From: Joel T. <joe...@ot...> - 2011-05-03 00:54:29
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Hi folks, I am looking at running virtual linux on a windows XP machine and I noticed that pymol runs but without graphics acceleration. Its all installed on the windows side and I have searched the web to see if I can activate enhanced graphics on a linux guest. I don't think you can do it with VMWare player but virtual box looks possible (not sure though) Comments appreciated J _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 |
From: Jason V. <jas...@sc...> - 2011-05-03 02:22:30
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Hi Joel, > I am looking at running virtual linux on a windows XP machine and I noticed > that pymol runs but without graphics acceleration. Its all installed on the > windows side and I have searched the web to see if I can activate enhanced > graphics on a linux guest. I don’t think you can do it with VMWare player > but virtual box looks possible (not sure though) If the VM software supports OpenGL acceleration in the VM then PyMOL will run using direct rendering. Otherwise, it falls back onto software. As I understand it only Parallels at this time offers OpenGL support in the Linux VM. (But, Parallels doesn't yet support OpenGL in Ubuntu 11.04 with Unity, it's planned for their next update.) Both Parallels and VMWare offer OpenGL for Windows. Good luck, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Ben E. <be...@hk...> - 2011-05-03 02:59:41
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Hi Jason and Joel, > As I understand it only Parallels at this time offers OpenGL support > in the Linux VM. (But, Parallels doesn't yet support OpenGL in Ubuntu > 11.04 with Unity, it's planned for their next update.) Both Parallels > and VMWare offer OpenGL for Windows. VirtualBox has some support for hardware accelerated OpenGL in linux guests: http://www.virtualbox.org/manual/ch04.html#guestadd-3d "OpenGL on Linux requires kernel 2.6.27 and higher as well as X.org server version 1.5 and higher. Ubuntu 10.10 and Fedora 14 have been tested and confirmed as working." Have fun. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | |
From: Martin H. <ma...@bl...> - 2011-05-03 20:00:25
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Dear all I would like to ask how it is possible to download the coordinate file for the biological assembly of a protein structure from the PDB. Naturally, this is not a question directly related to PyMOL, but I thought I'll be reaching at least a couple of Biochemists/Chrystallographers who know how to do this. As an example, when downloading the PDB file of "1AVD", I get a file with two chains. The biological assembly would be a tetramer, so I wonder what URL I would require to write into a script that does the downloading. Thanks for help on this. Martin |
From: Jason V. <jas...@sc...> - 2011-05-03 20:22:21
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Hi Martin, Do you mean something like this? If so, use the "type=" parameter with fetch. # grab the biological unit; this PDB1 is in # 2 states, so split them with multiplex fetch 1avd, type=pdb1, multiplex=1, async=0 # color the chains util.color_chains() # show as cartoon as cartoon Cheers, -- Jason On Tue, May 3, 2011 at 4:00 PM, Martin Hediger <ma...@bl...> wrote: > Dear all > I would like to ask how it is possible to download the coordinate file > for the biological assembly of a protein structure from the PDB. > Naturally, this is not a question directly related to PyMOL, but I > thought I'll be reaching at least a couple of > Biochemists/Chrystallographers who know how to do this. > As an example, when downloading the PDB file of "1AVD", I get a file > with two chains. The biological assembly would be a tetramer, so I > wonder what URL I would require to write into a script that does the > downloading. > > Thanks for help on this. > Martin > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Joel T. <joe...@ot...> - 2011-05-03 21:47:18
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Hi Martin, You can download the biological assembly directly from the pdb website. Under download files (RHS) usually the last entry is Biological Assembly. Once downloaded you can unzip it and change the file suffix back to pdb e.g. 1AVD.pdb1 ==> 1AVD_1.pdb Hope this helps Joel _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -----Original Message----- From: Martin Hediger [mailto:ma...@bl...] Sent: Wednesday, 4 May 2011 8:00 a.m. To: pym...@li... Subject: [PyMOL] Downloading the biological assembly from the PDB Dear all I would like to ask how it is possible to download the coordinate file for the biological assembly of a protein structure from the PDB. Naturally, this is not a question directly related to PyMOL, but I thought I'll be reaching at least a couple of Biochemists/Chrystallographers who know how to do this. As an example, when downloading the PDB file of "1AVD", I get a file with two chains. The biological assembly would be a tetramer, so I wonder what URL I would require to write into a script that does the downloading. Thanks for help on this. Martin ------------------------------------------------------------------------------ WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: Thomas H. <sp...@us...> - 2011-05-04 06:55:17
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Hi Martin, you may also consider these scripts from PyMOLWiki that generate the biological assembly from the asymmetric unit. http://pymolwiki.org/index.php/BiologicalUnit/Quat or http://pymolwiki.org/index.php/BiologicalUnit Cheers, Thomas Martin Hediger wrote, On 05/03/11 22:00: > Dear all > I would like to ask how it is possible to download the coordinate file > for the biological assembly of a protein structure from the PDB. > Naturally, this is not a question directly related to PyMOL, but I > thought I'll be reaching at least a couple of > Biochemists/Chrystallographers who know how to do this. > As an example, when downloading the PDB file of "1AVD", I get a file > with two chains. The biological assembly would be a tetramer, so I > wonder what URL I would require to write into a script that does the > downloading. > > Thanks for help on this. > Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: <li...@co...> - 2011-05-03 20:23:06
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http://www.rcsb.org/pdb/files/1avd.pdb1 The key is adding 1 to the suffix. Sometimes there is more than one biological unit, in which case, there is a pdb2, pdb3, etc. -David On May 3, 2011, at 4:00 PM, Martin Hediger <ma...@bl...> wrote: > Dear all > I would like to ask how it is possible to download the coordinate file > for the biological assembly of a protein structure from the PDB. > Naturally, this is not a question directly related to PyMOL, but I > thought I'll be reaching at least a couple of > Biochemists/Chrystallographers who know how to do this. > As an example, when downloading the PDB file of "1AVD", I get a file > with two chains. The biological assembly would be a tetramer, so I > wonder what URL I would require to write into a script that does the > downloading. > > Thanks for help on this. > Martin > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: Hongbo Z. <hon...@bi...> - 2011-05-04 07:38:50
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Yes, great trick: fetch 1avd, type=pdb1 On 05/03/2011 10:22 PM, li...@co... wrote: > http://www.rcsb.org/pdb/files/1avd.pdb1 > > The key is adding 1 to the suffix. Sometimes there is more than one biological unit, in which case, there is a pdb2, pdb3, etc. > > -David > > On May 3, 2011, at 4:00 PM, Martin Hediger<ma...@bl...> wrote: > >> Dear all >> I would like to ask how it is possible to download the coordinate file >> for the biological assembly of a protein structure from the PDB. >> Naturally, this is not a question directly related to PyMOL, but I >> thought I'll be reaching at least a couple of >> Biochemists/Chrystallographers who know how to do this. >> As an example, when downloading the PDB file of "1AVD", I get a file >> with two chains. The biological assembly would be a tetramer, so I >> wonder what URL I would require to write into a script that does the >> downloading. >> >> Thanks for help on this. >> Martin >> >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de |
From: Martin H. <ma...@bl...> - 2011-05-04 21:09:00
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Dear all thanks for the support, this is most helpfull. Kind regards Martin Am 04.05.11 09:38, schrieb Hongbo Zhu: > Yes, great trick: > > fetch 1avd, type=pdb1 > > On 05/03/2011 10:22 PM, li...@co... wrote: >> http://www.rcsb.org/pdb/files/1avd.pdb1 >> >> The key is adding 1 to the suffix. Sometimes there is more than one biological unit, in which case, there is a pdb2, pdb3, etc. >> >> -David >> >> On May 3, 2011, at 4:00 PM, Martin Hediger<ma...@bl...> wrote: >> >>> Dear all >>> I would like to ask how it is possible to download the coordinate file >>> for the biological assembly of a protein structure from the PDB. >>> Naturally, this is not a question directly related to PyMOL, but I >>> thought I'll be reaching at least a couple of >>> Biochemists/Chrystallographers who know how to do this. >>> As an example, when downloading the PDB file of "1AVD", I get a file >>> with two chains. The biological assembly would be a tetramer, so I >>> wonder what URL I would require to write into a script that does the >>> downloading. >>> >>> Thanks for help on this. >>> Martin >>> >>> ------------------------------------------------------------------------------ >>> WhatsUp Gold - Download Free Network Management Software >>> The most intuitive, comprehensive, and cost-effective network >>> management toolset available today. Delivers lowest initial >>> acquisition cost and overall TCO of any competing solution. >>> http://p.sf.net/sfu/whatsupgold-sd >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... |
From: Martin H. <ma...@bl...> - 2011-05-09 13:18:58
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I see, so if i get this right, every protein structure has at least one biological unit, sometimes it just conincides with the asymmetric unit. So it would be save to write .pdb1 in any case. Cool, thanks for pointing this out to me. Martin On 03.05.11 22:22, li...@co... wrote: > http://www.rcsb.org/pdb/files/1avd.pdb1 > > The key is adding 1 to the suffix. Sometimes there is more than one biological unit, in which case, there is a pdb2, pdb3, etc. > > -David > > On May 3, 2011, at 4:00 PM, Martin Hediger<ma...@bl...> wrote: > >> Dear all >> I would like to ask how it is possible to download the coordinate file >> for the biological assembly of a protein structure from the PDB. >> Naturally, this is not a question directly related to PyMOL, but I >> thought I'll be reaching at least a couple of >> Biochemists/Chrystallographers who know how to do this. >> As an example, when downloading the PDB file of "1AVD", I get a file >> with two chains. The biological assembly would be a tetramer, so I >> wonder what URL I would require to write into a script that does the >> downloading. >> >> Thanks for help on this. >> Martin >> >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... |