[Chimera-users] Unstructured residues disappear from sequence after save and reopen

Rob Blakemore robert.blakemore at tufts.edu
Mon Mar 23 07:02:02 PDT 2020


I'm encountering a problem wherein unstructured residues are present in the
sequence the first time I fetch it from PDB, but are omitted after I save
the file locally and reopen it. Has anyone else encountered this and would
you happen to know a workaround?

I'm running Chimera 1.14 (build 42094)  on MacOS Mojave V10.14.6
I'm using 6VXX as the PDB file.

When I fetch a structure by ID: (PDB mmCIF) and open a sequence (Tools -->
Sequence --> Sequence), it shows me a complete sequence containing both
residues present in the structure, as well as unresolved/unstructured
residues. The unresolved residues are outlined by a red border.

However, if I save this session to a file or save the structure to PDB and
then reopen it; if I then open the sequence, it only shows me the sequence
of residues present in the structure, and omits all of the unresolved /
unstructured residues. (All the red outlined residues are now gone)

Is there any way to preserve the unstructured residues when saving these

Thank you,
Rob Blakemore
robert.blakemore at tufts.edu
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