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Problems with modeling chimera


I try to model a chimeric protein based on FAQ 4

To test the method I took a PDB file and cut it in two parts and then try to model the complete molecule again based on an FAQ 4

I get the error: 

fit2xyz_E> number of equivalent positions < 3:     0
recover__> ERROR_STATUS >=  STOP_ON_ERROR:   1  1

As I understand it there are not enough overlapping residues in the alignment. But that is exactly the point, I try to model a chimeric protein based on the independent fragments exactly as in FAQ 4.

What is wrong?

Does the templates have to be overlapping, and is FAQ 4 wrong?

All files are attached

Thanks in advance


Kim Vilbour Andersen, PhD
Senior Scientist 
Agern Allé 1
DK-2970 Hørsholm
 <<model.top.gz>>  <<align.pir.gz>>  <<1GR3_A2.pdb.gz>>  <<1GR3_A1.pdb.gz>> 
Tel: +45 7020 5550
Direct: +45 4517 8473
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Fax: +45 7020 5530


Attachment: model.top.gz
Description: model.top.gz

Attachment: align.pir.gz
Description: align.pir.gz

Attachment: 1GR3_A2.pdb.gz
Description: 1GR3_A2.pdb.gz

Attachment: 1GR3_A1.pdb.gz
Description: 1GR3_A1.pdb.gz