Hi Everyone, I am getting this error, when i am running modeller. i posted this mail before but i did not get any reply. looking forward to it
Traceback (most recent call last): File "compare_1.py", line 32, in ? aln.malign3d() File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 329, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 1
On 11/25/2010 05:21 AM, bharat lakhani wrote: > I am getting this error, when i am running > modeller. i posted this mail before but i did not get any reply. ... > _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: > 1
Looks like you are trying to do a structural alignment of two proteins that are not aligned in sequence, e.g. your input alignment looks something like:
protein1 AAAAAAAA--------* protein2 -------BBBBBBBBB* protein3 CCCCCCCCCCCCCCCC*
There is no way that Modeller will be able to structurally align protein1 with protein2, because it needs at least 3 equivalent positions to do that (there is only one above).
Ben Webb, Modeller Caretaker
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bharat lakhani -
Modeller Caretaker