[Chimera-users] Hidden water molecules

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 15 09:32:55 PDT 2016

Hi Mike,
Yes, definitely!  You can select any set of atoms that you like and then use an option to save selected atoms only.  Or, you could delete all the other atoms and then save all the remaining atoms.

For example, you could select everything with chain ID C with a command (sel :.c) or the menu (Select… Chain… C) and then save with

(A) GUI: menu: File… Save PDB, with checkbox option “save selected atoms only”
- or -
(B) command “write” with “selected” option

With the other approach, you could first delete all the non-chain-C atoms. It could be done with the menu by selecting chain C, inverting selection, and deleting the resulting selection, or with one command:
 delete ~ :.c
(delete NOT chain C)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 15, 2016, at 1:22 AM, Michael Sharkey <michael.sharkey at ucd.ie> wrote:

> Hi Elaine
> Thank you for your reply.  I had manipulated the structure (opened in Swiss PDB Viewer and saved one chain of the asymmetric unit in a new file).  I hadn't realised that the waters didn't save with the protein structure (although the heteroatoms did). So that's why I couldn't see them!
> By-the-way, is there a way to select one chain (and associated molecules) and save it as a new PDB file through Chimera?  I haven't been able to find a way - hence the use of Swiss PDB Viewer.
> Kind regards
> Mike

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