[COOT] problem with refining DNA

[Norman Zhu]

hello there

   I am in the process of refining a protein structure complexed to DNA
promoter site.  I ran into difficulty as i try to move a few bases into
patch of electron density that is obviously meant for them.  dragging the
bases with real space refine zone and/or regularize zone neither break open
the phosphate back bone bounds or turn everything into knots.  
   I know there is nothing wrong with the naming convention of my bases
since I changed them from DT to Td after similar blog.  
  Any suggestion on this matter would be greatly appreciated.

Norm

Re: [COOT] DNA structure refining problem

[Norman Zhu]

Tim, 

  Yep, that was the problem.  thanks a lot.  

Norm

[COOT] Problem with decapitated protein

[Norman Zhu]

Hello everyone 

I am currently working with a protein shaped like dumbbell, with two
well folded domains connected by a fixable linker in meddle.  Anticipating
movement at the hinge I asked Phaser to treat these two domains as separate
entities.  Phaser provided me with a solution but it placed one of the
domain in the neighboring molecule.  Does anyone know a convenient way to
move that domain back into the same asymmetric unit?  


Norm

Re: [COOT] Problem with decapitated protein

[Norman zhu]

That's really clever.  i'll try that.  Norm

On Thu, Mar 4, 2010 at 12:27 AM, Pirkko Heikinheimo <
pirkko.heikinhe...@helsinki.fi> wrote:

> Norman,
> you can display the symmetry mates of the misplaced domain two in coot and
> then choose the one which is in the same molecule as domain one. Write the
> symmetry mate coordinates out in coot and edit into your coordinate file to
> describe your assymmetric unit with domain one.
>
> regards,
> Pirkko Heikinheimo
>
> Norman Zhu wrote:
>
>> Hello everyone
>>I am currently working with a protein shaped like dumbbell, with
>> two
>> well folded domains connected by a fixable linker in meddle.  Anticipating
>> movement at the hinge I asked Phaser to treat these two domains as
>> separate
>> entities.  Phaser provided me with a solution but it placed one of the
>> domain in the neighboring molecule.  Does anyone know a convenient way to
>> move that domain back into the same asymmetric unit?
>>
>> Norm
>>
>>
>
> --
> &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
>
> Pirkko Heikinheimo
>
> Structural Biology and Biophysics,
> Institute of Biotechnology,
> P. O. Box 65, FIN-00014 University of Helsinki, Finland
>
> Visit address:
> Biocenter 3, room 4320
> Viikinkaari 3, 00790 Helsinki, Finland
>
> http://www.biocenter.helsinki.fi/bi/xray/pirkko
> e-mail: pirkko.heikinhe...@helsinki.fi
> phone:  358-(0)9-191 58957
> gsm:358-(0)50-354 0713
> fax:358-(0)9-191 59940
>
> &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
>
>