Hello: To show the allowed torsion angles, run your protein through procheck (available at http://www.ccp4.ac.uk/main.html), this will show the allowed areas.
I would say that the convergence of an MD simlulation cannot be told by torsion angles since the protein conformation with the most allowed angles and/or fastest convergence to allowed regions isn't necessarily the correct one. I have seen some protein structures with a diverse array of torsion angles. What you may get is one of the conformations of the "ensemble" of the transition state to folding (read something by David Baker). Cheers, JTM On Thu, 1 Aug 2002 kkli...@gate.sinica.edu.tw wrote: > Dear pymolers, > > Many of you are interested in SS. > I think you must be experts on this. > So, although this is not a pymol problem, > I hope that you can give me some information. > > I've got some MD simulation results, > and I calculated the phi-psi angles of each amino acid. > (Yeah I know that phi-psi calculation is there in pymol. > I just wrote the program to check if I really understand it correctly.) > Then, with the data, you can say that I got the variation of > phi-psi angle 'on the fly'. > I can look at the change of their values with time in a movie. > > The problem is, I found that many of the amino acids > have phi-psi angles pairs that fall in the "forbidden area". > I think that you know what I mean by that. > Especially, there are a lot of valines in my model protein, > but often they have phi-psi angles in Glysine area or even > totally forbidden area. > Well maybe you will argue that the "forbidden" conformation > is only meaningful for native structures. > But what I wish to understand is the correlation between > the 'forbidden/allow" of phi-psi configuration and the > convergence of MD simulation, or even better, > one might point out the pathway of folding by looking at that. > > Anyway, to do further analysis, I wish to be able to obtain > the 'contour' of the chain conformation restriction map. > You know, when you go to the protein data bank and view the > Ramachandran diagram, in the background they show those area. > But where can I obtain information like that? > > Thank you in advance if you can provide me suggestions. > > Regards, > K.K.Liang > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > ************************* Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca *************************
