Re: [ccp4bb] No improvement in R-factor after Refmac.

2017-03-18 Thread Sudipta Bhattacharyya
Hi Satya Dev, You can feed the mtz output of SCALA to Phenix Xtriage and then see the presence of t-NCS and/or any other crystal pathologies. Another thing you can do is to merge and scale the data in P222 and then let the Phaser decide the best space group. Again, I am curious, when you ran point

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

2017-03-18 Thread Eleanor Dodson
I think CCP4MG does this very selectively? Eleanor Dodson On 17 March 2017 at 17:03, Xiao Lei wrote: > Dear All, > > Thanks for the information. > I tried the way suggested by pymol wiki, but pymol fail to display the > map. > This is what I did: Run Fft to generate simple mapin ccp4i, input mt

Re: [ccp4bb] No improvement in R-factor after Refmac.

2017-03-18 Thread Eleanor Dodson
You dont say whether there is Non cryst translation - that will be reported at various stages - the pointless/aimless/ctruncate task gives it. But if it exists and the translation ihas a component of .5 along any axis, that makes the SG estimate a bit uncertain - the absences could be due to the N

Re: [ccp4bb] No improvement in R-factor after Refmac.

2017-03-18 Thread Isupov, Michail
Hi, I have seen cases where in a correct space group 'R-work and R-free values 0.25 and 0.32 respectively' at 2 A resolution sound like not too bad values. In some of such cases when data from a different crystal in the same space group was available R-factors were much lower when the structure w

Re: [ccp4bb] No improvement in R-factor after Refmac.

2017-03-18 Thread Randy Read
Hi, I was just going to make the same point! The only thing to add is that, if there really is translational NCS (which is certainly possible with 4 copies in the a.u.), then it’s essential both to account for it (which current versions of Phaser should do automatically, if you search for all