The workaround works great, thanks!
And great that I could contribute to making Modeller even better ! ;-)
Cheers, Jan Kosinski
On Apr 5, 2012, at 7:40 PM, Modeller Caretaker wrote:
> 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage