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Hasanyone answered this? Possibilities 1) COOt by default may have written your CD to another coordinate file - usually called PointerAtoms.pdb 2) You got the atom into the pdb you want to refine but it is wrongly labelled. You need ATOM 471 N ASP A 81 23.896 6.780 5.956 1.00 60.81.. the atom label moved to the left, and the residue to be called CD and the atom type (last entry on ATOM line) to be CD ATOM 471 CD CD A 81 23.896 6.780 5.956 1.00 60.81.. The residue number must be different from any existing residue.. The REFMAC log will trell you what it disliked, but not very well marked.. On 11/28/2011 08:16 PM, Lu Yu wrote: > Hi ALL, > > This is the first structure I am working with. > As the title said, I was stuck in the middle of model building using coot, > and I found a big positive peak for Cadmium ion. The coot program doesn't > *know* the cadmium ion when I add a Cd atom there (under the "place atom at > pointer" menu--> "Other" ), and the refinement program doesn't *know* how > to refine this (failed when I refine the whole structure, and it may need > appropriate values as restraints, but I don't know how to add these values > ). > > So I am wondering any one can give me any suggestion about, how to add > cadmium ion in the position and do the refinement. > > Thanks in advance, > > Lu >