Re: [modeller_usage] structural alignment of models respect template(s)

[Modeller Caretaker <>]

On 6/10/10 12:30 PM, David Rodríguez wrote:
> I am interested in making a 3D structural alignment of the resulting
> models with their template(s). I have included the "a.final_malign3d =
> True" line in the script as stated in the manual, and the *_fit.pdb
> files were generated. However, none of the models are correctly aligned
> to the template.

That's intriguing, although I can't say for sure why it's happening 
without seeing your input files. My guess is that either a) you have 
very low sequence identity, so there is not enough conserved structure 
for malign3d to be able to make the correct alignment, or b) you have 
multiple templates which do not overlap well, and it's having a hard job 
aligning all of the models with all of the templates.

	Ben Webb, Modeller Caretaker
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