[Chimera-users] Delete pseudobonds

[Elaine Meng]

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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