I try to build a model with my own intial model, but it failed, here is the log file:
Traceback (most recent call last): File "single.py", line 36, in ? a.make() File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 427, in homcsr self.make_initial_model(aln) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 441, in make_initial_model self.generate_method(self, aln) File "/usr/lib64/python2.4/site-packages/modeller/automodel/generate.py", line 46, in read_xyz mdl.transfer_xyz(a, cluster_cut=-1.0) File "/usr/lib64/python2.4/site-packages/modeller/model.py", line 200, in transfer_xyz cluster_method) _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " "; atom file name: loop.pdb
On 07/09/2010 06:38 AM, albert wrote: > I try to build a model with my own intial model, but it failed, > here is the log file:
In order to reproduce your problem, we'll need to see all of your input files, not just the log. See http://salilab.org/modeller/9v8/manual/node10.html
> _modeller.ModellerError: rdpdb___303E> No atoms were read from the > specified input PDB file, since the starting residue number and/or chain > id in MODEL_SEGMENT (or the alignment file header) was not found; > requested starting position: residue number " ", chain " "; atom file > name: loop.pdb
Specification of an initial model is one way to help the optimizer find optimal solutions. In principle of course the optimizer will find the global solution, so the choice of initial model is irrelevant. That said, the initial model must be in the same format as the models generated by Modeller - i.e. the same amino acid sequence, residue numbering and chain IDs.
Ben Webb, Modeller Caretaker
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albert -
Modeller Caretaker