[phenixbb] Auto builiding
Jonathan Grimes
jonathan at strubi.ox.ac.uk
Fri Sep 11 03:50:02 PDT 2009
Dear Developers,
I have a molecular replacement solution with a model
that has 58 seq identity to my protein. There is 1 insertion
in my protein of 1 residue and 1 deletion of 4 residues
compared to the model.
There are 2 mols in the asym unit.
When I run autobuild with standard settings (but either
Auto or Yes for the rebuild in place) it falls over
with this error.
****************************************
AutoBuild Input failed
Sorry, the PDB file and sequence file could not be aligned
(with no gaps and >50.0% identity)
Please restart the wizard...
You have several possibilities to try ....
You can set rebuild_in_place=No
You can set input_sequence_file=None
You can edit your model to make sure it has no residues extending
N-terminal of the beginning of the corresponding sequences in
your sequence file
You can set min_seq_identity_percent to a lower value
You can set highest_resno to a higher value
You can specify start_chains_list if your
PDB file sequence starts with a residue number greater than the
number of residues in the sequence.
****************************************
It runs with
rebuild_in_place=No
but given the low resolution of the data (3.5A) I thought it would be
best to keep as much of the model as possible.
What am I doing wrong.
Thanks
Jon
--
Dr. Jonathan M. Grimes,
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK
Email: Jonathan at strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
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