[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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