[Chimera-users] Hidden water molecules

Michael Sharkey michael.sharkey at ucd.ie
Fri Apr 15 01:22:48 PDT 2016

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


On 6 April 2016 at 17:48, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> -OR-
> command: display
> -OR-
> 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
> -OR-
> 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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules
> >
> 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.
> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
> <http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html>
> I hope this helps,
> Elaine
> -----
> 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

Michael Sharkey PhD,
UCD School of Biomolecular and Biomedical Science,
Conway Institute,
University College Dublin,
Tel. 01-7166932
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