>ProBiS H2O and used through PyMOL Tcl-Tk<br />
GUI where plugin window supplements PyMOL default control and display windows.<br />
<br />
'''Important note''': Before first time usage use SETUP DB button to set up th working environment.<br />
<br />
<br />
== First Time Usage == <br />
<br />
In the lower left corner of the ProBiS H2O main window resides SETUP DB button. Before usage ProBiS H2O plugin<br />
requires up-to-date information on RCSB sequence clustering and ProBiS algorithm binary file. When SETUP DB button<br />
is pressed ProBiS H2O plugin creates /Probis_H2O/ folder in default working directory of PyMOL (default is user home<br />
directory) and downloads recent sequence clustering data from RCSB PDB Database. ProBiS H2O plugin also creates<br />
/Probis_H2O/.pro/ folder where ProBiS algorithm binary file is downloaded to achieve a final workspace:<br />
<br />
~/Probis_H2O/.pro/probis<br />
~/Probis_H2O/clusters50.txt<br />
~/Probis_H2O/clusters70.txt<br />
~/Probis_H2O/clusters90.txt<br />
~/Probis_H2O/clusters95.txt<br />
~/Probis_H2O/bc-30.out<br />
~/Probis_H2O/bc-40.out<br />
~/Probis_H2O/bc-50.out<br />
~/Probis_H2O/bc-70.out<br />
~/Probis_H2O/bc-90.out<br />
~/Probis_H2O/bc-95.out<br />
~/Probis_H2O/bc-100.out<br />
<br />
Final step is to grant probis binary executable rights:<br />
<br />
$sudo chmod +x ~/Probis_H2O/.pro/probis<br />
<br />
== Usage == <br />
<br />
Plugin is composed of three respective tabs:<br />
<br />
<br />
==== Define System Tab ==== <br />
<br />
Default workflow proceeds in following steps (all the data manipulation is performed in /Probis_H2O/ working directory<br />
that was configured using SETUP DB button):<br />
<br />
1. User inputs a desired PDB ID as examined system<br />
2. User presses “Find” button to display identified structures in cluster<br />
3. User downloads all relevant structures by pressing “Download” button (this step is in parentheses<br />
because this step is optional if the user already analysed a particular protein cluster and has the<br />
structures already downloaded. If it is a first time experiment, the “Download” button downloads the<br />
set from the PDB website)<br />
4. User identifies binding sites or chains of the examined system (1.)<br />
5. User selects desired binding site or chain from a list<br />
6. User proceeds with conserved water identification by pressing GO button<br />
<br />
<br />
==== Cluster Analysis Tab ==== <br />
<br />
After the calculation is finished ProBiS H2O switches to the cluster analysis tab and displays the results<br />
<br />
==== About/Help Tab ==== <br />
<br />
The users can get reference information on the About/Help tab. <br />
<br />
<br />
== Reference == <br />
<br />
'''If you are using ProBiS H2O in your work, please cite:'''<br />
<br />
Jukič, Marko, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, doi: 10.1021/acs.jcim.7b00443<br />
[https://pubs.acs.org/doi/10.1021/acs.jcim.7b00443]<br />
<br />
== Licensing == <br />
<br />
ProBiS H2O software is copyrighted by : <br />
<br />
:'''Marko Jukic''' <br />
:Fakulteta za farmacijo <br />
:Univerza v Ljubljani <br />
:Askerceva 7<br />
:SI-1000 Ljubljana <br />
:Slovenia.<br />
<br />
The terms stated in the following agreement apply to all files associated with the software <br />
unless explicitly disclaimed in individual files.<br />
<br />
# Copyright Notice<br />
# ================<br />
#<br />
# The PyMOL Plugin source code in this file is copyrighted, but you can<br />
# freely use and copy it as long as you don't change or remove any of<br />
# the copyright notices.<br />
#<br />
# ----------------------------------------------------------------------<br />
# This PyMOL Plugin is Copyright (C) 2017 by Marko Jukic <marko.jukic@ffa.uni-lj.si><br />
#<br />
# All Rights Reserved<br />
#<br />
# Permission to use, copy and distribute<br />
# versions of this software and its documentation for any purpose and<br />
# without fee is hereby granted, provided that the above copyright<br />
# notice appear in all copies and that both the copyright notice and<br />
# this permission notice appear in supporting documentation, and that<br />
# the name(s) of the author(s) not be used in advertising or publicity<br />
# pertaining to distribution of the software without specific, written<br />
# prior permission.<br />
#<br />
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,<br />
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN<br />
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR<br />
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF<br />
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR<br />
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR<br />
# PERFORMANCE OF THIS SOFTWARE.<br />
# ----------------------------------------------------------------------<br />
<br />
<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>MarkoJukic