https://pymolwiki.org/api.php?action=feedcontributions&user=LukasPravda&feedformat=atomPyMOLWiki - User contributions [en]2024-03-29T07:39:55ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=Main_Page&diff=12617Main Page2017-07-13T11:41:35Z<p>LukasPravda: </p>
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<div>__NOTOC__<br />
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|+ 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 />
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{| 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 />
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|- <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 />
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{| 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 />
! 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 />
! Official Release<br />
| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.<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 />
! Official Release<br />
| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.<br />
|-<br />
! PyMOL Open-Source Fellowship<br />
| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship<br />
|-<br />
! Official Release<br />
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.<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 />
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{| 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 />
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|}</div>LukasPravdahttps://pymolwiki.org/index.php?title=MOLE_2.0:_advanced_approach_for_analysis_of_biomacromolecular_channels&diff=12616MOLE 2.0: advanced approach for analysis of biomacromolecular channels2017-07-13T11:38:58Z<p>LukasPravda: </p>
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<div>[[File:Molelogo.png|80px|left|]] [[File:1jj2.png|400px|thumb|right|Example of channel system of 1JJ2]] [http://mole.chemi.muni.cz MOLE 2] is a successor of a popular software tool [http://lcc.ncbr.muni.cz/whitezone/development/mole/web/index.php Mole] for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate '''analysis of channels and transmembrane pores''' even ''' in large structures''' (hundreds of thousands of atoms). As a new feature, MOLE 2 '''estimates''' not only '''physicochemical properties''' of the identified channels, i.e., '''hydropathy, hydrophobicity, polarity, charge, and mutability''', but also physicochemical properties of the cavities. For thorough description of the functionality and instructions on working with MOLE 2 please consult the [http://dx.doi.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf manual].<br />
<br />
==MOLE 2.5 Update==<br />
Update of MOLE 2 with novel functionality and bug fixes has been released. The binaries and plugins are available for download from the [https://webchem.ncbr.muni.cz/Platform/App/Mole | main page].<br />
* Easily remove parts of the PDB entry with [https://webchem.ncbr.muni.cz/Wiki/PatternQuery:UserManual PatternQuery].<br />
* New PDB standard mmCIF is supported and recommended for all calculations.<br />
* New weight functions for tunnel/pore calculation.<br />
<br />
<br />
==Availability and Requirements==<br />
MOLE 2.5 is available as a [https://webchem.ncbr.muni.cz/Platform/App/Mole GUI application] with in-built molecular browser enabling user interactive work; [https://webchem.ncbr.muni.cz/Platform/App/Mole command-line application] and [https://webchem.ncbr.muni.cz/Platform/App/Mole PyMOL & Chimera plugin]. Some functionality is also available via online [http://beta.mole.upol.cz web service].<br />
<br />
* GUI application is available for Windows with [http://www.microsoft.com/en-us/download/details.aspx?id=17851 .NET 4.0 framework] or newer installed.<br />
* Command-line application and PyMOL&Chimera plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems [http://mono-project.com/Main_Page Mono framework] 2.10 or newer is required.<br />
<br />
<br />
[[File:Plugin.png|500px|thumb|center|MOLE 2.5 PyMOL plugin]]<br />
<br />
==References==<br />
<br />
# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: [http://dx.doi.org/10.1186/1758-2946-5-39 MOLE 2.0: advanced approach for analysis of biomacromolecular channels]. Journal of Cheminformatics 2013, 5:39.<br />
# Pravda,L., Berka,K., Svobodová Vařeková,R., Sehnal,D., Banáš,P., Laskowski,R.A., Koča,J. and Otyepka,M. (2014) [http://dx.doi.org/10.1186/s12859-014-0379-x Anatomy of enzyme channels]. BMC Bioinformatics, 15, 379.<br />
# Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: [http://dx.doi.org/10.1093/nar/GKS363 MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels]. Nucleic acids research 2012, 40:W222–7.<br />
<br />
[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=File:Plugin.png&diff=12615File:Plugin.png2017-07-13T11:21:42Z<p>LukasPravda: LukasPravda uploaded a new version of File:Plugin.png</p>
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<div>MOLE 2.0 plugin GUI</div>LukasPravdahttps://pymolwiki.org/index.php?title=Covers&diff=12509Covers2017-01-17T09:35:00Z<p>LukasPravda: added ValidatorDB article</p>
<hr />
<div>= PyMOL-created Journal Covers =<br />
Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.<br />
<br />
Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.<br />
<br />
<gallery perrow="5"><br />
<br />
<!-- Please consider using the following format: Image:filename.jpg|Brief description of the image (not necessarily the article title). [http://www.journal.org/url-to-issue-table-of-contents ''Journal'', Volume 338, Issue 6112, 7 Dec 2012]. --><br />
<br />
<!-- 2015 --><br />
Image:Jctcce v011i009.jpg|'''How Molecular Conformational Changes Affect Changes in Free Energy''' [http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00235 ''J. Chem. Theory Comput.'', Volume 11, Number 7, June 2015].<br />
Image:Nucl._Acids_Res.-2015-Front-Matter_DBissue.jpg|'''ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank''' [https://doi.org/10.1093/nar/gku1118 ''Nucl Acids Res'', Volume 43, Issue D1, January 2015].<br />
<br />
<!-- 2014 --><br />
Image:Hdgyp_cover.jpg|'''Structure of P. maritima HDGYP domain showing a novel tri-iron catalytic centre''' [http://onlinelibrary.wiley.com/doi/10.1111/mmi.12494/abstract ''Molecular Microbiology'', Volume 91, Number 1, January 2014].<br />
<br />
<!--2013--><br />
Image:cover_Paunescu.jpg|'''Protection and Deprotection of DNA — High-Temperature Stability of Nucleic Acid Barcodes for Polymer Labeling''' [http://onlinelibrary.wiley.com/doi/10.1002/anie.v52.15/issuetoc ''Angewandte Chemie International Edition'', Volume 52, Issue 15, 8 April 2013].<br />
<!--2012--><br />
Image:Proteins_08010_c1_sp_Ob.png|'''A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES''' [http://dx.doi.org/10.1002/prot.24113 Proteins, Volume 80, Issue 10, 2012].<br />
<br />
<!--2011--><br />
Image:Goldenberg cover.jpg|'''Protein Science''', Vol. 20, No. 12, Dec 2011<br />
Image:Polymer_physics_cover.png|'''Journal of Polymer Science''', Nov 15 2011<br />
Image:Biophysical_cover.png|'''Biophysical Journal''', Aug 3 2011<br />
Image:Science 2011 16.jpg|'''Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing''', [[http://www.sciencemag.org/content/333/6049.toc Science, Sept. 16, 2011]].<br />
Image:JExpBiol-214-4.jpg|'''Deconstructing honeybee vitellogenin''' [http://dx.doi.org/10.1242/jeb.048314 J. Exp. Biol., Volume 214, Issue 4, 2011].<br />
Image:FEBS-585-8.png|'''Binding of 14-3-3g to membranes''' [http://dx.doi.org/10.1016/j.febslet.2011.03.027 FEBS lett., Volume 585, Issue 8, 2011].<br />
Image:PNASCover.gif|Image of two short stretches of double-stranded DNA linked by a ruthenium 'light-switch complex', October 25, 2011; 108 (43) [[http://www.pnas.org/content/108/43.cover-expansion]]<br />
Image:Cen.jpg|'''PI3K Inhibitors''' C&EN, April 11, 2011.<br />
Image:Salam.jpg|'''Microbiology of article entitled "Genetic mapping of the interface between the ArsD metallochaperone and the ArsA ATPase.''' Volume 79, Feb, 2011, [http://onlinelibrary.wiley.com/doi/10.1111/mmi.2011.79.issue-4/issuetoc ''Molecular Microbiology'']<br />
<br />
<!--2010--><br />
<br />
<!--2009--><br />
Image:20091111_Structure_cover.jpg|Human antibodies coded by the VH3 gene and specific for V3 crown of the HIV-1 gp120 have an antigen-binding site shaped like a soup ladle. [http://www.cell.com/structure/issue?pii=S0969-2126%2809%29X0012-2 ''Structure'', Volume 17, Issue 11, 11 Nov 2009].<br />
Image:101209Nature.jpg|'''X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor''' [http://www.nature.com/nature/journal/v462/n7274/full/nature08624.html ''Nature'']<br />
Image:MMcoverMay2009.png|'''Impact of rRNA methylations on ribosome recycling and fidelity of initiation in ''Escherichia coli''.''' [http://www.ncbi.nlm.nih.gov/pubmed/19400784 ''Molecular Microbiology'']<br />
<br />
<!--2008--><br />
Image:jbc_mchu.jpeg|'''Crystal structure of the catalytic domain of the mitotic checkpoint kinase Mps1 in complex with SP600125'''. Chu ML, Chavas LM, Douglas KT, Eyers PA, Tabernero L. ''[http://www.ncbi.nlm.nih.gov/pubmed/18480048 J Biol Chem.'' 2008 Aug 1;283(31):21495-500]. Epub 2008 May 14.<br />
Image:JBC_Apr18_2008.jpg|'''Allosteric motions in structures of yeast NAD-specific isocitrate dehydrogenase.''' [http://www.ncbi.nlm.nih.gov/pubmed/18256028?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''J. Biol. Chem.'']<br />
<br />
<!--2007--><br />
Image:ACR_Jun_2007.jpg|'''Shall we dance? How a multicopper oxidase chooses its electron transfer partner.''' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17425282&query_hl=1&itool=pubmed_docsum ''Acc. Chem. Res.'']<br />
Image:ABB_May1_2007.jpg|'''Crystal structure of the yeast nicotinamidase Pnc1p.''' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17382284&query_hl=1&itool=pubmed_docsum ''Arch. Biochem. Biophys.'']<br />
<br />
<!--2006--><br />
<br />
<!--2005--><br />
<br />
<!--2004--><br />
Image:MolecularCell011.jpg|'''FLT3 Activation by an Oncogenic Insertion''' Molecular Cell, Volume 13 Number 2, January 30, 2004.<br />
<br />
<br />
<!--Ambiguous date or no date specified (need to look up)--><br />
Image:ParM.gif|'''End-on view of the atomic model of the bacterial actinlike ParM protein double-helical filament, generated from an electron microscopic reconstruction.''' [http://www.sciencemag.org/content/338/6112.toc A Bipolar Spindle of Antiparallel ParM Filaments Drives Bacterial Plasmid Segregation].<br />
Image:biochem_010110_cover.jpg|'''Crystal Structure of the Class D beta-lactamase OXA-1 in complex with doripenem''' [http://www.ncbi.nlm.nih.gov/pubmed/19919101 ''Biochemistry'']<br />
<br />
<!--Not yet sorted--><br />
Image:Cover_royal_soc_small.png|[http://pymolwiki.org/index.php/File:Cover_royal_soc_small.png Philosophical Transactions of The Royal Society, B : Biological Sciences Jan, 2009 ]<br />
Image:Image_large.png|[http://pymolwiki.org/index.php/File:Image_large.png MD simulation of protein-protein binding ]'''Pymol generated Movie is avialable inside pdf'''[[http://www.pymolwiki.org/index.php/File:SH3.pdf]] ''' or high quality AVI format'''[http://gepard.bioinformatik.uni-saarland.de/old_html/material/dl/SH3_large.avi]<br />
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]<br />
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]<br />
Image:080701_h.a.steinberg_biochemie.jpg|'''Targeting DNA''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236236%232008%23999099992%23693363%23FLA%23&_cdi=6236&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3e9cfd266720a7645cec65b2bfbd7645 BIOCHEMIE], July 1, 2008 Cover, Vol. 90.<br />
Image:080602cnen.pdf.jpg|'''Harnessing Helices''', [http://pubs.acs.org/cen/coverstory/86/8622aboutcover.html Chemical & Engineering News], June 2, 2008 Cover, Vol. 86, Issue 22.<br />
Image:080118_h.a.steinberg_JBC.jpg|''' Fusarium head blight (FHB)''', [http://www.jbc.org/content/vol283/issue3/cover.shtml JBC], January 18, 2008 Cover, Vol. 283, Issue 3.<br />
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.<br />
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.<br />
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.<br />
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007. <br />
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.<br />
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.<br />
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.<br />
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.<br />
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007<br />
Image:070803_h.a.steinberg_molec_cell.jpg|'''Paused transcription complexes''', [http://www.cell.com/molecular-cell/issue?pii=S1097-2765(07)X0175-8# Molecular Cell], August 3 2007 Cover, Vol. 27, Issue 3.<br />
Image:070415.h.a.steinberg_ABB.jpg|'''Vitamin D''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=6701&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=b9733feacdee17300b6b31649737997b&jchunk=460#460 ABB], April 14 2007 Cover, Vol. 460, Issue 2.<br />
Image:Jbc_20070413.gif|<b>''Mycobacterium tuberculosis'' PknD dimerization</b> [http://www.jbc.org/content/282/15 JBC], April 13 2007 Cover, Vol. 282, Issue 15.<br />
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.<br />
Image:070301_h.a.steinberg_protein_science.jpg|'''Glucose-1-phosphate uridylyltransferase''', [http://www.proteinscience.org/content/vol16/issue3/cover.shtml Protein Science], March 3, 2007 Cover, Volume 16 Issue 3.<br />
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.<br />
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.<br />
Image:061208_h.a.steinberg_molec_cell.jpg|'''Sen1 Control of RNA Pol II Termination''', [http://www.molecule.org/content/issue?volume=24&issue=5 Molecular Cell], December 8, 2006 Cover, Volume 24 Issue 5.<br />
Image:061201_h.a.steinberg_molec_micro.jpg|'''Transposon Loops''', [http://www.blackwell-synergy.com/toc/mmi/62/6 Molecular Microbiology], December 1, 2006 Cover, Volume 62 Issue 6.<br />
Image:060904cnen.pdf.jpg|'''Glycosylation Engineering''', [http://pubs.acs.org/subscribe/journals/cen/84/i36/toc/toc_i36.html Chemical & Engineering News], Sept. 4th, 2006.<br />
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.<br />
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.<br />
Image:060101_h.a.steinberg_protein_science.jpg|'''Poly (2S-proline)''', [http://www.proteinscience.org/content/vol15/issue1/cover.shtml Protein Science], January 1, 2006 Cover, Volume 15, Issue 1.<br />
Image:050624_h.a.steinberg_JMB.jpg|'''Ribonuclease A''', [http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996459998%23609160%23FLA%23&_cdi=6899&_pubType=J&view=c&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=9623405850d13617453adb034fb10a81 JMB], November 18, 2005 Cover, Volume 354, Issue 1.<br />
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.<br />
Image:050923_h.a.steinberg_JBC.jpg|'''GalNAc kinase''', [http://www.jbc.org/content/vol280/issue38/cover.shtml JBC], September 23, 2005 Cover, Volume 280, Issue 38.<br />
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.<br />
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.<br />
Image:050624_h.a.steinberg_jmb1.jpg|[http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236899%232005%23996509994%23597371%23FLA%23&_cdi=6899&_pubType=J&_auth=y&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bc37bcef231976694d0fbe8920ef596 JMB], June 24, 2005 Cover, Volume 349, Issue 5.<br />
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.<br />
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.<br />
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.<br />
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.<br />
Image:apr2003_ProtSci.png|<b>''Pae'' SmAP1</b> 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].<br />
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]<br />
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]<br />
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.<br />
Image:Iapp.gif|<b>Cross-Beta Spine of IAPP</b>, [http://www3.interscience.wiley.com/journal/121603721/issue ''Protein Science'', September 2008].<br />
Image:JBC 080406 no31 proof.png|<b>Calcium Sensor</b>, [http://www.jbc.org/content/281/31 ''JBC'', August 4, 2006].<br />
Image:AngewChemIntEd_Comm_Cover_R_Cighetti.jpg |[http://pymolwiki.org/index.php/File:AngewChemIntEd_Comm_Cover_R_Cighetti.jpg, <b>LPS coated nanoparticle</b>, ''Angew.Chem.Int.Ed.'', January 17, 2011]<br />
Image:Structure_cover_Dec2010.jpg|<b>DAXX helical bundle (DHB) and DHB/Rassf1C structures</b>, [http://www.cell.com/structure/issue?pii=S0969-2126%2810%29X0013-2 ''Structure'', December 2010].<br />
<br />
<br />
</gallery></div>LukasPravdahttps://pymolwiki.org/index.php?title=File:Nucl._Acids_Res.-2015-Front-Matter_DBissue.jpg&diff=12508File:Nucl. Acids Res.-2015-Front-Matter DBissue.jpg2017-01-17T09:30:37Z<p>LukasPravda: </p>
<hr />
<div></div>LukasPravdahttps://pymolwiki.org/index.php?title=MOLE_2.0:_advanced_approach_for_analysis_of_biomacromolecular_channels&diff=11433MOLE 2.0: advanced approach for analysis of biomacromolecular channels2013-09-22T10:50:39Z<p>LukasPravda: wrong url corrected</p>
<hr />
<div>[[File:Molelogo.png|80px|left|]] [[File:1jj2.png|400px|thumb|right|Example of channel system of 1JJ2]] [http://mole.chemi.muni.cz MOLE 2.0] is a successor of a popular software tool [http://lcc.ncbr.muni.cz/whitezone/development/mole/web/index.php Mole] for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate '''analysis of channels and transmembrane pores''' even ''' in large structures''' (hundreds of thousands of atoms). As a new feature, MOLE 2.0 '''estimates''' not only '''physicochemical properties''' of the identified channels, i.e., '''hydropathy, hydrophobicity, polarity, charge, and mutability''', but also physicochemical properties of the cavities. For thorough description of the functionality and instructions on working with MOLE 2.0 please consult the [http://dx.doi.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf manual].<br />
<br />
<br />
==Availability and Requirements==<br />
MOLE 2.0 is available as a [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_ui.zip GUI application] with in-built molecular browser enabling user interactive work; [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_cmd.zip command-line application] and [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_pymol.zip PyMOL plugin]. Some functionality is also available via online [http://mole.upol.cz web service].<br />
<br />
* GUI application is available for Windows with [http://www.microsoft.com/en-us/download/details.aspx?id=17851 .NET 4.0 framework] or newer installed.<br />
* Command-line application and PyMOL plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems [http://mono-project.com/Main_Page Mono framework] 2.10 or newer.<br />
<br />
<br />
<br />
[[File:Plugin.png|500px|thumb|center|MOLE 2.0 PyMOL plugin]]<br />
<br />
==References==<br />
<br />
# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: [http://dx.doi.org/10.1186/1758-2946-5-39 MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics 2013, 5:39.]<br />
# Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: [http://dx.doi.org/10.1093/nar/GKS363 MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic acids research 2012, 40:W222–7.]<br />
<br />
[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=MOLE_2.0:_advanced_approach_for_analysis_of_biomacromolecular_channels&diff=11431MOLE 2.0: advanced approach for analysis of biomacromolecular channels2013-09-10T12:47:55Z<p>LukasPravda: typos correction</p>
<hr />
<div>[[File:Molelogo.png|80px|left|]] [[File:1jj2.png|400px|thumb|right|Example of channel system of 1JJ2]] [http://mole.chemi.muni.cz MOLE 2.0] is a successor of a popular software tool [http://lcc.ncbr.muni.cz/whitezone/development/mole/web/index.php Mole] for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate '''analysis of channels and transmembrane pores''' even ''' in large structures''' (hundreds of thousands of atoms). As a new feature, MOLE 2.0 '''estimates''' not only '''physicochemical properties''' of the identified channels, i.e., '''hydropathy, hydrophobicity, polarity, charge, and mutability''', but also physicochemical properties of the cavities. For thorough description of the functionality and instructions on working with MOLE 2.0 please consult the [http://doi.dx.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf manual].<br />
<br />
<br />
==Availability and Requirements==<br />
MOLE 2.0 is available as a [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_ui.zip GUI application] with in-built molecular browser enabling user interactive work; [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_cmd.zip command-line application] and [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_pymol.zip PyMOL plugin]. Some functionality is also available via online [http://mole.upol.cz web service].<br />
<br />
* GUI application is available for Windows with [http://www.microsoft.com/en-us/download/details.aspx?id=17851 .NET 4.0 framework] or newer installed.<br />
* Command-line application and PyMOL plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems [http://mono-project.com/Main_Page Mono framework] 2.10 or newer.<br />
<br />
<br />
<br />
[[File:Plugin.png|500px|thumb|center|MOLE 2.0 PyMOL plugin]]<br />
<br />
==References==<br />
<br />
# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: [http://dx.doi.org/10.1186/1758-2946-5-39 MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics 2013, 5:39.]<br />
# Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: [http://dx.doi.org/10.1093/nar/GKS363 MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic acids research 2012, 40:W222–7.]<br />
<br />
[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=MOLE_2.0:_advanced_approach_for_analysis_of_biomacromolecular_channels&diff=11430MOLE 2.0: advanced approach for analysis of biomacromolecular channels2013-09-10T12:44:39Z<p>LukasPravda: </p>
<hr />
<div>[[File:Molelogo.png|80px|left|]] [[File:1jj2.png|400px|thumb|right|Example of channel system of 1JJ2]] [http://mole.chemi.muni.cz MOLE 2.0] is a successor of a popular software tool [http://lcc.ncbr.muni.cz/whitezone/development/mole/web/index.php Mole] for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate '''analysis of channels and transmembrane pores''' even ''' in large structures''' (hundreds of thousands of atoms). As a new feature, MOLE 2.0 '''estimates''' not only '''physicochemical properties''' of the identified channels, i.e., '''hydropathy, hydrophobicity, polarity, charge, and mutability''', but also physicochemical properties of the cavities. For thorough description of the functionality and instructions on working with MOLE 2.0 please consult the [http://doi.dx.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf manual].<br />
<br />
<br />
==Availability and Requirements==<br />
MOLE 2.0 is available as a [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_ui.zip GUI application] with in-built molecular browser enabling user interactive work; [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_cmd.zip command-line application] and [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_pymol.zip PyMOL plugin]. Some functionality is also available via online [http://mole.upol.cz web service].<br />
<br />
* GUI application is available for Windows with [http://www.microsoft.com/en-us/download/details.aspx?id=17851 .NET 4.0 framework] or newer installed.<br />
* Command-line application and PyMOL plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems [http://mono-project.com/Main_Page Mono framework] 2.10 or newer.<br />
<br />
<br />
<br />
[[File:Plugin.png|500px|thumb|center|MOLE 2.0 PyMOL plugin]]<br />
<br />
==References==<br />
<br />
# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: [http://doi.dx.org/10.1186/1758-2946-5-39 MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics 2013, 5:39.]<br />
# Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: [http://doi.dx.org/10.1093/nar/GKS363 MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic acids research 2012, 40:W222–7.]<br />
<br />
[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=Main_Page&diff=11429Main Page2013-09-10T12:41:29Z<p>LukasPravda: added information about the new plugin MOLE for PyMOL</p>
<hr />
<div>__NOTOC__<br />
{| align="center" style="padding-bottom: 4em;"<br />
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
| New accounts: email jason (dot) vertrees (@) gmail dot com<br />
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"<br />
|}<br />
{| align="center" width="45%" style="background: #EDEBD5; 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: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links<br />
|- <br />
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''<br />
|-<br />
| style="font-size: 1.1em; color #61021F; 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; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''<br />
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')<br />
||'''[[GoogleSearch]]'''<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 />
| [[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 />
! New Plugin<br />
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.<br />
|-<br />
! New Software<br />
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.<br />
|-<br />
! New Script<br />
| [[cgo_arrow]] draws an arrow between two picked atoms.<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.<br />
|-<br />
! New Script<br />
| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.<br />
|-<br />
! New Script<br />
| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.<br />
|-<br />
! New Script<br />
| [[DistancesRH|Distances RH]]<br />
|-<br />
! PyMOL on the iPad<br />
| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.<br />
|-<br />
! OS X Compatibility<br />
| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].<br />
|-<br />
! New Script<br />
| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file<br />
|-<br />
! New Script<br />
| [[b2transparency]] can set surface transparency based on atom b-factor<br />
|-<br />
! New Extension<br />
| [[psico]] is a python module which extends PyMOL with many commands<br />
|-<br />
! New Script<br />
| [[uniprot_features]] makes named selections for sequence annotations from uniprot<br />
|-<br />
! New Plugin<br />
| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.<br />
|-<br />
! New Script<br />
| [[set_phipsi]] can set phi/psi angles for all residues in a selection<br />
|-<br />
! New Script<br />
| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack. <br />
|-<br />
! New Script<br />
| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!<br />
|-<br />
! New Script<br />
| [[cyspka]] is an experimental surface cysteine pKa predictor.<br />
|-<br />
! New Plugin<br />
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].<br />
|-<br />
! New Script<br />
| [[spectrum_states]] colors states of multi-state object<br />
|-<br />
! New Script<br />
| [[TMalign]] is a wrapper for the TMalign program<br />
|-<br />
! Gallery Updates<br />
| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering<br />
|-<br />
! New Script<br />
| [[save_settings]] can dump all changed settings to a file<br />
|-<br />
! Tips & Tricks<br />
| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.<br />
|-<br />
! Wiki Update<br />
| Wiki has been updated. Please report any problems to the sysops.<br />
|-<br />
! New Scripts<br />
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]<br />
|-<br />
! New Script<br />
| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. <br />
|-<br />
! New Script<br />
| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]]. <br />
|-<br />
! New Script<br />
| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.<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 />
<DPL><br />
namespace=<br />
category=Commands|Plugins|Script_Library|Settings<br />
includepage=*<br />
includemaxlength=1050<br />
escapelinks=false<br />
resultsheader=__NOTOC__ __NOEDITSECTION__<br />
randomcount=1<br />
mode=userformat<br />
addpagecounter=true<br />
listseparators=,<h3>[[%PAGE%]]</h3>,,\n<br />
</DPL><br />
</div><br />
<div style="clear: both;"></div><br />
|}<br />
|<br />
|style="vertical-align: top; width: 18%"|<br />
<DPL><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 />
</DPL><br />
<br />
|}</div>LukasPravdahttps://pymolwiki.org/index.php?title=Mole&diff=11428Mole2013-09-10T12:38:23Z<p>LukasPravda: added information about the new version of software MOLE</p>
<hr />
<div>====There is a new version of MOLE [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|check it out]]!====<br />
<br />
<br />
[http://mole.chemi.muni.cz MOLE] is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in molecular structures. The core of MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is a powerful software (overcomming some limitations of [[Caver]] tool) for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories (AMBER ascii traj and parm7 are supported) in which analysis of a large number of snapshots is required.<br />
<br />
Program is available as standalone application for Linux(Unix), MacOS and Windows. Plugin for pyMol enables calling the MOLE program via an user friendly interface and allows results visualization. The on-line interface provides another interactive and easy-to-use interface to analyze molecular channels.<br />
<br />
[http://mole.chemi.muni.cz/web/docs/doc_pymolplugin.php Tutorial] is also available.<br />
<br />
References:<br />
<br />
Petrek M., Kosinova P., Koca J., Otyepka M.: [http://dx.doi.org/10.1016/j.str.2007.10.007 MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure 2007, 15, 1357-1363]<br />
<br />
[[Image:KscA.png]]<br />
<br />
[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=MOLE_2.0:_advanced_approach_for_analysis_of_biomacromolecular_channels&diff=11427MOLE 2.0: advanced approach for analysis of biomacromolecular channels2013-09-10T12:29:04Z<p>LukasPravda: </p>
<hr />
<div>[[File:Molelogo.png|80px|left|]] [[File:1jj2.png|400px|thumb|right|Example of channel system of 1JJ2]] [http://mole.chemi.muni.cz MOLE 2.0] is a successor of a popular software tool [http://lcc.ncbr.muni.cz/whitezone/development/mole/web/index.php Mole] for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate '''analysis of channels and transmembrane pores''' even ''' in large structures''' (hundreds of thousands of atoms). As a new feature, MOLE 2.0 '''estimates''' not only '''physicochemical properties''' of the identified channels, i.e., '''hydropathy, hydrophobicity, polarity, charge, and mutability''', but also physicochemical properties of the cavities. For thorough description of the functionality and instructions how working with MOLE 2.0 please consult the [http://doi.dx.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf manual].<br />
<br />
<br />
==Availability and Requirements==<br />
MOLE 2.0 is available as a [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_ui.zip GUI application] with in-built molecular browser enabling user interactive work; [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_cmd.zip command-line application] and [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_pymol.zip PyMOL plugin]. Some functionality is also available via online [http://mole.upol.cz web service].<br />
<br />
* GUI application is available for Windows with [http://www.microsoft.com/en-us/download/details.aspx?id=17851 .NET 4.0 framework] or newer installed.<br />
* Command-line application and PyMOL plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems [http://mono-project.com/Main_Page Mono framework] 2.10 or newer.<br />
<br />
<br />
<br />
[[File:Plugin.png|500px|thumb|center|MOLE 2.0 PyMOL plugin]]<br />
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==References==<br />
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# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: [http://doi.dx.org/10.1186/1758-2946-5-39 MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics 2013, 5:39.]<br />
# Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: [http://doi.dx.org/10.1093/nar/GKS363 MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic acids research 2012, 40:W222–7.]<br />
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[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=Mole2&diff=11426Mole22013-09-10T12:28:41Z<p>LukasPravda: moved Mole2 to MOLE 2.0: advanced approach for analysis of biomacromolecular channels</p>
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<div>#REDIRECT [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=MOLE_2.0:_advanced_approach_for_analysis_of_biomacromolecular_channels&diff=11425MOLE 2.0: advanced approach for analysis of biomacromolecular channels2013-09-10T12:28:41Z<p>LukasPravda: moved Mole2 to MOLE 2.0: advanced approach for analysis of biomacromolecular channels</p>
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<div>=MOLE 2.0: advanced approach for analysis of biomacromolecular channels=<br />
[[File:Molelogo.png|80px|left|]] [[File:1jj2.png|400px|thumb|right|Example of channel system of 1JJ2]] [http://mole.chemi.muni.cz MOLE 2.0] is a successor of a popular software tool [http://lcc.ncbr.muni.cz/whitezone/development/mole/web/index.php Mole] for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate '''analysis of channels and transmembrane pores''' even ''' in large structures''' (hundreds of thousands of atoms). As a new feature, MOLE 2.0 '''estimates''' not only '''physicochemical properties''' of the identified channels, i.e., '''hydropathy, hydrophobicity, polarity, charge, and mutability''', but also physicochemical properties of the cavities. For thorough description of the functionality and instructions how working with MOLE 2.0 please consult the [http://doi.dx.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf manual].<br />
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==Availability and Requirements==<br />
MOLE 2.0 is available as a [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_ui.zip GUI application] with in-built molecular browser enabling user interactive work; [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_cmd.zip command-line application] and [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_pymol.zip PyMOL plugin]. Some functionality is also available via online [http://mole.upol.cz web service].<br />
<br />
* GUI application is available for Windows with [http://www.microsoft.com/en-us/download/details.aspx?id=17851 .NET 4.0 framework] or newer installed.<br />
* Command-line application and PyMOL plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems [http://mono-project.com/Main_Page Mono framework] 2.10 or newer.<br />
<br />
<br />
<br />
[[File:Plugin.png|500px|thumb|center|MOLE 2.0 PyMOL plugin]]<br />
<br />
==References==<br />
<br />
# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: [http://doi.dx.org/10.1186/1758-2946-5-39 MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics 2013, 5:39.]<br />
# Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: [http://doi.dx.org/10.1093/nar/GKS363 MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic acids research 2012, 40:W222–7.]<br />
<br />
[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=MOLE_2.0:_advanced_approach_for_analysis_of_biomacromolecular_channels&diff=11424MOLE 2.0: advanced approach for analysis of biomacromolecular channels2013-09-10T12:26:47Z<p>LukasPravda: Created page with "=MOLE 2.0: advanced approach for analysis of biomacromolecular channels= left| Example of channel system of 1JJ2 [h..."</p>
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<div>=MOLE 2.0: advanced approach for analysis of biomacromolecular channels=<br />
[[File:Molelogo.png|80px|left|]] [[File:1jj2.png|400px|thumb|right|Example of channel system of 1JJ2]] [http://mole.chemi.muni.cz MOLE 2.0] is a successor of a popular software tool [http://lcc.ncbr.muni.cz/whitezone/development/mole/web/index.php Mole] for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate '''analysis of channels and transmembrane pores''' even ''' in large structures''' (hundreds of thousands of atoms). As a new feature, MOLE 2.0 '''estimates''' not only '''physicochemical properties''' of the identified channels, i.e., '''hydropathy, hydrophobicity, polarity, charge, and mutability''', but also physicochemical properties of the cavities. For thorough description of the functionality and instructions how working with MOLE 2.0 please consult the [http://doi.dx.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf manual].<br />
<br />
<br />
==Availability and Requirements==<br />
MOLE 2.0 is available as a [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_ui.zip GUI application] with in-built molecular browser enabling user interactive work; [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_cmd.zip command-line application] and [http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_pymol.zip PyMOL plugin]. Some functionality is also available via online [http://mole.upol.cz web service].<br />
<br />
* GUI application is available for Windows with [http://www.microsoft.com/en-us/download/details.aspx?id=17851 .NET 4.0 framework] or newer installed.<br />
* Command-line application and PyMOL plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems [http://mono-project.com/Main_Page Mono framework] 2.10 or newer.<br />
<br />
<br />
<br />
[[File:Plugin.png|500px|thumb|center|MOLE 2.0 PyMOL plugin]]<br />
<br />
==References==<br />
<br />
# Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: [http://doi.dx.org/10.1186/1758-2946-5-39 MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics 2013, 5:39.]<br />
# Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: [http://doi.dx.org/10.1093/nar/GKS363 MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic acids research 2012, 40:W222–7.]<br />
<br />
[[Category:Surfaces and Voids|Mole]]<br />
[[Category:Biochemical_Properties]]<br />
[[Category:Plugins]]<br />
[[Category:Pymol-script-repo]]</div>LukasPravdahttps://pymolwiki.org/index.php?title=File:Plugin.png&diff=11423File:Plugin.png2013-09-10T12:18:37Z<p>LukasPravda: MOLE 2.0 plugin GUI</p>
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<div>MOLE 2.0 plugin GUI</div>LukasPravdahttps://pymolwiki.org/index.php?title=File:Molelogo.png&diff=11422File:Molelogo.png2013-09-10T12:08:40Z<p>LukasPravda: Mole 2.0 logo</p>
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<div>Mole 2.0 logo</div>LukasPravdahttps://pymolwiki.org/index.php?title=File:1jj2.png&diff=11421File:1jj2.png2013-09-10T11:46:14Z<p>LukasPravda: Example of channel system of large ribosomal subunit (1JJ2)</p>
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<div>Example of channel system of large ribosomal subunit (1JJ2)</div>LukasPravda