[phenixbb] Generate sequence files of homodimer protein or double strand DNA for phaser MR

[Alex Lee]

Dear Phenixbb members,

I am using Phaser MR for solving a homodimer DNA binding protein with dsDNA
complex structure. I'd like to use sequence file rather then molecular
weight in the component definition of ASU.  As there are solved homodimer
protein structures (amino acid identity 100%) on PDB, I can download seq
file (fasta form) from PDB webpage, but the seq file is only for one
protein chain.  I also tried online tools like "make sequence from PDB
file" (http://swift.cmbi.ru.nl/servers/html/soupir.html), when I put the
protein dimer bound to dsDNA pdb into the online tool, the outtput pir
sequence file only shows a single protein chain and dna which dose not
seems like two strands, rather then just put two 23base dna together for a
46 base length single strand DNA.

I am asking is there a way to generate sequence file for a homodimer and
dsDNA? or I have to generate sequence file for each chain separately (there
will be four sequence files in this case, two protein chains and two dna
chains)?

Thanks.

Alex












Alex
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