[Chimera-users] [chimera-dev] alignment + missing residues

Eric Pettersen 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.


                         Eric Pettersen
                         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  
> 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
> Germany
> +49 (3834)-864392
> _______________________________________________
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