[Chimera-users] alignment + missing residues

Gesa Volkers gesa.volkers at uni-greifswald.de
Fri Jul 16 03:06:56 PDT 2010

Additionally I downloaded 1JFF and did an alignment with another 
tubulin-structure. And still the numbering does not recognize this gap 
between 34 and 61.

Gesa Volkers schrieb:
> 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?
> Thanks,
> Gesa
> 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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