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.

Pavel

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 <[email protected]> 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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