On 4/5/12 4:00 AM, Jan Kosinski wrote:
I cannot get Chain.join() working properly for multi-chain PDB files. For example, for PDB code 2YFH, which has chains A, B, C, D, E, F,: * when I join D and E I get A, B, C, D, F as expected * but if I try to join A and B I get A, F only
Yes, you're right. There is a bug that affects joining adjacent chains when the second chain is *not* the last chain in the PDB (but as you noticed, joining non-adjacent chains works fine). The fix for this will be in the next release (out within about a month). Below is a
workaround you can use in the meantime:
from modeller import *
from modeller.scripts import complete_pdb
env = environ()
env.libs.topology.read('${LIB}/top_heav.lib')
env.libs.parameters.read('${LIB}/par.lib')
mdl = model(env)
mdl.read(file='2yfh')
mdl.chains['B'].name = 'A'
mdl.write(file='out.pdb', no_ter=True)
mdl = complete_pdb(env, 'out.pdb')
Note that even using Chain.join() you would still need to write out the
file then read it back with complete_pdb(), in order to rebuild the
topology (Chain.join() does not remove OXT atoms, for example).
Note that the workaround uses no_ter=True. This generates a PDB file containing no TER records. When complete_pdb() reads in such a model, it has to assume that chain breaks occur between residues in differently-named chains. Since we forced the B chain to also be labeled 'A', it will merge the two 'A' chains at this point.
Ben Webb, Modeller Caretaker
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