On Thu, 2011-08-04 at 13:06 +0530, vandana kukshal wrote: > in a PDB with 2 A resolution many atoms of side chan if argenine and > aspartate , lysine and glutamate are missing due to weak electron > density
Aha! Take that, non-believers in the wisdom of the "end user"! :) Hope it does not revive the hopelessly deadlocked discussion of what to do with disordered side chains (guilty as charged). On the practical side, there are many ways to do it, mine would be: 1) Use COOT to fill in partial residues (if it's a fairly recent deposition it must be accompanied by the experimental data, and you can use that to obtain the most fitting conformers). REFMAC can also fill in the missing atoms, but afaiu it will not do any real space fitting so you may end up with unreasonable conformations - after all, there is presumably no density to fit into. 2) If you want to be fancier, do a quick MD simulation designed specifically for the purpose of orienting side chains. If you are looking forward to something fast, relatively easy to learn, and free, try GROMACS - you can restrain everything in the protein except the side chains in question and run a full solvation MD on a medium sized protein in under 24 hours on a $500 linux box. It is interesting if the results will be detectably different from above (I doubt it), but it will give your presentation a scientific aftertaste, so to speak. What to do depends on your goals. From my limited experience I can conclude (perhaps incorrectly) that the electrostatic potential maps usually give you very similar outcome to just coloring by atom (if you choose blue-to-red color scheme in both cases): negative potential where aspartates and glutamates are and positive near arginines and lysines. Look, however, at this http://web.mit.edu/tidor/www/residual/grasp.html If you manage to get GRASP running, of course - last time I enjoyed it on an SGI and windows version has never worked in my hands, but I am dumb after all and last time I tried was couple of years ago. So you may be more lucky. Of course, pymol should be good too. Good luck. Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
