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? I tried this but the resulting model did not preserve the quaternary architecture of the homologous template (the two additional domains were rigidly moved away). I thought a good idea would be to use as input model (inifile) the X-ray structure of my target protein and refine the two additional models using the whole homologous proteins as template. I also defined the selection to model as explained in: https://salilab.org/modeller/9.23/manual/node23.html
Anyway I got the following:
No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " "; atom file name: INI_MOD.pdb
(Where INI_MOD.pdb is the input model defined in inifile) Why did I get this? Thank you very much for your support,
Stefano
Il giorno mar 25 feb 2020 alle ore 22:59 Modeller Caretaker < modeller-care@salilab.org> ha scritto:
> On 2/25/20 7:26 AM, Stefano Motta wrote: > > I'm trying to build a model of a hetero-dimer starting from an X-ray > > structure. Each monomer have 3 domains (6 in total). An X-ray structure > > of part of the complex (two domains of each monomer) exist and I want to > > complete the model with the two missing domains (one for each monomer). > > I would use the X-ray of homologous proteins for which all 6 domains are > > available. Which would be the best approach? I want to keep the X-ray > > part as frozen as possible, and only model the two missing domains from > > the template (both structure and orientation in the complex). > > This should a straightforward application of multiple-template modeling. > You may just need to manually modify the alignment if you get conflicts > (e.g. don't align the model with the 6-domain template in some regions > if it doesn't align well with your X-ray structure). > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >