Hi, > Visualization software can sometimes assign the secondary structure > incorrectly.
There has been an interesting discussion on this on the Pymol user list years ago (http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg01574.html). Secondary structure assignment is foremost human defined. You can use different metrics to obtain assignments, and should be careful to take any one of them as 'correct'. For instance, it makes a difference whether you assign three types (helical, sheet, loop), as Pymol does, or like seven types, as DSSP does. In pymol you can set the secondary structure type manually, but I find that the internal command 'dss' usually does a good job. Note that it only works on one frame and then uses the assignment for that frame on all of them, although there may be a workaround (I'll check; something with discrete_states). The frame to use for the assignment can be given to the 'dss' command through the argument state=N, where N is the frame number. If dss doesn't give the assignment you want, you can also try 'util.ss' that uses a different metric. Hope it helps, Tsjerk >> On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: >> Hi, >> >> I had done 10ns simulation, >> >> by dssp, can see the beta-sheet appeared very apparently, before it's >> alpha-helix. >> >> there were 5000 frames, I based on the time of the picture got from dssp, I >> can guess around which frames is supposed to have those beta sheets. >> >> After I took few frames which I thought might be representive, but under >> pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, >> I really do not know which one is most representive. >> >> Or maybe some parts I understand wrong. >> >> Thanks for any advice and if I am wrong please let me know, >> >> We've really no idea of the detail of what you've done, so can't guess. Just >> about anything could be the problem - all the way from "you are looking at >> the wrong files", to "pymol's definition of a beta sheet doesn't agree with >> dssp". >> >> If you can't report the command lines you used easily, then your method was >> not reproducible enough, or not recorded well enough :-) >> >> Mark >> > > > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
