[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


   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.


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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