problems with linking structure of the modelled protein with sequence

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

Hi Piotr.

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:

···

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

Oops.

I forgot to finish this email.

James Procter wrote:
<snip>

A quick work around is to add in a

.. 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