Re: [PyMOL] XYZ trajectory file - unbond two atoms, insert a new one, and create new bonds.

[Thomas H. <tho...@sc...>]

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 <gni...@gm...> 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.