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 ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&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
