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...that is, take the model pdb and my
alignment file and generate a model for my protein of interest?
yong,
sounds like you might want to try Chainsaw within CCP4i. It isn't available
for Windows (unless this has changed recently), but works fine in Linux.
Also, you can try an online program called CASPR, which does molrep for you,
and can then output the final model to have the correct sequence of your
protein of interest (this option is under Expert User). the link is below.
http://igs-server.cnrs-mrs.fr/Caspr2/index.cgi?step=0
If all else fails, a more laborious approach is to do it manually within
Coot, which make this process really fast and painless, in my opinion. Even
if your protein is large, you can accomplish this in less than a day. I am
sure there are other programs or approaches, but these have worked for me in
the past.
Hope some of this helps! Best of Luck and please let me know if I can help
further.
Cheers,
Nick
----- Original Message -----
From: "Yong Tang" <[EMAIL PROTECTED]>
To: <[email protected]>
Sent: Friday, December 15, 2006 3:42 PM
Subject: [ccp4bb]: structural modeling with manual sequence alignment
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Dear all,
I have a protein that has a homolog with known crystal structure. I
aligned them manually and very carefully to make sure that we get what
we have known right. I want to now replace the conserved residues in
the model into those of my protein of interest and hopefully also do
some sort of positional minimization so that I could have a rough idea
about the surface of my protein of interest. Would there be any
program doing this for me - that is, take the model pdb and my
alignment file and generate a model for my protein of interest? If
not, would you be kind enough to share your protocol with me if you
have done this by hand. Happy Holidays!
Thanks! -yong
