[phenixbb] AutoBuild can't align sequence file

Tom Terwilliger terwilliger at lanl.gov
Wed May 27 07:39:12 PDT 2009

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
 >>>optionally start another chain


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 (terwilliger at lanl.gov)  
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, <Moritz.Metlitzky at sbg.ac.at> 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:   
> NOTE: chain A (residues 1-304)  
> 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
> phenixbb at phenix-online.org
> 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: terwilliger at LANL.gov
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

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