Hi everyone,
I'm relatively new to Modeller, so please bear with me. I have specific applications in-mind for the future, but for now as an exercise I'm trying to accomplish basic tasks.
Right now, I'm trying to accomplish some basic multi-chain modeling. Let's say I have two target protein sequences, and I have found a PDB template that is appropriate for modeling them via PSI-BLAST. However, unlike the 2-chain example here: http://salilab.org/modeller/manual/node29.html the two chains that are homologous to my target sequences are not A and B in a two-chain PDB. They are C and E, or worse, F and B. My question: Is there any way to use the PIR format en route to automodel.make() to specify two chains that aren't contiguous in a template?
The example given below assumes that the two chains in 2abx are the first two, but what if they were chains C and A?. I could flip their order to get them to be in the order they appear in the PDB file, but there's still the issue that chain B doesn't factor into my modeling step, and so I would like modeller to ignore it? Is there any way to not use chain B without altering the original PDB file to only include the two chains I want to use for modeling?
>P1;2abx structureX:2abx: 1 :A:74 :B:bungarotoxin:bungarus multicinctus:2.5:-1.00 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG*
>P1;1hc9 sequence:1hc9: 1 :A:148:B:undefined:undefined:-1.00:-1.00 IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG/ IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG*
Furthermore, is there any way to use align2d to perform the two sequence-two chain alignment in one step to create the appropriate PIR file for multi-chain modeling. Right now, I'm doing two align2d commands to create two separate PIR files, and then mashing them together afterward.
Thanks!
Michael