[Chimera-users] alignment + missing residues
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?
> 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 Pettersen
>> UCSF Computer Graphics Lab
Institut für Biochemie, Molekulare Strukturbiologie
More information about the Chimera-users