Dear Dhiraj,
you may want to check our web service dnatco.datmos.org where you can
also generate 3D constraints for refinement in Phenix.
Best regards,
Bohdan, bs.structbio.org
On 2021-03-30 3:52, Srivastava, Dhiraj wrote:
Thank you everyone for the help. I am sorry about phenix related
question. But since the question was refinement related I thought it
will be ok to ask on ccp4bb.
Thank you
Dhiraj
-----------------------------------------------------------------
*From:* Oleg Sobolev <[email protected]>
*Sent:* Monday, March 29, 2021 6:18 PM
*To:* Srivastava, Dhiraj <[email protected]>
*Cc:* [email protected] <[email protected]>
*Subject:* [External] Re: [ccp4bb] phenix refinement for bent DNA
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the
structure using phenix. do I need to turn off the DNA secondary
structure restraints during refinement?
Application of secondary structure restraints depends on the quality of
the experimental data. The most basic parameter to consider would be a
resolution. For lower-resolution SS restraints might help to keep a
reasonable geometry of the structure. The bent DNA should also work fine
with SS since they are restraining base pairs and stacking pairs which
normally don't distort too much.
P.S. There is a separate bulletin board for Phenix-specific questions:
http://www.phenix-online.org/mailman/listinfo/phenixbb
Best regards,
Oleg Sobolev.
Thank you
Dhiraj
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