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
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MPI for Developmental Biology
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