Hi: I use 'model-segment.py' to build the structure of my target protein, the following is the script: from modeller import * from modeller.automodel import * log.verbose() class mymodel(automodel): def select_atoms(mdl): return selection(mdl.residue_range('37:A','63:A'), mdl.residue_range('74:A','96:A'), mdl.residue_range('111:A','133:A'), mdl.residue_range('153:A','173:A'), mdl.residue_range('203:A','224:A'), mdl.residue_range('250:A','274:A'), mdl.residue_range('287:A','308:A')) env=environ() env.io.atoms_files_directory='./:../atom_files' env.edat.nonbonded_sel_atoms=2 a=mymodel(env, alnfile='1u19-tm.ali', knowns='1u19', sequence='mrg-tm') a.starting_model=1 a.ending_model=1 a.make() after running the scripts, it appears some errors: Traceback (most recent call last): File "selection.py", line 22, in ? a.make() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 118, in make atmsel = self._check_select_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 483, in _check_select_atoms atmsel = self.select_atoms() File "selection.py", line 6, in select_atoms return selection(mdl.residue_range('37:A','63:A'), File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 64, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 165, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v1/modlib/modeller/util/modutil.py", line 76, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 50, in _indxres raise KeyError, ("No such residue: %s" % indx) KeyError: 'No such residue: 37:A' The residue numbers in the model are really the same as residue numbers in the template. After 'mod9v1 model-segment.py', it produce the 'tm-mrg.ini' and 'tm-mrg.scr'files, if the script is wrong, dose it produce results else? ps: is there any diffference between the .ini files and .pdb files?
jinlian05@lzu.cn wrote: > after running the scripts, it appears some errors: ... > KeyError: 'No such residue: 37:A'
Yes, that's the same error you reported before. Please read my previous post.
> The residue numbers in the model are really the same as residue numbers in the > template.
No - they're not. You are building a single-chain model, so Modeller will not assign it a chain ID. And the residue numbers would only match if your alignment contained no gaps.
> After 'mod9v1 model-segment.py', it produce the 'tm-mrg.ini' and > 'tm-mrg.scr'files, if the script is wrong, dose it produce results else?
You will also get one or more .pdb files if the script runs to completion.
> ps: is there any diffference between the .ini files and .pdb files?
Of course - the .ini file is simply the target sequence threaded onto the template structure. It is unoptimized.
Ben Webb, Modeller Caretaker
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jinlian05＠lzu.cn -
Modeller Caretaker