Yes, you can use a template containing more than one chain for modelling.

Use a modeller script to extract the protein sequence from the pdb file containing both chains and use that for your alignment.

READ_MODEL FILE = 'pdb_file_name' #Without the extension SEQUENCE_TO_ALI ALIGN_CODES = 'pdb_file_name', ATOM_FILES = ALIGN_CODES WRITE_ALIGNMENT FILE = 'pdb_file_name.seq'

The above script should do that for you. You can also produce a model of a complex provided you have a template containing the two proteins.

Cvetan

Quoting Himanshu Grover hgrover_00@iiita.ac.in:

> Hullo, > am a novice user of modeller... need some help for a problem described > below... > > my target protein contains 2 chains which need to be modelled. I am > currently modelling them independently and then concatenating their pdbs > to get the complete protein. > > Firstly, is is possible to model the 2 chains together, rather than > independently, since that would mean taking one chain into context while > modelling the other... > > Secondly, after generating the protein, i need to check its binding to > another protein, with which it is always found complexed. For instance, in > case of immunoglobulins, we have 2 chains to be modelled, and then these > chains are always found complexed with a peptide-MHC... So I need that the > optimization of the chains and loop refinement of the heavy and the light > chains should take place taking into consideration the peptide-MHC as > well. > > The reason i want to do this is that I tried to generate the structure of > some xyz protein through modeller, whose crystallographic structure is > also available. so i took xyz(crystallographic) as the template and tried > to generate the same structure with modeller. the new struc. has an rmsd > value of 0.19 as compared to the actual structure, which is quite good. > however, at the binding site, there are some side chains that are not > nicely fitting on top of the actual structure. and some interactions have > gone down, resulting in poor binding. is there a way to rectify this > problem?? i was thinking of doing the simulated annealing part taking into > context the entire complex... that is, say, after we > concatenate the light and heavy chain of immunoglobulin with p-MHC, and > then applying molecular dynamics taking into consideration p-MHC > also...but am not sure whether that is possible or not... any say?? > > sincerely, > himan... > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >