[phenixbb] Generating cif file for DNA basepairing in PHENIX

Oleg Sobolev osobolev at lbl.gov
Wed Apr 22 09:20:56 PDT 2015

Dear Xiang,

The simplest way to restrain basepairs in DNA would be option
secondary_structure.enabled=True. If this  doesn't work for you in the way
you are expecting, try to generate basepairs to restrain by using
phenix.secondary_structure_restraints <your_model.pdb>. This will output
restraints in form of phil file. You may inspect it to make sure basepairs
are correct. Then you can supply this file to geometry minimization along
with secondary_structure.enabled=True
secondary_structure.find_automatically=False options. This should do the
work. You will need relatively fresh version of Phenix, I'd recommend
dev-2006 nightly build.

This is relatively new feature, so feel free to provide feedback and get
back to us if something doesn't work as you expecting.

Best regards,
Oleg Sobolev.

On Wed, Apr 22, 2015 at 8:34 AM, 李翔 <lixiang1642 at gmail.com> wrote:

> Hi everyone,
> I am trying to build some DNA duplex models with different pitches by
> 3DNA. After changing the pitches from the original duplex model, I refined
> the duplex in PHENIX with geometry minimization. However, the basepairing
> get completely distorted.
> Is there a quick way to generate the cif file for basepairing in PHENIX or
> are there any other better ways to keep the basepairing restraint during
> the model refinement?
> Thank you very much for your kind help!
> Sincerely,
> Xiang
> --
> Li Xiang
> Department of chemistry,
> University of Michigan
> Email:lixiang1642 at gmail.com
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