Re: [PyMOL] How to visualize coarse-grained pdb file with CONECT ?

[Thomas H. <sp...@us...>]

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 5:45 AM, Tsjerk Wassenaar wrote:
> 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 <all...@gm...> 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!!