[phenixbb] Generating cif file for DNA basepairing in PHENIX

Pavel Afonine pafonine at lbl.gov
Wed Apr 22 11:49:29 PDT 2015


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 <osobolev at lbl.gov 
> <mailto: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
>     <mailto: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 <mailto:lixiang1642 at gmail.com>
>
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>
>
>
>
> -- 
> Li Xiang
> Department of chemistry,
> Purdue University
> Email:lixiang1642 at gmail.com <mailto:lixiang1642 at gmail.com>
>
>
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