[]
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 a
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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molecule looks like, could it be automorphism?
-Original Message-
From: Baptiste Legrand
Sent: Wednesday, July 25, 2018 9:17 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
from a docking
Dear all,
I tried to calculate
Dear all,
I tried to calculate a rmsd value between ligands from a crystal
structure and after docking. The two molecules share similar
nomenclatures and are really well superimposed. I think that the RMSD
should be < 1 A. I used the following lines:
alter all,segi=""
alter all,chain =""
Dear all,
I wounder to know about possible ways to measure chi1, chi2 dihedral
angles on a set of structures. For example, I opened 10 pdb files and
the phi_psi command allows us to easily obtain the phi and psi values:
Ex: To obtain the phi and psi values of the residue 288 of the chain A
in
Dear all,
I have a small helical pseudopeptide with mixed alpha and beta
amino-acids. How can I make a cartoon representation of this helix with
Pymol? For the moment, I have selected the peptide backbone atoms and
tried the alter command to force pymol to recognize the helix but it
do not
Thanks Joseph and Thomas for your replies. When I use the as cartoon
commands, all my molecule disappear. My *pdb file could be the problem as it
is a *cif crystal structure file (converted with mercury) from the cambridge
crystal data.
Cheers,
Baptiste
2011/8/16 Thomas Holder
