[Chimera-users] Hidden water molecules

david gae ddgae at ucdavis.edu
Fri Apr 15 21:24:10 PDT 2016


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 at 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 at ucsf.edu <mailto:DavidHyon.Gae at 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 at ucd.ie <mailto: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
> >
> > --
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> 
> 
> 
> 
> -- 
> Michael Sharkey PhD,
> UCD School of Biomolecular and Biomedical Science,
> Conway Institute,
> University College Dublin,
> Tel. 01-7166932
> 

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