RE: [ccp4bb]: how to prepare a structure-based sequence alignment

["Frank Vondelft" <Frank.Vondelft@syrrx.com>]

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Hi Zahngfan:

http://www-cryst.bioc.cam.ac.uk/~joy

Or more automatic:

http://www-cryst.bioc.cam.ac.uk/~jiye/evoltrace/evoltrace.html

which will, amongst others, produce the JOY alignment you're after.  And
a very handy evolutionary tree, so you can include non-structure
sequences, which are often handy to have aligned. 

Cheers
phx.




> -----Original Message-----
> From: fan zhang [mailto:zhangfan1980@hotmail.com]
> Sent: Tuesday, July 02, 2002 8:04 AM
> To: ccp4bb@dl.ac.uk
> Subject: [ccp4bb]: how to prepare a structure-based sequence alignment
> 
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear All,
> 
> I'm very sorry it is not a question closely related to protein 
> crystallography.
> Recently, I want to prepare a 
> structure-based-sequence-alignment figure, but 
> I don't know how to do it. In addition, how should I deal with those 
> residues that are of similar physicochemical properties but 
> are not of equal 
> positions.
> 
> Hope your kind replies!
> 
> Best,
> 
> Zhangfan
> 
> Life School of Peking University
> P. R. China
> 
> 
> 
> 
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