[phenixbb] AutoBuild can't align sequence file
terwilliger at lanl.gov
Wed May 27 07:39:12 PDT 2009
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,
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
> 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
> Any suggestions would be appreciated.
> phenixbb mailing list
> phenixbb at phenix-online.org
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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