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 back to atomistic? 

Cheers,

Tsjerk



On Mon, Oct 14, 2013 at 2:32 AM, Aiqun Huang <allanqunzi@gmail.com> wrote:
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, 1
show spheres
show sticks


But still I can not see the bonds showing in the image.  I searched a lot but still have no clue how to show the bonds between the coarse-grained beads.

Can anyone help me? Thanks!!

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--
Tsjerk A. Wassenaar, Ph.D.