Hi, Thanks for your advice! My problem has been solved, coot has cadmium ion (which I didn't know at first), and the reason that it didn't work at first is I put Cd instead of CD (should be *upper case*) under the "place atom at pointer" menu, so the refmac and coot don't recognize it. Now I learned new things!
Many thanks! Lu On Wed, Nov 30, 2011 at 5:56 AM, Eleanor Dodson <c...@ysbl.york.ac.uk>wrote: > 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 >> >>
