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

[Randy Read]

Dear Alex,

For Phaser, it doesn’t matter whether your sequences of a particular type are in one or more files.  You can’t mix protein and nucleic acid sequences, but you can concatenate several chains of either protein or nucleic acid in one file.  The reason is that Phaser is only using this information to determine the overall composition of the asymmetric unit of your crystal; it is not relating the sequences you provide to the models.

If you have a sequence file for one chain and you know you should have two, then you can provide that sequence file and simply say that there are two copies in the GUI (or in command-line scripts or Python scripts, if you prefer).

I hope that helps!

Randy Read
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research    Tel: +44 1223 336500
Wellcome Trust/MRC Building                         Fax: +44 1223 336827
Hills Road                                                            E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

> On 8 Jan 2016, at 18:21, Alex Lee <alexlee198609 at GMAIL.COM> wrote:
> 
> 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
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> Alex
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