Re: [PyMOL] 60-mer virus capsid (need computing power!)
Hi Shane, With PyMOL v1.5 and later, and a reasonable machine you should be able to use large systems (250,000, and upward of 1,000,000+ atoms) without much of a problem. Using the following simple test script: fetch 2xpj, type=pdb1, async=0 split_states 2xpj delete 2xpj orient For these 240,000 atoms on a Dell T5500 with a very nice video card, I get: * 30 FPS as lines * 28 FPS using cartoons * 30 FPS a ribbons * 30 FPS as surface For these 240,000 atoms on a (1 year old) MacBookPro (with ATI Radeon HD 6770) I get * 60 FPS as lines * 33 FPS as cartoon * 36 FPS as ribbon * 27 FPS as surface 30--60 FPS is surely in the realm of interactive. Earlier versions of PyMOL would have a tough time with these data. (Plus the new versions of PyMOL have nicer rendering in real time.) Next, you wrote: Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A With Moore's Law still in effect, nothing is overkill. However, consider value for money: the recent announcements from Apple centered around the MacBookPro -- not the MacPro. It should be clear that those who financially support PyMOL are responsible for this level progress. The diff from v1.4 to v1.5 was in the range of 50,000+ lines -- and we couldn't have done that work without our supporters. So, a special thanks goes out to them! Cheers, -- Jason On Wed, Jun 13, 2012 at 2:32 PM, Shane Neeley shane.nee...@gmail.com wrote: Hi, Does anyone use pymol for very large structures, such as a full virus 60-mer capsid? If so, what processing power, memory, graphics card, etc. do you need to render these large files and manipulate them without any slowing? PyMol takes about 1 minute to think after trying to spin one of these full capsids, and that is on a dual-core 8gb ram laptop. Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A Has anyone built other machines to do this sort of work? Appreciate your input, Shane Neeleu -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 60-mer virus capsid (need computing power!)
Hi Jason, Thanks a lot for the performance info. I think that a full capsid would be around 300,000 atoms, so your info is very helpful. We will probably invest in the newest version of pymol when we purchase the computer. On Fri, Jun 15, 2012 at 12:19 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Shane, With PyMOL v1.5 and later, and a reasonable machine you should be able to use large systems (250,000, and upward of 1,000,000+ atoms) without much of a problem. Using the following simple test script: fetch 2xpj, type=pdb1, async=0 split_states 2xpj delete 2xpj orient For these 240,000 atoms on a Dell T5500 with a very nice video card, I get: * 30 FPS as lines * 28 FPS using cartoons * 30 FPS a ribbons * 30 FPS as surface For these 240,000 atoms on a (1 year old) MacBookPro (with ATI Radeon HD 6770) I get * 60 FPS as lines * 33 FPS as cartoon * 36 FPS as ribbon * 27 FPS as surface 30--60 FPS is surely in the realm of interactive. Earlier versions of PyMOL would have a tough time with these data. (Plus the new versions of PyMOL have nicer rendering in real time.) Next, you wrote: Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A With Moore's Law still in effect, nothing is overkill. However, consider value for money: the recent announcements from Apple centered around the MacBookPro -- not the MacPro. It should be clear that those who financially support PyMOL are responsible for this level progress. The diff from v1.4 to v1.5 was in the range of 50,000+ lines -- and we couldn't have done that work without our supporters. So, a special thanks goes out to them! Cheers, -- Jason On Wed, Jun 13, 2012 at 2:32 PM, Shane Neeley shane.nee...@gmail.com wrote: Hi, Does anyone use pymol for very large structures, such as a full virus 60-mer capsid? If so, what processing power, memory, graphics card, etc. do you need to render these large files and manipulate them without any slowing? PyMol takes about 1 minute to think after trying to spin one of these full capsids, and that is on a dual-core 8gb ram laptop. Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/A Has anyone built other machines to do this sort of work? Appreciate your input, Shane Neeleu -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] 60-mer virus capsid (need computing power!)
Hi, Does anyone use pymol for very large structures, such as a full virus 60-mer capsid? If so, what processing power, memory, graphics card, etc. do you need to render these large files and manipulate them without any slowing? PyMol takes about 1 minute to think after trying to spin one of these full capsids, and that is on a dual-core 8gb ram laptop. Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/Ahttps://mail.ohsu.edu/owa/redir.aspx?C=a84e20fef7e04111bec08a76775f0093URL=http%3a%2f%2fstore.apple.com%2fus_smb_78313%2fconfigure%2fMD771LL%2fA Has anyone built other machines to do this sort of work? Appreciate your input, Shane Neeleu -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] 60-mer virus capsid (need computing power!)
Hi Shane, I've been playing with a virus 60mer on an intel core i7 workstation with 6Gb memory with good response. Just make sure you use the latest incentive or open source version and have a good graphics card. Cheers, Tsjerk On Jun 14, 2012 11:49 PM, Shane Neeley shane.nee...@gmail.com wrote: Hi, Does anyone use pymol for very large structures, such as a full virus 60-mer capsid? If so, what processing power, memory, graphics card, etc. do you need to render these large files and manipulate them without any slowing? PyMol takes about 1 minute to think after trying to spin one of these full capsids, and that is on a dual-core 8gb ram laptop. Is a 12-core mac like this overkill? http://store.apple.com/us_smb_78313/configure/MD771LL/Ahttps://mail.ohsu.edu/owa/redir.aspx?C=a84e20fef7e04111bec08a76775f0093URL=http%3a%2f%2fstore.apple.com%2fus_smb_78313%2fconfigure%2fMD771LL%2fA Has anyone built other machines to do this sort of work? Appreciate your input, Shane Neeleu -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
