Re: [ccp4bb] phenix refinement for bent DNA

On 30/03/2021 02:52, Srivastava, Dhiraj wrote: I am sorry about phenix related question. But since the question was refinement related I thought it will be ok to ask on ccp4bb. For the record, it's not wrong, it just that questions about Phenix are more likely to get accurate and timely respon

Re: [ccp4bb] [External] Re: [ccp4bb] phenix refinement for bent DNA

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 Sent: Monday, March 29, 2021 6:18 PM To: Srivastava, Dhiraj Cc

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 param

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? > probably not, unless you have reasons to do so otherwise. P.S.: There is a Phenix mailing list for Phenix specifi

Re: [ccp4bb] refmac twin refinement vs resolution limit

Well - I am not sure whether this has anything to do with twin refinement but resolution limits are often a bit iffy. First the low resolution discrepancy. The Free R is generated to a lower and higher resolution than any observation. The FreeR set is meant to be complete for any possible index re

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[ccp4bb] phenix refinement for bent DNA

Hi 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? Thank you Dhiraj To unsubscribe from the CCP4BB list

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[ccp4bb] refmac twin refinement vs resolution limit

When I use refmac restrained refinement with intensity based twin refinement, resolution limit has been changed from 71.4519- 1.9996 to 47.392-1.986. From Log file, before refinement, Scaling and SigmaA resln: 71.4519 1.9996, seems to be correct. But in the middle of log file, around Fom and Sigm