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Re: [PyMOL] MD analysis (distance, dihedral etc)
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From: Baptiste L. <bap...@gm...> - 2020-09-04 14:26:56
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Thanks Tamas, I will have a look on this. Best, Baptiste Le 04/09/2020 à 15:55, Tamas Hegedus a écrit : > It is. > > ---------- > > Pseudo code: > sel1 = u.select_atoms... > sel2 = u.select_atoms... # it is important to make the selection out > of the loop > > for t in u.trajectory: > d = numpy.norm(sel1.center_of_geometry - sel2...) > > ---------- > dihedral is somwhat more complex: > > SEL = "resid %i and name %s" > > C0 = SEL % (RESI-1, 'C') > N1 = SEL % (RESI, 'N') > CA = SEL % (RESI, "CA") > C1 = SEL % (RESI, "C") > N2 = SEL % (RESI+1, "N") > > phiL = [] > psiL = [] > > u = MDA.Universe(GRO, TRJ) > phi = sum([u.select_atoms(atom) for atom in [C0, N1, CA, C1]]).dihedral > psi = sum([u.select_atoms(atom) for atom in [N1, CA, C1, N2]]).dihedral > > for f in u.trajectory: > phiL.append(phi.value()) > psiL.append(psi.value()) > > > On 9/4/20 9:02 AM, Baptiste Legrand wrote: >> Hi all, >> >> Is it possible to monitor distances, dihedrals etc. in a protein >> trajectory? to finally plot distances or something else versus time. >> (as VMD or others) >> Thanks. >> >> Best, >> >> Baptiste >> >> >> >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym...@li... >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
