[ccp4bb] structure based superposition
Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
Re: [ccp4bb] structure based superposition
normaly you can do it in the pymol. In the main interface, on the left menu, there is a:A button, click it, then looking for Aliagn. Then you can do it. But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any region you want to do superpose.
Re: [ccp4bb] structure based superposition
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Suda, You can use - - lsqkap - - lsqman - - tools available in coot - - pymol - - probably something like phenix.superpose ... Cheers, Tim On 08/18/2011 11:10 AM, Suda Ravindran wrote: Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOTOKYUxlJ7aRr7hoRAoh8AJ9Kx2qWJAXEDvyxnSt7bnAk54rfPwCg15AN +yV/DvZS4+oVGUkQfTufIOs= =zj1/ -END PGP SIGNATURE-
Re: [ccp4bb] structure based superposition
... and in ccp4mg On 18 Aug 2011, at 10:55, Shilong Fan wrote: normaly you can do it in the pymol. In the main interface, on the left menu, there is a:A button, click it, then looking for Aliagn. Then you can do it. But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any region you want to do superpose.
Re: [ccp4bb] structure based superposition
Hi Shilong, On Thu, Aug 18, 2011 at 5:55 AM, Shilong Fan fanshil...@hotmail.com wrote: normaly you can do it in the pymol. In the main interface, on the left menu, there is a:A button, click it, then looking for Aliagn. Then you can do it. But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any region you want to do superpose. PyMOL can indeed perform alignments. It has three different methods and I'd like to take a second to clear up the differences. First, the align command (A Align ) performs a sequence alignment followed by a few rounds of fitting throw away outliers to improve the fit. The super command is similar to align, but if you indicate seq=0 then PyMOL will ignore the sequence. It then uses a dynamic programming strategy to find the best fit. Last, PyMOL also offers access to the structure-only cealign method as well. Of course, if you already know your paired atoms you can just use any of the 'fit' commands to do the fitting. Here are links to the PyMOLWiki pages for reference: * -- http://www.pymolwiki.org/index.php/Align * -- http://www.pymolwiki.org/index.php/Super * -- http://www.pymolwiki.org/index.php/Cealign * -- http://www.pymolwiki.org/index.php/Fit Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] structure based superposition
You can do structure based sequence alignments using STRAP. It's java based and free. On Aug 18, 2011 5:20 AM, Suda Ravindran biobud...@gmail.com wrote: Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
Re: [ccp4bb] structure based superposition
Check out Theseus: http://www.theseus3d.org/ You will need a sequence based alignment. This alignment can be provided automatically by muscle if you have it installed (http://www.drive5.com/muscle/)--this is different from pymol. Pymol seems to do an SVD to obtain the alignment. I'm not up to date on what all the other programs are using, but I think most use least-squares, so you need to provide a sequence based alignment for these programs Theseus results are always as good or better (subjectively speaking) than straight least-squares superposition. I don't know how the Theseus/muscle combo compares to pymol's use of SVD in terms of alignment quality because I haven't compared them directly. James On Aug 18, 2011, at 3:10 AM, Suda Ravindran wrote: Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
Re: [ccp4bb] structure based superposition
Hi Suda, You can do this in Coot by loading the two structures, then using the tool Calculate- SSM superpose. The rmsd value and sequence identity should be reported within your terminal window. Hope that helps. -Joe Date: Thu, 18 Aug 2011 14:40:32 +0530 From: biobud...@gmail.com Subject: [ccp4bb] structure based superposition To: CCP4BB@JISCMAIL.AC.UK Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
