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 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
