[Chimera-users] alignment + missing residues

Eric Pettersen pett at cgl.ucsf.edu
Wed Jul 14 10:32:34 PDT 2010

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

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