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
On 2/25/20 11:45 PM, Stefano Motta wrote: > > 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 mailto: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 mailto: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 mailto:s.motta17@campus.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). > _________________________________________________________________ > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage