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
[PyMOL] Protein Parameters?
Hi, This is unrelated to PyMol, but I just wanted to spam the community to see what they think about different protein parameters. Let me know if this sort of question is inappropriate for the forum. I have thousands of randomly generated 7 amino acid peptide sequences that are within a virus. As we subject this virus to reproduction selective pressure in cell lines, we get back functional viruses with certain 7 amino acid sequences, while most random sequences are null mutations. So I am now testing the the positive sequences to see what they have in common, or what is most important. I am doing this with a likely structural sequence and a likely surface sequence. So far I have these params from http://web.expasy.org/protparam/ and ConSurf 1) Isoelectric Point 2) Molecular Weight (may mean bulkiness) 3) GRAVY: grand average of hydropathicity 4) Conservation of AAs at given locations Do any of you protein experts know of other parameters that I could be testing? Maybe something like Phi-value analysis? -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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] color_by_mutation needs identical atom counts?
Hi, I am using color_by_mutations on PyMol 1.3. http://www.pymolwiki.org/index.php/Color_By_Mutations I get this error: PyMOLrun color_by_mutation.py PyMOLcolor_by_mutation aav2, aav8 ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs 30227) Executive: Error -- no atoms left after refinement! ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs 30227) Executive: Error -- no atoms left after refinement! Selector-Error: Invalid selection name __aln. ( aav2 and name CA and __aln )-- Selector-Error: Invalid selection name __aln. ( aav8 and name CA and __aln )-- Selector-Error: Invalid selection name __aln. ( aav2 and name CA and __aln )-- Selector-Error: Invalid selection name __aln. ( aav8 and name CA and __aln )-- Selector-Error: Invalid selection name __aln. ( aav2 and name CA and __aln )-- Selector-Error: Invalid selection name __aln. ( aav8 and name CA and __aln )-- How could there every be an exact atom count between two unidentical structures anyways? -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] AttributeError: 'module' object has no attribute 'super'
AttributeError: 'module' object has no attribute 'super' I am trying to run color_by_mutation http://www.pymolwiki.org/index.php/Color_By_Mutations But I get that error. Maybe my version of Mac PyMol from 2006 doesn't have that superimpose command? How do I fix this? Thank you. Shane -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] fink install pymol help
Thanks Guys I just had to self update fink. On Thu, Mar 15, 2012 at 4:46 PM, Shane Neeley shane.nee...@gmail.comwrote: Hi, S.S. Thanks for your help. It says, Failed: no package found for specification 'pymol-py27'! null-b88d121ba616:~ chimpsarehungry$ fink list pymol Information about 312 packages read in 1 seconds. null-b88d121ba616:~ chimpsarehungry$ It doesn't appear to be a package available to me. On Thu, Mar 15, 2012 at 4:27 PM, S. Shunmugasundararaj raj_...@yahoo.comwrote: Try fink install pymol-py27 -- *From:* Shane Neeley shane.nee...@gmail.com *To:* pymol-users@lists.sourceforge.net *Sent:* Thursday, March 15, 2012 4:53 PM *Subject:* [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http://pymol.sourceforge.net/newman/user/S0120install.html In terminal I type sudo -s apt-get *pymol install* * * But it did not work. Do you know how I could install it with fink? -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] fink install pymol help
I've installed all of the packages for pymol-py27 with fink. And my terminal went back to normal. Now what? How do I make PyMol an application? On Thu, Mar 15, 2012 at 5:28 PM, Shane Neeley shane.nee...@gmail.comwrote: Thanks Guys I just had to self update fink. On Thu, Mar 15, 2012 at 4:46 PM, Shane Neeley shane.nee...@gmail.comwrote: Hi, S.S. Thanks for your help. It says, Failed: no package found for specification 'pymol-py27'! null-b88d121ba616:~ chimpsarehungry$ fink list pymol Information about 312 packages read in 1 seconds. null-b88d121ba616:~ chimpsarehungry$ It doesn't appear to be a package available to me. On Thu, Mar 15, 2012 at 4:27 PM, S. Shunmugasundararaj raj_...@yahoo.com wrote: Try fink install pymol-py27 -- *From:* Shane Neeley shane.nee...@gmail.com *To:* pymol-users@lists.sourceforge.net *Sent:* Thursday, March 15, 2012 4:53 PM *Subject:* [PyMOL] fink install pymol help I installed Fink on my mac because apparently it has pymol as a port so that I can download a newer version. According to this: http://pymol.sourceforge.net/newman/user/S0120install.html In terminal I type sudo -s apt-get *pymol install* * * But it did not work. Do you know how I could install it with fink? -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] How to tell what amino acids are in view?
Hi, Does anyone know of a way to tell which amino acids are currently in view? I am imagining something that highlights the the parts of the sequence that are visible as you rotate the molecule around. It may be much more complex than I am describing. Shane -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] New to PyMol. Want to extract sequence from .pse file w/ colors.
Hi Pymol Network, I would appreciate someones help in extracting the sequence in the viewer above the protein. I have gone through the sequence and changed AAs to different colors based on their position. I would ideally like to be able to copy that sequence with the colors that they are coded so that I could export it to an excel file. Is this possible? Thanks very much. Shane -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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
