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

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

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

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

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

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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

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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