Hi Tsjerk & Aiqun,
very good find, puzzled me as well. There is a setting "pdb_unbond_cations"
which seems to be implemented a bit buggy, I think it should only prevent
distance-based connectivity of cations, and not interfere with explicit CONECT
records.
Cheers,
Thomas
On Oct 15, 2013, at
Hi Aiqun Huang,
It puzzled me for a while. I found that renaming all 'K' atoms to 'C' the
bonds are drawn correctly. That still puzzles me, but at least it offers a
way to get the desired view.
Are you actually running simulations with this model? And are you
interested in converting the CG model
Hi dear PyMol users,
I am new to PyMol. I have a pdb file(see attached cg_dna.pdb) for a
coarse-grained model of DNA,
this file includes the "CONECT" section which specifying the connectivity
of the coarse-grained beads.
I have tried the following commands:
load cg_dna.pdb, cg
set connect_mode,
