[Chimera-users] alignment + missing residues

Gesa Volkers gesa.volkers at uni-greifswald.de
Fri Jul 16 02:58:48 PDT 2010

Dear Eric,

thanks for your suggestions. Unfortunately removing the SEQRES record 
did not help. I also downloaded and installed the new chimera-version 
today. The false numbering in the alignment still occurs. Also when I 
remove the SEQRES record and try with the new chimera version the false 
numbering appears. Quite annoying... The pdb-file is not in the protein 
data bank yet.

Any more suggestions? Could I add "dummy atoms" in the structure?


Eric Pettersen schrieb:
> On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote:
>> Dear All,
>> I observed an issue with the alignment function of Chimera.
>> I loaded a crystal structure where in between a loop is not modelled 
>> due to low electron density- so these residues are missing in the 
>> structure and the numbering also has this gap. When I align this 
>> structure with others, the missing residues are not recognized and 
>> chimera just overrides the numbering so after this loop all the 
>> numbers in the alignment do not fit anymore to the residues they 
>> should belong to although the structure and numberings are shown in 
>> the right way in the graphics window. How can I overcome this issue? 
>> Should I change the pdb-file? In which way?
>> Thanks for all responses!
> Hi Gesa,
> I had a similar problem reported with 1JFF 12 days ago and haven't yet 
> worked on fixing it.  It seems to only happen for a small subset of 
> structures.  1JFF has a missing loop and also exactly one missing 
> residue at the N terminus.  Is your structure like that?  Is it a 
> standard PDB entry (if so, what's the ID code)? I'll add you to the 
> recipient list for the ticket we have open in our bug database for 
> this (#8585) so you will be notified when it gets fixed.  It'll 
> probably be fairly soon.
> Until then the only workaround that occurs to me is for you to remove 
> the SEQRES records from the PDB file before you open it.  Then the 
> Sequence viewer will depict only the residues physically present in 
> the structure -- no gaps (incorrect or otherwise) will be depicted.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu

Gesa Volkers
Institut für Biochemie, Molekulare Strukturbiologie
Felix-Hausdorff-Straße 4
17489 Greifswald
+49 (3834)-864392

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