From: Thomas Holder <speleo3@us...> - 2012-07-15 14:52:46
if you load the molecules as "discrete" objects, then the states will be
independant and each state will have its own connectivity.
load testm.pqr, mov, discrete=1
PyMOL by default calculates connectivity based on distances. If you want
to make sure that only your own CONECT records are used, then set
connect_mode to 1. http://pymolwiki.org/index.php/Connect_mode
T.S: wrote, On 07/12/12 05:32:
> Dear PyMOL users,
> I´m looking for an option to generate animations with changing bonds.
> So far:
> = 2 objects with correct bonding from "conect" entries
> load testm.pqr, mov
> load testm1.pqr, mov
> = trajectory, but only connection table from 1st frame seems to be used
> small test structures (only 1 bond removed) are attached, overall
> simulations consists of larger structures with substitution reactions
> and a large number of time steps - therefore a loop for loading the
> files should be possible. The "conect" entries per time frame are
> calculated in the simulation, the pqr files are generated using this
> information, either as single file/time step or as one file holding all
> time steps. Connection table reads are not necessary every single time
> step, but would be nice every n iterations based on typical structures
> changes in the simulations.
> I'm rather new to PyMOL, so hopefully you can guide me to a solution.
> Kind regards,
MPI for Developmental Biology