Hi Sean, If you're doing this for illustrative purposes, why not just build the inferred backbone? You could use BBQ, among many others:
http://biocomp.chem.uw.edu.pl/tools/bbq FWIW, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Sean Law <magic...@hotmail.com<mailto:magic...@hotmail.com>> Date: Wednesday, June 4, 2014 4:17 PM To: "Sampson, Jared" <jared.samp...@nyumc.org<mailto:jared.samp...@nyumc.org>> Cc: "pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>" <pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure Jared, For now, we are using different colors to indicate the SS assignments but it's not pretty. We would prefer to show the SS for both sheets and helices. Can you elaborate on what you mean by "radially symmetric". Are there other cartoon modes where I would be able to get both helices and sheets after altering the residue's SS assignment by hand? I see what you mean by not being able to define the flat plane though. Best, Sean ________________________________ From: jared.samp...@nyumc.org<mailto:jared.samp...@nyumc.org> To: magic...@hotmail.com<mailto:magic...@hotmail.com> CC: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure Date: Wed, 4 Jun 2014 20:03:54 +0000 Hi Sean - I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s part. Rather, I think it may have something to do with two facts: 1) unlike loops, sheets represented in automatic mode are not radially symmetric; and 2) unlike helices, the orientation of the sheet at a particular CA atom cannot be determined by its immediate neighbors. I haven’t had a chance to look at the relevant source, so I can’t confirm this at the moment, but it seems likely to me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane of a sheet, and without this information, instead of guessing at its orientation, it omits the sheet entirely. (This also appears to be the case for other non-radially symmetric modes, including dumbbell, rectangle, and oval.) Could you get by using different colors to indicate your SS assignments in another cartoon mode? Cheers, Jared Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 4, 2014, at 1:50 PM, Sean Law <magic...@hotmail.com<mailto:magic...@hotmail.com>> wrote: Hi PyMOLers, I have a c-alpha only model and I would like to visualize both helices and sheets based on my own custom SS assignments (via "alter"). Altering a residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be visualized. However, altering a residue's SS assignment to sheet (ss="S") causes that residue to disappear. Again, this is c-alpha only and I am visualizing in "cartoon automatic" mode. Any suggestions for visualizing the sheets in this case would be greatly appreciated. Best, Sean ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech_______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto: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<http://www.mail-archive.com/pymol-users%40lists.sourceforge.net> ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ 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
