My question pdb files which contain alpha-carbons only ... like 1alm.pdb Q: Is it possible to calculate a vector which is orthogonal to the backbone if one is only given a chain of alpha-carbons?
To draw backbones/traces, we only need the alpha carbon positions. In order to draw ribbons/strands/cartoons, we need to calculate an orthogonal vector that points to the edge of the ribbon. When the entire NCCO amino acid backbone is present then the relative position of the carbonyl oxygen is used to calculate this vector. In a helix structure, one could calculate such a vector by using the angle formed by three successive alpha carbons. It is not clear to me whether or not the same thing would work in other structures. If someone wants to read up on this, the following paper seems to do some useful and related types of calculations: Micheal Levitt and Jordon Greer, 1977 Automatic identification of secondary structure in globular proteins http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf Miguel ------------------------------------------------------- This SF.Net email is sponsored by Sleepycat Software Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver higher performing products faster, at low TCO. http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
