Hi Simon - Glad you figured out a method that worked for you.
However, I'm wondering why you ended up with "un-smoothed" helices using the `cartoon_smooth_loops` method. Are you sure you typed the last two commands in my example correctly (`alter` and `rebuild`)? I'm getting a single, relatively straight tube for all the helices. Here's a link to a working (for me) .pml script and sample output images: https://www.dropbox.com/sh/jstq1ngshyqn4fj/Cx1ehJbFtr Just curious to see what the difference might be. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Dec 2, 2013, at 11:16 AM, Simon Schweizer <schwei...@tum.de> wrote: > Hi Carlos and Jared, > > thanks for your answers! > Jared, your method is quick to do, but the ribbon follows every > turn of a helix, which I wanted do avoid. > Carlos, your method did what I wanted. I commented > out amino acids which c-alphas I did not want to be included, > and ran the script zero_residues.py. However, I had to manually > delete some lines and did a manual renumbering (easy to do > with vim's ctrl+a and ctrl+x functions do decrease/increase > a number. > > Cheers, > Simon > > > Am 14.11.13 14:41, schrieb Simon Schweizer: >> Dear all, >> >> I have a complex protein (with a knot in the polypeptide chain) >> and want to show the rough course of the chain, so everyone can >> easily see that there is a knot inside. >> >> I don't know how to draw such a complex 3D object in a drawing >> program, so I want to do that in PyMol (or another similar program). >> >> What I did is copying a part of the protein sequence and transformed >> it in a new object. I want to superimpose the new object drawed >> in ribbons with the whole protein in cartoon representation. I made >> the ribbons big. How can I make it transparent, too, by the way? >> >> For showing the rough course of the polypeptide chain, the ribbon >> should not follow every alpha-helix, loops and so on. What I want to >> do is like box filtering the chain. >> I tried to delete atoms, but then the ribbon is broken. How can >> I connect these atoms, must the c-alpha carbons be connected >> by peptide bonds so the ribbon is drawed? But I want to delete >> atoms, so the connections between the remaining atoms that >> form the ribbon will have larger distances than normal bonds. >> Is that possible to do that at all in PyMol? >> >> Another option would be: taking some c-alpha carbons that >> show the rough course of the chain, and building a povray >> file that draws it like a ribbon or flexible tube, and input that >> povray code into the povray-file of the rendered protein. >> >> Any help is greatly apprechiated! >> Thanks! >> Simon >> > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk > _______________________________________________ > 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 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. ================================= ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk _______________________________________________ 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
