Re: [modeller_usage] Minimize structure energy

[danashah AT post.tau.ac.il]

P.S: When I tried using the same sequence for the alignment file, I  
received this message on the .log file:

read_al_373E> Protein specified in ALIGN_CODES(i) was not found
              in the alignment file; ALIGN_CODES(       1) =   
model_for_modeller.pdb

Thank you,
Dana.

Quoting danashah AT post.tau.ac.il:

> Hi all,
>
> I've only joined this mailing list lately, so pardon me if this  
> question was asked and answered before.
>
> We wish to perform energy minimization to a model we created. We  
> were wondering whether we can use your automodel for that, via "use  
> your own initial model":
> http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel
>
> If it's possible, what should be the alignment file, since the  
> sequence we want to use is the same as the model?
>
> Thank you,
> Dana.
>
> __
> Dana Sachyani
> Joel Hirsch's Lab
> Faculty of Life Sciences
> Tel Aviv University
> Ramat Aviv, Israel
> e-mail: danashah AT post.tau.ac.il