[Chimera-users] Delete pseudobonds

[Justin Prado]

Thank you so much for getting back to me. I was able to delete those files,
but it did not really solve my issue. The thing is, I am trying to add a
peptide into a protein but not by the end of the protein. There is a part
of the structure that is missing which is about 20 amino acids, so I am
trying to fit a peptide inside that section. I keep running into an error
that says "Unexpected branching atom ( ) connected to C-terminal carbon. I
just assumed it was that pseudo bond that was put to fill that empty space.
I deleted those CONECT lines but I still got the same error. Do you have
any other suggestions?

On Tue, Mar 14, 2023 at 9:43 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Justin,
> You just open the PDB file in your favorite text editor and then delete
> all the lines that start with CONECT.  It is not something you would do
> using Chimera or ChimeraX.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Mar 13, 2023, at 9:52 PM, Justin Prado via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Good evening,
> >
> > I am emailing on behalf of a message that was responded to in 2018. It
> involved the deleting of CONECT records from a PDB file. I was wondering if
> there were instructions on how that was done? I look forward to hearing
> from you.
> >
> > Thank you
> > Justin Prado
>
>
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