[PyMOL] surfaces
Hello: Okay, I got the surface from Grasp read in by ungrasping it in Raster3d. Now the read in surface loses its electrostatic potential colouring - is there any way to fix this? Cheers, JTM * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca *
[PyMOL] grasp surfaces
Hello: This might have been asked before but is there anyway to load an electrostatic surface from grasp into pymol? Cheers, JTM * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca *
Re: [PyMOL] cartoon_smooth_loops
Hello: You can create more than one object of the same protein, make one smooth loops and display only a small section of that one. Cheers, JTM On Sat, 10 Aug 2002, Bartholomeus Kuettner wrote: > Hello there! > > Is it possible to assign "cartoon_smooth_loops" to specific residues of a > protein? Let's say, you want to draw cartoons for only one loop directly > through the CA positions (set ...=0) but want to show smoothed loops > (set...=1) for the remaining molecule. > It seems to be a global modifier since an local assigment (set ...=0, > "residues xyz") does not work. > > Thank you! > > Greetings, > Bartholomeus Kuettner > > > --- > 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 *
Re: [PyMOL] Polypeptide conformation restriction
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 *
[PyMOL] Re: fitting residues
Hello: I am trying to color residues off a cartoon loop and want to color the sticks version of the residue down to the Ca, but not the Ca itself (ie. the residue and the cartoon are different colors). The problem is that if I color the Ca, then that section of the cartoon also gets colored. If I don't color the Ca, then the cartoon loop color comes halfway up the bond to the Cbeta. Does anybody have any suggestions, that is if I haven't made the question so convoluted you can understand it. Thanks in advance. Cheers, JTM * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca *
[PyMOL] fitting residues
Hello: I was wondering if there was anyway to make the cartoon backbone match the real backbone to a greater extent. Now I have residues displayed as sticks and a backbone displayed as loop and the loop doesn't really come near the residue so it looks like the residue is floating in space. I am looking for a command similar to defining the secondary structure as "turn" in molscript which forces the cartoon through the actual backbone. Thanks in advance. Cheers, JTM * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca *
Re: [PyMOL] pymol without GL
Hello: pymol.com -c scriptname But you have to get your view first somehow. Cheers, JTM * Jason Thomas Maynes MD/PhD Program Faculty of Medicine University of Alberta ja...@biochem.ualberta.ca * On Tue, 16 Jul 2002, Nathaniel Echols wrote: > > quick question: I'm trying to do batch jobs on a server. Obviously, > there's no X or OpenGL installed. Is there any way to build PyMOL without > any graphical frontend, and just use it as a raytracer? I don't want to > go through the trouble of adding in these libraries... > > thanks, > Nat > > > > --- > This sf.net email is sponsored by: Jabber - The world's fastest growing > real-time communications platform! Don't just IM. Build it in! > http://www.jabber.com/osdn/xim > ___ > 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 *
