El 20 Oct 2005 a las 0:31, Timothy Driscoll escribió: > hi Angel, > > just curious: that atom naming system is not familiar to me. is it > specific to lipids?
Hi, Tim As far as I know, it's not standard. There are few lipids in the PDB or in other databases, so I don't think there is a standard nomenclature. These PDB files are a lipid bilayer with 200 phospholipid molecules, obtained through molecular dinamics simulation and geometric duplication of molecules. H. Heller, M. Schaefer & K. Schulten [Theoretical Biophysics Group, Beckmann Institute, University of Illinois, Urbana-Champaign, U.S.A.] "Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases", J. Phys. Chem. 97:8343-60, 1993 http://www.lrz-muenchen.de/~heller/membrane/membrane.html Links via Protein Explorer: http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/cutc2.pdb http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/cutg2.pdb http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/cutf2.pdb I don't know how the authors decided to label the atoms, but since it is a manually-made PDB I suspect they simply wanted to assign a unique, reasonably comprehensible name to each. I checked against the PDB file format description and it is according to it, but the use of the first number and its character position is not frequently used in most models (proteins, nucleic); that's the reason Jmol gets funny about them. BTW, I solved the problem using wilcards in the atom selector. · · · · · · · · · · · · · · · · · · · · · · · · · · · · · Dr. Angel Herraez Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain fax: +34-91 885 45 85 ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
