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
