Gaps in the PDB file

["Fabio Passetti" <fabiopassetti AT hotmail.com>]

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"

If any of you know how to handle with this, please e-mail me.

Regards,

Fabio

=======================================================================================
Fabio Passetti, PhD student

Instituto do Coração - HCFMUSP
Laboratório de Cardiologia e Genética Molecular
Grupo de Bioinformática

Rua Dr. Enéas de Carvalho Aguiar, 44
05403-010 São Paulo - SP - Brazil

fabiopassetti AT hotmail.com
======================================================================================





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