Hi Liang: The most up-to-date contour on the Ramachandran plot you can find at the molprobity website: http://kinemage.biochem.duke.edu/molprobity/
It's a bit indirect, you have to submit a structure and then it will give back a Ramachandran plot - but this plot agrees pretty well with what we tend to see in Xray structures. Better than the procheck (etc.) plots. Good luck phx. > -----Original Message----- > From: kkli...@gate.sinica.edu.tw [mailto:kkli...@gate.sinica.edu.tw] > Sent: Thursday, August 01, 2002 12:06 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Polypeptide conformation restriction > > > 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 > ---------- This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version.
