Hi

Did you check the tutorial?

I think this is what you are looking for (at the end)

https://salilab.org/modeller/wiki/Missing%20residues

"Because either automodel or loopmodel will build a comparative model using your input PDB as a template, potentially all of the atoms in your final model could move. If you really don't want the non-missing residues to move, you can override the select_atoms method to select only the missing residues with a script similar to that below"

I hope this helps

OCS

Oscar Conchillo Solé
Computational Biology Group
Data Center Manager, Sysadmin and Bioinformatics
Institut de Biotecnologia i Biomedicina (UAB)
mail: ocs@bioinf.uab.es
telf:0034 93586 8939; 0034 93581 4431

No. As you discovered you'll lose information that way. I would just
align the two templates together and go from there. 

But this means that the four domains for which I have the X-ray of my target would be moved a little and I want to avoid it. Can I tell modeller not to move them?

That won't work (as you saw) since the inifile has to have exactly the
same sequence as the final model.

Indeed I added the two missing domains (manually aligned with the template). In this way my infile has  exactly the same residues present in the alignment file for the target sequence, but I expect modeller to refine only the two domains I manually add.

Thank you very much for your support,

Stefano  

Il giorno mar 25 feb 2020 alle ore 23:37 Modeller Caretaker <modeller-care@salilab.org> ha scritto:

On 2/25/20 2:33 PM, Stefano Motta wrote:
> Thanks for your answer. Do you mean that I should remove the 4 domains
> present in the X-ray of my target protein from the homologous template?

No. As you discovered you'll lose information that way. I would just
align the two templates together and go from there.

> I thought a good idea would be to use as input
> model (inifile) the X-ray structure of my target protein

That won't work (as you saw) since the inifile has to have exactly the
same sequence as the final model.

        Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

--

________________________________________________________________

Stefano Motta PhD

Email: stefano.motta@unimib.it
Field of study: Molecular Modeling, and Proteins Molecular Dynamics

 
Università degli Studi di Milano Bicocca
Department of Earth and Environmental Sciences

Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).

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