Indeed, both of them (ConSurf, ALINE) worked very well. Although I found ConSurf to be exact what I asked for, but I was also looking for program like ALINE which aligns the sequences with secondary structure labelling. 

Thanks a lot 



On Fri, Jun 4, 2010 at 8:47 PM, Folmer Fredslund <folmerf@gmail.com> wrote:
Dear Humayun,


On 4 June 2010 13:30, humayun scherrif <hum.one@gmail.com> wrote:
> Dear All,
> Is there any way of color coding sequence conservation of a protein onto
> structure by using multiple sequence alignment and structure in pymol ?
>

It might be possible to do this in PyMOL, but I would strongly advise
you to have a look at ALINE:
http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/

Here you can color the alignment and export the colors to a PyMOL script.

This is at least one way to do it.

Best regards,
Folmer Fredslund



>
> Thanks in advance
>
> --
> Best Regards,
>
> Humayun Sharif
> MS student
> Protein Structure and Function Laboratory
> Gwangju Institute Of Science & Technology,
> Gwangju, 500-712, Republic of Korea
> Tel (Res) :+82-62-718-4176
> Tel (Lab) : +82-62-970-2549
> Email: hum.one@gmail.com
>
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--
Best Regards,

Humayun Sharif
Research Assistant
Protein Structure and Function Laboratory
Gwangju Institute Of Science & Technology,
Gwangju, 500-712, Republic of Korea
Tel (Res) :+82-62-718-4176
Tel (Lab) : +82-62-970-2549
Email: hum.one@gmail.com