[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.
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 <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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