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" 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 :

...

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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