Re: [ccp4bb] align structure in Pymol based on dsDNA helix

[Thirugnanasambandam Arunachalam]

Dear Xiao Lei,

You can try the command given below to align structures. Before you do that
you have to create mobile and target chains to different objects.

align mobile, targeted, transform=0/1; transform=0(without) / 1(with
superposition)

For more options refer the pymol wiki (https://pymolwiki.org/index.php/Align
)


Best regards,

Thiru

On Mon, May 15, 2017 at 10:34 PM, Stefan Gajewski 
wrote:

> Dear Xiao Lei,
>
> You might want to consider UCSF Chimera for this task
>
> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/
> matchalign/matchalign.html
>
> Best,
> Stefan
>

Re: [ccp4bb] align structure in Pymol based on dsDNA helix

[Stefan Gajewski]

Dear Xiao Lei,

You might want to consider UCSF Chimera for this task

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html

Best,
Stefan

Re: [ccp4bb] align structure in Pymol based on dsDNA helix

[Tim Gruene]

Dear Xiao Lei,

In my opinion, lsqman from the Uppsala Software Factory is the most flexible 
program for aligning structures. Aligning based on dsDNA should also be 
possible in lsqkap, I guess.

Best,
Tim

On Saturday, May 13, 2017 1:29:27 PM CEST Xiao Lei wrote:
> Dear All,
> 
> I was wondering in Pymol is there a way to align various NCS protein dsDNA
> complex structure in asymmetric unit based on the double helix of DNA?
> 
> I can do the align with the protein part with action-->align--> to molecule
> or to selection. But this way does not work out if I select dsDNA and do
> the align to selection. I also tried to used command align obj 01 and chain
> X, obj 02 and chain Y to align dsDNA, but still failed with message
> "invalid selection for alignment".
> 
> thanks ahead for any input.

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/104
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

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[ccp4bb] align structure in Pymol based on dsDNA helix

[Xiao Lei]

Dear All,

I was wondering in Pymol is there a way to align various NCS protein dsDNA
complex structure in asymmetric unit based on the double helix of DNA?

I can do the align with the protein part with action-->align--> to molecule
or to selection. But this way does not work out if I select dsDNA and do
the align to selection. I also tried to used command align obj 01 and chain
X, obj 02 and chain Y to align dsDNA, but still failed with message
"invalid selection for alignment".

thanks ahead for any input.