[phenixbb] Generating cif file for DNA basepairing in PHENIX

李翔 lixiang1642 at gmail.com
Wed Apr 22 11:19:23 PDT 2015

Hi Oleg,

Thanks for  the email. I tried to add "option secondary_structure.enabled=
True" in the geometry minimization but it does not work. I also tried to
prepare the restraint file with the same command your provide above.
However, on my computer it says cif file is required and it does not
recognize the generated restraint file.

Maybe there is something wrong with my laptop or setting and I will also
try the newest version of PHENIX. Currently I am using PHENIX-1.9-1692.

Thanks for your kind help!


2015-04-22 12:20 GMT-04:00 Oleg Sobolev <osobolev at lbl.gov>:

> 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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Li Xiang
Department of chemistry,
Purdue University
Email:lixiang1642 at gmail.com
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