Dear bulletin board,
I am trying to run Pandda on a set of about 50 data sets. I asked our system
manager to roll back to CCP4 update 047 and by using unique and refmac, I could
fix the problem of a few missing low resolution reflections.
However, then Pandda crashes apparently during alignment of the structures with
the following - for me not very helpful - error messages:
Failed to align dataset x10
Traceback (most recent call last):
File
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/pandda/analyse/functions.py",
line 68, in run
alignment = model.align_to(other_hierarchy=other.hierarchy, method=method,
require_hierarchies_identical=False)
File
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/dataset.py",
line 96, in align_to
self.alignment = align_structures_flexible(mov_hierarchy=self.hierarchy,
ref_hierarchy=other_hierarchy, **kwargs)
File
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
line 254, in align_structures_flexible
l_ali = align_chains_flexible(chn_mov=chn_mov, chn_ref=chn_ref,
altlocs=altlocs, cutoff_radius=cutoff_radius)
File
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
line 285, in align_chains_flexible
chn_ref_cr, chn_mov_cr = common_residues(chn_ref_cb, chn_mov_cb)
File
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/select.py",
line 79, in common_residues
assert (max(m_seq_1)<len(alignment.a)) and (max(m_seq_2)<len(alignment.b)),
'Something has gone wrong: selecting residue index greater than chain length'
AssertionError: Something has gone wrong: selecting residue index greater than
chain length
The same message is repeated for 47 more data sets.
Does anyone has an idea what the problem is? Did the rollback to update 047
fail? All pdb files have the same sequence, but there may sometimes be one or
two residues missing at the N- or C-terminus. Also in some cases, some
side-chains may be missing. There is only a single protein chain and a few
calcium ions. In most cases, the calcium ions have the same chainID as the
protein (as in the reference pdb file), but sometimes the calcium ions have a
separate chainID.
Any help will be greatly appreciated!
Herman
