Not quite sure what you mean but I suppose you refined with NCS restraints and the red bar means that your chains in those regions are not identical. I would turn NCS restraints off during refinement, with your resolution there is no real good reason to include them. You probably have to do some manual tweaking in those regions with red NCS bars.
Bert ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Vipul Panchal <panchal.vi...@igib.in> Sent: 24 April 2017 09:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] NCS difference I am not from any structure biology related group. So I have followed literatures for the structure solution and analysis. At this level all stereochemical and geometry looks good. The only parameter I could see with some red bar was NCS difference. Through literature, I couldn't understand if some red bars in NCS DIFFERENCE window should be a concern. So it would be helpful if some of you can suggest me some relevant literature or practice regarding NCS difference. On 24-Apr-2017 1:25 PM, "Pavel Afonine" <pafon...@gmail.com<mailto:pafon...@gmail.com>> wrote: Minimizing a red bar may be tricky.. Have you tried to make it less red (blue or may be green)? Otherwise Rw/Rf~20/25 is just fine at 2.2A resolution. What exactly your worry is about? Pavel On Mon, Apr 24, 2017 at 12:48 AM, Vipul Panchal <panchal.vi...@igib.in<mailto:panchal.vi...@igib.in>> wrote: Hi all, I am solving structure of one of the acyltransferse protein. We have collected data at 2.16A resolution. Currently the Rfree is 0.2508 and Rwork is 0.2042. My query is regarding NCS difference. Under validation tool of coot while looking for NCS differene, i can find some residues with red bar. Can some one suggest me how may i minimize it if i am expected to do it? -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372 On 24-Apr-2017 1:25 PM, "Pavel Afonine" <pafon...@gmail.com<mailto:pafon...@gmail.com>> wrote: Minimizing a red bar may be tricky.. Have you tried to make it less red (blue or may be green)? Otherwise Rw/Rf~20/25 is just fine at 2.2A resolution. What exactly your worry is about? Pavel On Mon, Apr 24, 2017 at 12:48 AM, Vipul Panchal <panchal.vi...@igib.in<mailto:panchal.vi...@igib.in>> wrote: Hi all, I am solving structure of one of the acyltransferse protein. We have collected data at 2.16A resolution. Currently the Rfree is 0.2508 and Rwork is 0.2042. My query is regarding NCS difference. Under validation tool of coot while looking for NCS differene, i can find some residues with red bar. Can some one suggest me how may i minimize it if i am expected to do it? -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372
