[Chimera-users] structure editing query

Elaine Meng meng at cgl.ucsf.edu
Sat Sep 10 11:36:28 PDT 2011

Yes, did you try it?

To add atoms to a molecule, keep adding hydrogens and changing their types in "modify structure" and then after all the atoms are present, if you still need to add a bond, you can use the "adjust bonds" part.

On Sep 10, 2011, at 10:34 AM, Bala subramanian wrote:

> 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,
> Bala
> 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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