Hi Chetan, Unless the model is horrendously far away from the final result, I would do the following instead of the chain copying: - Start from chain A with NCS ghosts in COOT and go through the model residue by residue. Refine 3-residue windows. If you see NCS deviation. Cycle through the other chains and NCS match things unless the maps clearly tell you otherwise. - After the first ~200 residues, move to the difference density peaks. Fix what you can fix. - Refine the model in Refmac and with local NCS. - Go to COOT and repeat with the next residues until you have seen the entire model.
If you keep notes of the things you are unsure of you can revisit those residues later. With hotkeys in COOT and some practice, you can do a COOT session in about an hour. You'll see it will get easier soon. To give your model a first kick you can also try pdb-redo to see if if can improve you model stats a bit. You never know with early models, but it doesn't take much time to try. HTH, Robbie PS 8 is a nice number, are you sure your space group is correct? On 4 Dec 2018 07:33, Chetan A <[email protected]> wrote: Hello All, I am trying to refine some protein structure and right now my structure's R-free is not coming down from 37% even the R-work is lowering in each round of refinements. When phasing done, it created 8 chains for dimer protein (~750 aa's per unit). So I am using NCS for refinement in each cycle. My question is that how to choose the best chains to refine in coot before I do the SSM superpose, Merge and then run the refinement. I am also trying to try auto-build if R-values don't come down. Any suggestions or education is welcomed. Thanks and cheers. Chetan Arya Instem, Bangalore India 560065 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
