[phenixbb] Phenix command to align the PDB sequence and input sequence

[Gabor Bunkoczi]

Hi Smith,

if you are happy to use a GUI, then try the "Mutiple sequence alignment" 
available from the "Utilities" menu (not the Utilities sidebar!) in the 
main Phenix window. This will automatically extract the sequence from 
your PDB file.

I am not sure whether there is a command line tool that does the same. 
However, you can always use phenix.print_sequence to extract the 
sequence of a PDB and then use phenix.muscle to do the alignment.

HTH, Gabor

On 2015-04-10 10:06, Smith Liu wrote:
> Dear All,
> 
> I mean the Phenix command to extract the sequence from the PDB file
> and align it with the input sequence for refine.
> 
> Smith
> 
> At 2015-04-10 16:20:23, "Folmer Fredslund" <folmerf at gmail.com> wrote:
> 
>> Hi Smith,
>> 
>> PHENIX uses muscle (http://www.drive5.com/muscle/ [2]) to align
>> sequences
>> 
> (https://www.phenix-online.org/documentation/phenix_gui.html#other-tools
>> [3]).
>> 
>> You can access muscle with "phenix.muscle" on the command line.
>> 
>> Hope this helps,
>> Folmer Fredslund
>> 
>> 2015-04-10 9:20 GMT+02:00 Smith Liu <smith_liu123 at 163.com>:
>> 
>>> Dear All,
>>> 
>>> Will you please tell me the Phenix command to align the PDB
>>> sequence and input sequence?
>>> 
>>> I am looking forward to getting your reply.
>>> 
>>> Smith
>>> 
>>> _______________________________________________
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>> 
>> --
>> 
>> Folmer Fredslund
> 
> 
> 
> Links:
> ------
> [1] http://phenix-online.org/mailman/listinfo/phenixbb
> [2] http://www.drive5.com/muscle/
> [3] 
> https://www.phenix-online.org/documentation/phenix_gui.html#other-tools
> 
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