Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

On 25/08/10 23:24, Garib Murshudov wrote: However 1) coot uses 2mFo-DFc maps Typically yes, but it uses whatever Refmac (or other programs) provide (of course) 2) you should be able to feed any map you want to coot Yes. so it is nice place for experimenting this kind of calculation

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

Well - that is exactly what COOT does isnt it? Eleanor Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards,

[ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't realize this before, sorry again. Best Regards, Hailiang

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I found some comments saying minimizing the difference between 2mFo-DFc and Fc may be better, thats why I am asking

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

I mean the density of 2mFo-DFc or Fc maps. On Wednesday 25 August 2010 03:13:53 pm Hailiang Zhang wrote: Hi Garib: Actually I tried coot real space refine zone, but the model seems not sliding into the best density map (I also tried dragging it around, but still not working fine). Then I

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

On Wednesday 25 August 2010 03:19:53 pm zhan...@umbc.edu wrote: I mean the density of 2mFo-DFc or Fc maps. I still don't understand. Real space refinement will minimize a fit of model to density in whatever map you give it. It's up to you which coefficients are used to calculate the map you

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

Ethan, I still don't understand. Real space refinement will minimize a fit of model to density in whatever map you give it. It's up to you which coefficients are used to calculate the map you are refining against. This is true. However, I guess, the way it is implemented in Coot is a bit

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

I think Paul (Emsley) is better qualified to answer to this question. However 1) coot uses 2mFo-DFc maps 2) you should be able to feed any map you want to coot so it is nice place for experimenting this kind of calculation 3) You may try to relax gemetry 4) Usually if the model does not

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

But equation given in slide #4 is exactly least-square equation with some modified maps. Just use Pareval's theorem, then for case of 2mFo- Dfc you will have sum_{reflection used) (2mFo-DF_{c current) -k F_{model})^2 F_model is equal to F_{c current} at the point of calculation. All