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Re: Gaps in the PDB file

On Wed, Sep 18, 2002 at 11:34:32AM -0300, Fabio Passetti wrote:
> Dear Modeller users,
> I have found problems to run Modeller 6.2. I have a PDB file (chain A of 
> the PDB entry 1LDJ) that has two gaps: the first between the 56th and the 
> 83rd and the second between the 150th and the 156th aminoacids. I have 
> tried to find a command in Modeller to warn it that the PBD file has gaps, 
> but I was not able to do so. Even if I replace the missed aminoacids from 
> the PDB file in the input .ali file, the program log stills give a message 
> error, as follows:
> "rdpir___648E> Alignment sequence not found in PDB file:        2  
> ./cullin1.atm   recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       
> 1"

This error is saying some identifier is mislabeled in your .ali.
It hasn't gotten to the point of complaining about missing residues yet.

If you are missing residues, just remove them from the alignment.

Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology
Yale University School of Medicine
Center for Medical Informatics | Research Assistant