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.
On 10/2/14, 3:06 PM, Michael Meyer wrote: > 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?
If the chains are in the right order (e.g. A, C) you can include the full sequence of chains A, B and C and then align the B chain with a set of gaps in the model:
template AAAAAAAA/BBBBBBBB/CCCCCCCC* model aaaaaaaa/--------/cccccccc*
If the chains are in the wrong order (e.g. C, A) then you can treat them as two separate templates:
template1 CCCCCCCC/--------* template2 --------/AAAAAAAA* model cccccccc/aaaaaaaa*
Note however that this will discard any interactions (distance restraints) between chains A and C.
Otherwise, your only option is to edit the PDB file and reorder the chains.
> 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.
You can certainly try to align both chains at the same time. align2d (as long as you use a recent version of Modeller) will try to line up the gaps, but since it's basically trying to globally align the two sequences it could get confused if your chains are of very different lengths or you do something crazy like try to align one chain in the template with two in the model. Aligning the chains separately probably works the best in this case.
Ben Webb, Modeller Caretaker