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
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 d
You can do structure based sequence alignments using STRAP. It's java based
and free.
On Aug 18, 2011 5:20 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.
Hi Shilong,
On Thu, Aug 18, 2011 at 5:55 AM, 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. Y
Dear all,
Thanks a lot helping me out. I shall try it out... :)
-Suda
On Thu, Aug 18, 2011 at 3:52 PM, Phil Evans wrote:
> ... 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" butt
... 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. Y
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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/pr
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.
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
