No atoms were read form the specified input pdb file
Dear All,
While running the model-single.py, I am getting the following error---
No atoms were read form the specified input pdb file since the starting residue no and/ or chain ID in Model_Segment <or the alignment file header> was not found; requested starting position residue no "0" chain "A"
My model file starts with residue no 4.
Please help. Thanks J
Can you show the alignment file you are using?
Regards,
João [...] Rodrigues @ http://stanford.edu/~joaor/
On Sun, Dec 13, 2009 at 2:33 AM, james09 pruza james09xtal@gmail.comwrote:
> Dear All, > > While running the model-single.py, I am getting the following error--- > > No atoms were read form the specified input pdb file since the starting > residue no and/ or chain ID in Model_Segment <or the alignment file header> > was not found; requested starting position residue no "0" chain "A" > > My model file starts with residue no 4. > > Please help. > Thanks > J > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
On 12/13/2009 02:33 AM, james09 pruza wrote: > While running the model-single.py, I am getting the following error--- > No atoms were read form the specified input pdb file since the starting > residue no and/ or chain ID in Model_Segment <or the alignment file > header> was not found; requested starting position residue no "0" chain "A"
OK, so in that case your alignment file header must be instructing Modeller to read from residue 0:A. See http://salilab.org/modeller/9v7/manual/node445.html for a description of the format (the example at that URL tells Modeller to read 5fd1 from residue 1:A through 106:A).
> My model file starts with residue no 4.
Sounds like you just need to edit the alignment file header to reflect this.
Ben Webb, Modeller Caretaker
participants (3)
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james09 pruza -
João Rodrigues -
Modeller Caretaker