[Chimera-users] alignment + missing residues

Gesa Volkers gesa.volkers at uni-greifswald.de
Wed Jul 14 06:53:25 PDT 2010

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!

Gesa Volkers
Institut für Biochemie, Molekulare Strukturbiologie
Felix-Hausdorff-Straße 4
17489 Greifswald
+49 (3834)-864392

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