[Chimera-users] Delete pseudobonds

[Justin Prado]

I did exactly as you instructed and it worked perfectly. Thank you so much
for your help, I really appreciate your time.

Best
Justin Prado

On Wed, Mar 15, 2023 at 9:29 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> HI Justin,
> You could start with a PDB file that has the last part deleted, so you
> only have the first part and can build the middle part (you could open the
> last part as another PDB file if you need to see where it is while you are
> building).  Then you can save the PDB file with the first part + middle
> that you built.  Then text-edit it to put the last part back in.  That is
> just one way.
>
> Another way if the missing part is not too long is to open the whole
> sequence from a sequence file (e.g. FASTA format) and open the PDB with the
> first and last parts in it, and then use Modeller to build the missing
> loop.  See the help:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html
> >
>
> 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 14, 2023, at 6:23 PM, Justin Prado via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > 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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