Re: [PyMOL] MD analysis (distance, dihedral etc)

[Tamas H. <bio...@gm...>]

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
>
>
>
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