PyMOL Wiki - User contributions [en]

File:Movie.gif

2009-12-31T01:38:02Z

Sawaya: movie of a helicase unwinding DNA

movie of a helicase unwinding DNA

File:Interface02 labeled.png

2009-12-31T01:26:29Z

Sawaya: Interface of PE-PPE complex

Interface of PE-PPE complex

File:Density-stereo.png

2009-12-31T00:30:55Z

Sawaya: electron density map of dUTPase

electron density map of dUTPase

File:Overlay03.png

2009-12-30T23:54:52Z

Sawaya: overlay of alpha carbon traces of LovD

overlay of alpha carbon traces of LovD

File:Dutpase active02-labeled.png

2009-12-30T00:26:24Z

Sawaya: Active Site image of dUTPase

Active Site image of dUTPase

File:Csos3-stereo01.png

2009-12-30T00:01:56Z

Sawaya: stereo image of CsoS3 fold

stereo image of CsoS3 fold

Covers

2009-12-29T23:43:27Z

Sawaya:

= PyMOL-created Journal Covers =
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.

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.

<gallery perrow="5">
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.'']
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.'']
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.'']
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 ]
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]
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]
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.
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.
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.
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007.
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007
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.
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.
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.
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.
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.
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.
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.
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.
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.
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.
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.
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.

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.
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.
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.
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.
Image:apr2003_ProtSci.png|''Pae'' SmAP1 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.
Image:Iapp.gif|Cross-Beta Spine of IAPP, [http://www3.interscience.wiley.com/journal/121603721/issue ''Protein Science'', September 2008].
Image:JBC 080406 no31 proof.png|Calcium Sensor, [http://www.jbc.org/content/281/31 ''JBC'', August 4, 2006].
</gallery>

File:JBC 080406 no31 proof.png

2009-12-29T23:36:34Z

Sawaya: DaLoop Cover of JBC, Augus 4, 2006.

DaLoop Cover of JBC, Augus 4, 2006.

Covers

2009-12-29T23:27:04Z

Sawaya:

Covers

2009-12-29T23:20:50Z

Sawaya:

= PyMOL-created Journal Covers =
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.

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.

<gallery perrow="5">
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.'']
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.'']
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.'']
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 ]
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]
Image:Cover_JCIM_2008_48-10.png|[http://pubs.acs.org/action/showLargeCover?issue=329743592 J. Chem. Inf. Model., 2008, 48 (10)]
Image:Science090410.jpg|[http://www.sciencemag.org/content/vol324/issue5924/index.dtl Protein Dynamics]
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.
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.
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.
Image:071213nature.pdf.jpg|'''Pumping Ions''', [http://www.nature.com/nature/journal/v450/n7172/index.html Nature], Dec. 13th, 2007.
Image:0712channels.jpg|[http://www.landesbioscience.com/journals/channels/toc/1/6], Dec 2007.
Image:071123science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5854/index.dtl Science], Nov. 23rd, 2007.
Image:071120pnas.jpg|'''Sensing Calciums'''[http://www.pnas.org/content/104/47.toc], Nov 20th, 2007.
Image:071113Structure.png|'''Aminoacyl-tRNA synthetases from human mitochondria'''[http://www.cell.com/structure/issue?pii=S0969-2126(07)X0180-1], Nov. 13th, 2007.
Image:071009science.pdf.jpg|[http://www.sciencemag.org/content/vol318/issue5849/index.dtl Science], Oct. 19th, 2007.
Image:070920nature.pdf.jpg|'''Sensing Acid''', [http://www.nature.com/nature/journal/v449/n7160/index.html Nature], Sept. 20th, 2007.
Image:070816nature.pdf.jpg|'''Form Finds Function?''', [http://www.nature.com/nature/journal/v448/n7155/index.html Nature], Aug. 16thm 2007.
Image:Largecover.gif|[http://www.nature.com/neuro/journal/v10/n8/abs/nn1942.html Nature Neuroscience] Vol. 10 No. 8 Aug. 2007
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.
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.
Image:070405nature.pdf.jpg|'''Auxin Action Revealed''', [http://www.nature.com/nature/journal/v446/n7136/index.html Nature], April 5, 2007.
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.
Image:070219cnen.pdf.jpg|'''How Ribosomes Work''', [http://pubs.acs.org/cen/coverstory/85/8508aboutcover.html Chemical & Engineering News], Feb. 19th, 2007.
Image:070215nature.pdf.jpg|'''HIV's Hidden Weakness''', [http://www.nature.com/nature/journal/v445/n7129/index.html Nature], Feb. 15th, 2007.
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.
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.
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.
Image:060817nature.pdf.jpg|'''Chromatin Code Decoded''', [http://www.nature.com/nature/journal/v442/n7104/index.html Nature], Aug. 17th, 2006.
Image:060522cnen.pdf.jpg|'''Halogenases''', [http://pubs.acs.org/subscribe/journals/cen/84/i21/toc/toc_i21.html Chemical & Engineering News], May 22nd, 2006.
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.
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.
Image:051020nature.pdf.jpg|'''The B to Z of DNA''', [http://www.nature.com/nature/journal/v437/n7062/index.html Nature], Oct. 20th, 2005.

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.
Image:050908nature.pdf.jpg|'''Neurotransmission''', [http://www.nature.com/nature/journal/v437/n7056/index.html Nature], Sept. 8th, 2005.
Image:050722science.pdf.jpg|[http://www.sciencemag.org/content/vol309/issue5734/index.dtl Science], July 22nd, 2005.
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.
Image:050609nature.pdf.jpg|'''Probing Prions''', [http://www.nature.com/nature/journal/v435/n7043/index.html Nature], June 9th, 2005.
Image:050429science.pdf.jpg|[http://www.sciencemag.org/content/vol308/issue5722/index.dtl Science], April 29th, 2005.
Image:040910science.pdf.jpg|[http://www.sciencemag.org/content/vol305/issue5690/index.dtl Science], Sept., 10th, 2004.
Image:040123science.pdf.jpg|[http://www.sciencemag.org/content/vol303/issue5657/index.dtl Science], Jan. 23rd, 2004.
Image:apr2003_ProtSci.png|''Pae'' SmAP1 14-mers, [http://www3.interscience.wiley.com/journal/121602086/issue ''Protein Science'', April 2003].
Image:Ribbon_hh1.png|[http://www.chembiol.com/content/issue?volume=15&issue=4 Chem. Biol.]
Image:0903_1_1.jpg|[http://pubs.acs.org/journals/achre4/covers/36/articleWindow.achre4.091603.html Accounts of Chemical Research]
Image:CRP_nature_cover1.jpg|''Nature'', April 27th, 2006.
Image:Iapp.gif|Cross Beta Spine of IAPP, ''Protein Science'', September 2008.
</gallery>

File:Iapp.gif

2009-12-29T22:35:43Z

Sawaya: Cover of Protein Science, September 2008

Cover of Protein Science, September 2008