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: "> 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 <" moz-do-not-send="true">> 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
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Field of study: Molecular Modeling, and Proteins Molecular Dynamics
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