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: [email protected], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
Hi Jon, I think you're doing everything right, but autobuild has a very simple alignment tool and it can't edit your model. The best thing to do is to edit your PDB file to match your sequence manually or with another tool, and then give autobuild your modified PDB file and no sequence file or a matching sequence file. Then it should run fine with rebuild-in-place. All the best, Tom T
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: [email protected], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
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participants (2)
-
Jonathan Grimes -
Thomas C. Terwilliger