[Chimera-users] Hidden water molecules

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 6 09:48:01 PDT 2016

Hi Michael,
We try to present an initial view that is not too confusing, so it doesn’t automatically show all the atoms.  However, you can show whichever atoms you want, and there are many ways.  I’ll mention a few:

To show all atoms:

menu: Actions… Atoms/Bonds… show
command: display
menu: Presets…. Interactive 2 (all atoms)

In the all atom preset, however, the waters will be small dots and probably hard to see unless you change them into some representation other than wire.  If you do either of the first two right after opening the structure, atoms will already be in stick representation, which for singletons is small balls and easier to see than the dots.

To show waters specifically:

menu: Select… Structure… solvent
menu: Actions… Atoms/Bonds… show
command: display solvent
-OR- (if residue name is HOH)
command: display :hoh

If you ALWAYS want to see alll the atoms when you open the structure instead of the simplified view, however, you can set that in the preferences.  Menu:  Favorites… Preferences, category: New Molecules, set “smart initial display” to “false”, click Save if you want this setting to apply to later uses of Chimera.

You may want to take a look at one of the getting-started tutorials to become familiar with how to specify sets of atoms, residues, etc.

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 6, 2016, at 7:38 AM, Michael Sharkey <michael.sharkey at ucd.ie> wrote:

> Hi 
> I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D).  They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2).
> What am I missing?
> Thanks in advance
> Mike

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