Re: [modeller_usage] problem with Chain.join()

[Jan Kosinski <>]

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
> -- 
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage