[Chimera-users] [chimera-dev] alignment + missing residues
pett at cgl.ucsf.edu
Tue Jul 20 13:06:19 PDT 2010
This message and the one before it reappeared due to a malfunction in
our mailing-list software. That problem has been fixed. Sorry for
the spam. The problem in the mail itself has been fixed also, as per
the response I sent to the original messages.
UCSF Computer Graphics Lab
On Jul 16, 2010, at 2:58 AM, Gesa Volkers wrote:
> 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
> numbering appears. Quite annoying... The pdb-file is not in the
> 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
>> 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
> Gesa Volkers
> Institut für Biochemie, Molekulare Strukturbiologie
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