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