[phenixbb] AutoBuild can't align sequence file

Moritz.Metlitzky at sbg.ac.at Moritz.Metlitzky at sbg.ac.at
Wed May 27 04:39:13 PDT 2009


Hi all, i'm currently trying to solve my structure with phenix and i tried to do it via AutoMR. At first everything works fine, it finds a MR solution, but then i get this error:

Chain too short or poor match to sequence:  MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL

NOTE: chain A (residues 1-304) MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL
did not match the input sequence...
ignoring alignment and rebuilding segment without sequence information.
***************************************
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 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.


what can i do now? the pdb file has nearly the same sequence (2 mutations) but he says that he can't align them, i use a .dat file for this is this correct? i also have a fasta line in it >... but it doesn't work without this line either.
i tried with different phenix versions and have always the same problem
Any suggestions would be appreciated. 

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