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

[Eric Pettersen]

Dear Gesa,
	I suspect you are using a Mac, since the daily builds failed last  
night for the Mac platforms.  You need to get a daily build dated July  
16 or later.  I tried opening the sequence view for 1JFF in one of the  
successful daily builds and it was correct, e.g.:



You can see that the interior gap is correctly recognized now.   
Hopefully the daily builds on the Mac platforms will work tonight.

>> 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.

Ah, the "remove SEQRES records" hack will only work for the single- 
sequence viewer, not an alignment.  I tested that in the 1.4.1 release  
and it indeed worked as I expected:



The whole sequence is smushed together with no gaps, but the  
correspondences are correct.  You could then align additional  
sequences to the smushed sequence and the correspondences would remain  
correct.  Nonetheless it's probably simply better to wait for a daily  
build to succeed than to use the hack now.  So make sure you check the  
date in the download table.  If you still have problems with a release  
later than July 16, let me know.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Jul 16, 2010, at 3:06 AM, Gesa Volkers wrote:

> 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
> Germany
> +49 (3834)-864392
>
>




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