Hi Xiang, Oleg's email says "I'd recommend dev-2006 nightly build". So please use that version of Phenix and it should work. If it doesn't please get back to us and we will do our best to make it work. Again, it will not work in "PHENIX-1.9-1692". All the best, Pavel On 4/22/15 11:19 AM, 李翔 wrote:

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!

Sincerely, Xiang

2015-04-22 12:20 GMT-04:00 Oleg Sobolev mailto:[email protected]>:

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 . 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 mailto:[email protected]> 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：[email protected] mailto:[email protected]

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

-- Li Xiang Department of chemistry, Purdue University Email：[email protected] mailto:[email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]