Hi Pawel,
only "discrete" objects have per-state bonding. In discrete objects, states
have independent atom sets, which comes down to similar memory consumption like
individual objects (split_states).
PyMOL> load example.xyz, discrete=1
If you want to make a movie, instead of using one discrete object, I would
create two objects. One for state 1-X, and one for X-N.
PyMOL> load example1to4.xyz, obj1
PyMOL> load example5to10.xyz, obj2, state=5
PyMOL> mset 1-10
Hope that helps.
Cheers,
Thomas
On 01 Jan 2015, at 13:11, Pawe? Gniewek <gniewko.pa...@gmail.com> wrote:
> Hi all,
>
> I am having some troubles with the following problem:
>
> I have a trajectory stored in a file having XYZ format - let's assume it has
> 10 states in total.
>
> At the very beginning I have 5 atoms connected in a loop (like in
> cyclopentane):
>
> ATOM1 - ATOM2
> ATOM2 - ATOM3
> ...
> ATOM5 - ATOM1
>
> I create bonds by:
> "bond ATOM1, ATOM2"
> and so on.
>
> However in my simulations at some point (let's say in state #4) a new element
> is introduced.
> If that happens I must break a bond ("unbond" command) between e.g. "ATOM1 -
> ATOM5" and then then create two new bonds:
> "ATOM1-ATOM6"
> and
> "ATOM5-ATOM6"
>
> So what I want to obtain is a bond between atoms 1 and 5 up to the state #4,
> at the time of #4 I want to break a bond and create two new ones, and from
> that moment proceed with the new bonds' topology - so I can render every
> frame with a correct bonds network.
>
> Moreover my trajectory files are usually too large to use "split_states".
>
> Any ideas how to work this problem out?
>
> Thanks,
> Pawel
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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