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@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@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@post.tau.ac.il
On 1/27/13 3:11 AM, danashah@post.tau.ac.il wrote: > 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
You could use automodel for that if you wanted; just give it a simple alignment containing two copies of your sequence (100% identical), e.g.
>P1;orig structureX:my_model.pdb:::::::: AAAAA*
>P1;seq sequence::::::::: AAAAA*
Then set knowns='orig' and sequence='seq' in your Modeller script (my_model.pdb is your input model). You don't need to feed in an initial model, since the initial model is simply the template already. Note though that Modeller builds models that aim to resemble the template structure, so it's not going to be able to improve upon the original template backbone.
Ben Webb, Modeller Caretaker
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danashah＠post.tau.ac.il -
Modeller Caretaker