[Chimera-users] structure editing query

Bala subramanian bala.biophysics at gmail.com
Sat Sep 10 10:34:18 PDT 2011

Hi Elaine,
Thanks for the detailed information. I just want to make the same linkage as
in the pdb i sent in another pdb ie. in a different model.
C2'-oxygen-C6'-C4' ?. As per your suggestions i just need to add hydrogens
one by one and then change it to the element i need right ?

Best regards,

On Sat, Sep 10, 2011 at 5:57 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> HI Bala,
> I see C2' is bonded to three atoms so it might have one more. It is not
> clear from what you said whether you want to add one new oxygen to that
> carbon, or to bond this molecule to some other molecule that already has the
> oxygen.
> To bond two different models you would use the "join models" tab.  You'd
> need to add hydrogens first so that the H on C2' would then be replaced
> during the join.
> To bond two atoms that already exist in the same model you would use the
> "adjust bonds" tab.
> To simply add one oxygen to C2' you would use the "modify structure" tab in
> two steps.
> (a) select C2', change it to element C bonds 4 geometry tetrahedral.  While
> this does not actually change the atom since that is what it already is, it
> will add a hydrogen to it.
> (b) then select that hydrogen, change it to element O bonds 2 geometry
> tetrahedral, which will change it to OH.
> ...or instead of part (a) just add hydrogens to the whole thing.
> 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 Sep 10, 2011, at 3:47 AM, Bala subramanian wrote:
> > Friends,
> > I am trying to modify the sugar of a nucleotide. I am interested in
> making a linkage of two carbons in the sugar as in the attached pdb. I tried
> to use the Build structure -> modify structure option but it does not work
> in the sense that when i select carbon atom (c2') and tried to connect it to
> an oxygen, chimera says that it is already bonded and hence some bonds to
> create a new one. Is there any way to make such linkages as in the pdb ?
> >
> > Thanks,
> > Bala
> > <A.pdb>
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