[phenixbb] restraints for dna planarity

Pavel Afonine pafonine at lbl.gov
Fri Sep 12 15:18:16 PDT 2014

Hi John,

just to add to Oleg's reply.. This option will enable three types of DNA 
specific restraints:

- restraints to mimic hydrogen bonds between interacting base pairs;
- planarity restraints for interacting base pairs;
- parallelity restraints will gently enforce stacking bases to be 
approximately parallel.


On 9/12/14 3:10 PM, Oleg Sobolev wrote:
> Dear John,
> Can you please try to use option
> "nucleic_acid_restraints.enabled=True"
> if you run phenix.refine from command line. This is fairly new option 
> so you should have recent nightly build.
> Since the option is new, your feedback will be greatly appreciated. If 
> it does not do the job, I'll be happy to look at your files (off list) 
> and will try to solve the issue.
> Best regards,
> Oleg Sobolev.
> On Fri, Sep 12, 2014 at 2:42 PM, John Lee <jklee at umn.edu 
> <mailto:jklee at umn.edu>> wrote:
>     Hi,
>     I'm refining a low resolution structure of a dna-protein complex
>     (3.7A)  & wondering if someone could help me with setting
>     restraints in Phenix to maintain the base-pair planarity of the dna?
>     With the restraints I have, even with a reference model, I'm
>     getting 'puckering' of the base-pairs. Although the h-bonding
>     distances seem to hold over time, I can't seem to find a way to
>     keep the planarity intact.
>     Thanks in advance for your help.
>     -John
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