Hi Laurie,
The list of bonds is accessible with cmd.get_model(), see
https://pymolwiki.org/index.php/Get_Model
PyMOL> m = cmd.get_model()
PyMOL> print m.bond[0].index
[0, 1]
PyMOL> print m.bond[0].order
1
Cheers,
Thomas
On 26 Jan 2017, at 13:50, Laurence Williams wrote:
> Dear pymol users,
Dear pymol users,
I understand that pymol does not explicitly need connectivity data to visualise
molecules as bonds are drawn when two atoms are within in a given distance.
However, once those bonds are drawn for the molecule, is connectivity data
stored somewhere whilst the file is in use? I
Hallo
Thanks for the answer. So could PyMol generate the connectivity it sees?
So this could be used for a subsequent force field computation?
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Dear Martin,
On Thu, 05 Aug 2010 10:44:45 +0200 Martin Hediger wrote:
> I am confused about the requirement of providing connectivity data in a
> pdb file to properly render a protein with PyMol.
> Right now, I am displaying a pdb file not containing any connectivity
> data but still the prote
Dear all
I am confused about the requirement of providing connectivity data in a
pdb file to properly render a protein with PyMol.
Right now, I am displaying a pdb file not containing any connectivity
data but still the protein seems perfectly valid.
My question is: how does PyMol know how to pr
I am using Pymol to visualize a "pseudo polymer" generated by some
brownian dynamics code. We take the coordinate files generated by our
simulation and convert them into a PDB file using the hetatm
representation and having explicit connections defined with conect. For
example:
HETATM
