A small bugfix is going into the next release which fixes this.
Jalview's PDB parser relied on finding a meaningful PDB ID from the TITLE entry in the file, and Modeller doesn't write this in. I only discovered this myself after a half hour of frustration after building some models.
A quick work around is to add in a
Piotr Cieplak wrote:
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I ma having problems with linking structure to the sequence in Jalview
alignment. I can successfully do that for "real" pdb structures taken
from PDB, I cannot do this for proteins structure that is a model build
by some modeler tools (for example modeler).
Is there any solution for that?
Thanks
Piotr Cieplak
.. dummy line in the PDB file that you are trying to read in:
HEADER 9mdlXX
This will ensure the (broken) parser puts in a valid string into the PDB ID variable, and so avoiding the exception that leads to Jalview thinking it cannot read this file as a PDB file.
cheers.
Jim
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J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk