Hi Moritz,

I'm sorry for the trouble!  Yes, certainly if you have only 2 mutations the sequence should get aligned.  Somehow it seems that your input sequence is not getting read properly, as you are guessing.

Your formats sound ok.  The format for a sequence file is:

>>> optional text about this chain 
ONELETTERCODEFORSEQUENCE
>>>optionally start another chain
NEWCHAIN

ANOTHERNEWCHAINSIGNALLEDBYEMPTYLINEABOVE

where all spaces or characters that are not amino acids are ignored, and capitalization is ignored.  You can indicate a new chain with an empty line or with one or more ">".

If this doesn't help and you'd like to send me ([email protected]) your sequence file and the PDB file and the exact command you used I can run it here and see what is going on.

All the best,
Tom T


On May 27, 2009, at 5:39 AM, <[email protected]> wrote:


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.

_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: [email protected]
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss