[Chimera-users] mmCIF lacks peptide bonds

Michael Blaisse mblaisse at berkeley.edu
Fri Apr 8 10:49:20 PDT 2016


I'm solving a crystal structure and as I'm preparing to submit the final
structure to PDB, I used the PDB_Extract tool to convert my final refined
.pdb to an mmCIF file as per the request of PDB. After I do this, however,
I noticed that if I open the CIF file in Chimera, it does not have any
connectivity between the residues. This does not appear to be a problem in

Less importantly, I also had a question about the Sequence view in Chimera.
I have a break in my chain due to unmodelled residues, and I noticed that
if I float my cursor over a residue in the sequence, it shows the correct
residue number at the bottom of the window, however the numbering at the
side of the sequence view window is wrong after the break because it does
not take the chain break into account.

I appreciate any advice/help people can offer.

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