I have an input alignment, two structures, and a subset of residues I would like to use to perform a superposition. When I perform the superposition using all residues in the alignment I am successful. However, when I attempt to perform the superposition using a subset, I get error messages:
The script:
from modeller import * env = environ() log.very_verbose() env.io.atom_files_directory = '.' aln = alignment(env, file='reference.1dlf_L.pir', align_codes=('1ck0', '1dlf')) mdl1 = model(env, file='1ck0', model_segment=aln['1ck0'].range) mdl2 = model(env, file='1dlf', model_segment=aln['1dlf'].range) atmsel = selection(mdl1.residue_range('19', '23'), mdl1.residue_range('35', '39')) r = atmsel.superpose(mdl2, aln) mdl2.write(file='1dlf.subset.pdb')
The alignment: >P1;1ck0 structureX:1ck0:FIRST:L:LAST:L:Ab:species:: DIQLTQSPS-SLAVSAGEKVTMNCKSSQNLLHSITR--KNYLAWYRQKPGQSPKLLIYW---ASTRGSGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC---KQSYNL-YTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR * >P1;1dlf structureX:1dlf:FIRST:L:LAST:L:Ab:species:: DVVMTQ-TPLSLPVSLGNQASISCRSSQS---LVHSNGNTYLHWYLQKPGQSPKLLIYK---VSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFC---SQSTHVPFTFGSGTKLEIKR------------------------------------------------------------------------------------------------------- *
The Error:
Traceback (most recent call last): File "modelscript.1ck0.1dlf.py", line 10, in ? atmsel = selection(mdl1.residue_range('19', '23'), mdl1.residue_range('35', '39')) File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 71, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 198, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v3/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 56, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 19'
I was able to determine the source of the error: I had to specify the chain:
atmsel = selection(mdl1.residue_range('19:L', '23:L'), mdl1.residue_range('35:L', '39:L')).only_atom_types('CA')
The initial set of examples on http://salilab.org/modeller/manual/node216.html showed only residue selections, but the later examples included the format listed above. I humbly withdraw my question.
Jake
On Fri, Apr 18, 2008 at 4:47 PM, Jake Gunn-Glanville dr.jake@gmail.com wrote:
> I have an input alignment, two structures, and a subset of residues I > would like to use to perform a superposition. When I perform the > superposition using all residues in the alignment I am successful. However, > when I attempt to perform the superposition using a subset, I get error > messages: > > The script: > > from modeller import * > env = environ() > log.very_verbose() > env.io.atom_files_directory = '.' > aln = alignment(env, file='reference.1dlf_L.pir', align_codes=('1ck0', > '1dlf')) > mdl1 = model(env, file='1ck0', model_segment=aln['1ck0'].range) > mdl2 = model(env, file='1dlf', model_segment=aln['1dlf'].range) > atmsel = selection(mdl1.residue_range('19', '23'), > mdl1.residue_range('35', '39')) > r = atmsel.superpose(mdl2, aln) > mdl2.write(file='1dlf.subset.pdb') > > The alignment: > >P1;1ck0 > structureX:1ck0:FIRST:L:LAST:L:Ab:species:: > > DIQLTQSPS-SLAVSAGEKVTMNCKSSQNLLHSITR--KNYLAWYRQKPGQSPKLLIYW---ASTRGSGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC---KQSYNL-YTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR > * > >P1;1dlf > structureX:1dlf:FIRST:L:LAST:L:Ab:species:: > > DVVMTQ-TPLSLPVSLGNQASISCRSSQS---LVHSNGNTYLHWYLQKPGQSPKLLIYK---VSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFC---SQSTHVPFTFGSGTKLEIKR------------------------------------------------------------------------------------------------------- > * > > The Error: > > Traceback (most recent call last): > File "modelscript.1ck0.1dlf.py", line 10, in ? > atmsel = selection(mdl1.residue_range('19', '23'), > mdl1.residue_range('35', '39')) > File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 71, in > residue_range > start = self.residues[start]._num > File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 198, in > __getitem__ > (self.offset, self.length, self.suffix)) > File "/usr/lib/modeller9v3/modlib/modeller/util/modutil.py", line 19, in > handle_seq_indx > int_indx = lookup_func(*args) > File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 56, in > _indxres > raise KeyError("No such residue: %s" % indx) > KeyError: 'No such residue: 19' > >
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Jake Gunn-Glanville