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 <[email protected]> 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!! ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
