Hi Mike, No problem. You can also save each chain and heteroatom in CHIMERA by doing “select:.a” -> GUI-> Save PDB and “select:.b”->GUI-> Save PDB OR run a simple script below: f = open('chainA.pdb','w') f2= open('chainB.pdb','w') pdb = open("1c1d.pdb","r") for line in pdb: if line[:4] == 'ATOM' and line[21:22] == "A": f.write(line) if line[:6] == 'HETATM' and line[21:22] == "A": f.write(line) if line[:4] =='ATOM' and line[21:22] =="B": f2.write(line) if line[:6] == 'HETATM' and line[21:22] == "B": f2.write(line) Hope this helps, Dave

On Apr 15, 2016, at 1:16 AM, Michael Sharkey <michael.sharkey@ucd.ie> wrote:

Thanks Dave

I had saved a copy containing one of the two chains in the asymmetric unit, not realising that the waters didn't come with the protein (and heteroatoms).

Problem solved

Thanks again (for a very swift response)

Mike

On 6 April 2016 at 16:23, Gae, David Hyon <DavidHyon.Gae@ucsf.edu <mailto:DavidHyon.Gae@ucsf.edu>> wrote: Hi Mike,

If you haven’t messed around the PDB file in WordPad. i think doing “ disp: hoh “ in command line should show the water.

Hope this help, Dave

...

On Apr 6, 2016, at 7:38 AM, Michael Sharkey <michael.sharkey@ucd.ie <mailto:michael.sharkey@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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