Hello everyone, I know that coot reads in the pdb file and figures out the ncs relationships upon loading . When you run refmac from inside coot and click the button, I am assuming it uses the computed NCS relationships as restraints during refinement . My pdb file does have the NCS definitions in the header , but I was not sure if coot was using those if I checked the box.
Also, in pdb file I have four bound chloride ions to my four protein chains A,B,C,D . The new chlorides were assigned to 4 new chains E,F.G,H when I added them , for some reason refmac run from inside coot seems to have issues with that and stopped with some error . I am sorry I didnt note down the error , But assigning those Cl atoms to their respective chains a la the new pdb style got refmac from inside coot to chug right along and refine the model.. Thanks for your help and comments Hari
