[phenixbb] sugar puckering in DNA

Maia Cherney chern at ualberta.ca
Fri Oct 24 10:52:29 PDT 2008


Hi Yu Seon.
I would appreciate it very much if you send me your added restraints to 
the cif file.
Maia

YS. Chung wrote:
> Hi Maia,
> I had the same problem when I was refining with phenix. I ended up
> looking at the torsions that were used in 3DNA (the program I used to
> analyze the puckerings) and manually added the restraints to the .cif
> files used in phenix. I can send you an example if you'd like. The
> puckerings improved a lot when I used the modified .cif files.
> Yu Seon
>
> On Fri, 24 Oct 2008 10:43:44 -0600
>  "chern" <chern at ualberta.ca> wrote:
>  
>> Sorry, I gave a wrong subject name in my previous e-mails. Should've
>> been sugar puckering in DNA.
>> I am wondering why the default .cif file for DNA does not include all
>>
>> information about sugar puckers.
>> I do not have some fancy nucleotides. They are regular.
>>
>> Maia
>>
>> ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" 
>> <rwgk at cci.lbl.gov>
>> To: <phenixbb at phenix-online.org>
>> Sent: Friday, October 24, 2008 10:03 AM
>> Subject: Re: [phenixbb] elbow
>>
>>
>>    
>>>> The answer is yes but there may be better options.  Ralf is the
>>>>         
>> best
>>    
>>>> person to answer this question but one option is to start with the
>>>>         
>> .cif
>>    
>>>> file in the monomer library.
>>>>         
>>> This is more a chemistry question than a formatting question.
>>> Since I'm not deeply familiar with the DNA chemistry, I was
>>>       
>> pointing
>>    
>>> Maia to phenixbb in hopes that someone may already have figured out
>>> the list of torsion angle restraints to fix sugar puckers.
>>>
>>> What Maia really wants is:
>>>
>>>      
>>>> could you please send me a specific example of how to modify a cif
>>>>         
>> file
>>    
>>>> to specify the sugar puckers in DNA (I want them C2'-endo).
>>>>         
>>> Has anyone on this list done this already?
>>>
>>> Ralf
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>       
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>>     
>
>   




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