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

Marta Perez Illana marta.perez at cnb.csic.es
Mon Mar 23 10:20:35 PDT 2020

Hi Rob

I was having exactly the same situation as you mention... Same here if I 
save those mmCIFs in regular chimera as PDBs, unstructured sequence is 
somehow lost.

The only think I could do was use *chimerax, where the unstrucutred 
sequence is kept after saving it as a mmCIF format*.

  *   and then I open it and the whole sequence is kept. If I play
    around with the mmCIF in chimerax everything is fine and kept and 
    can use it normally.
  * But If I would open it in traditional chimera, unstructured sequence
    would be kept, but again, when saving it, the unstructured sequence
    is lost....

But this is NOT when saved in PDB format. Like if you would save in PDB 
format in chimerax no unstructured sequence is neither kept, as in 
traditional chimera...

I think ( and this is just a practical opinion, since I lack the theory 
underneath) that this has something to do with the new mmCIF files 
format. At least everything that I usually fetch nowadays are mmCIF 
already (even if in the past they were initially PDBs in the data base).

If there is an alternative way I would also be more than interested :)



On 23.03.20 15:02, Rob Blakemore wrote:
> Hi,
> 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?
> Details
> 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 files?
> Thank you,
> Rob Blakemore
> robert.blakemore at tufts.edu <mailto:robert.blakemore at tufts.edu>
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Marta Pérez Illana, Ph. D. student
Dept. of Macromolecular Structures Lab 15
Centro Nacional de Biotecnología (CNB-CSIC)
Darwin, 3
28049-Madrid (SPAIN)
Email:  marta.perez at cnb.csic.es
Phone:  (0034) 91 585 4508

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