Re: [PyMOL] Dynamic Bonds based on connection table ?

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

Hi Thomas,

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

Cheers,
   Thomas

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:
> cmd.load("testm.pqr")
> cmd.load("testm1.pqr")
> = 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,
> Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen