Re: [PyMOL] Retain order for select segment and write trajectory

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

Hi Kelly,

With retain_order=1, PyMOL will sort by rank, which is the order of time of loading the structure. By setting all rank values to the same value, you'll get segi/chain/resi sorting. So to preserve rank based sorting only for non-solvent, you can do this:

set retain_order
alter solvent, rank=-1
sort

This will sort solvent to the beginning. To put it to the end, pick a number which is beyond the atom count. 

set retain_order
alter solvent, rank=9999
sort

The atom ID is never used for sorting. But you could incorporate it in the ranks:

set retain_order
alter solvent, rank=9999 + ID
sort

Cheers,
  Thomas

> On Jul 18, 2017, at 2:09 PM, Kelly Tran <kn...@ge...> wrote:
> 
> Hi,
> 
> I'm using PSICO to write a DCD. Is it possible to retain the original order for one segment (protein) while sorting by atom ID for another segment (water).
> 
> Thank you,
> 
> Kelly

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.