Hi Vincent,
can you load the 400 copies of your ligand into the same object? For example by
creating a multi-model PDB file, or using a trajectory format. In that case,
the 400 conformations will share the topology (the atoms and bonds) and you
only have to form the bond once.
Also, the
Dear everyone,
I have a MD simulation of coarse grain molecules, therefore not defined
as typically for normal protein/ligands, but as beads.
I want to represent it using Pymol, and need to define bonds between the
beads.
The problem is that I have 400 copies of my ligand, and all with the
Hi kmeatball,
If you append all structures to the same model, which is what you do
by loading each under the same name into different states, the
connectivity will be determined by the first state. That is, the
topology information (read bond map) is global, and applies to all
states. If you want
Hi,
I'm loading a sequence of .pdb files into a movie using the script:
for file in file_list:
cmd.load(file,mov)
cmd.mset(1 -%d%len(file_list))
The problem is that some bonds (conect records in the .pdb files)
are persisting in the movie even after they are no longer in the
Hey
I'm trying to make bonds.. or lines/connections
between the C-alphas of various residues. I found that
bond can do this, however the bond color is adopted
from the color of the atoms that the bond connects. Is
there a way to isolate a bond object and set the color
of it independent of the
Hi all!
I've written a script to position all atoms into a simulation box, but
the connectivity stays, thus generating a beautiful image of bonds all
across the box. Though not too clear. Is there a way to update the
connectivity directly (other than saving the coordinates and reloading)?
