Delete all waters, then run refmac to get a difference density map, delete Chain A or B of your molecule and pick waters. Since it will only pick those close to your molecule you can get waters around A and waters around B. But why would you like to do this ? Jürgen
On Sep 5, 2011, at 8:31 AM, Ida Noemi Simon wrote: Dear All, I have a protein with two molecules in the asymmetric unit, denoted as chain A and B and I have a 3rd chain with all the water molecules. My question is how can I assign the waters in Wincoot to the 2 different protein chains according to their distance from the protein? I tried the WATER TIDY in CCP4, but it results in several water molecules with different coordinates compared to the water molecules find in Wincoot (and I also have problems with reading the Watertidy output file). The only thing I can do now is to inspect all the waters in Wincoot, measure the distance from the protein chains and change the water chain id to A or B in the pdb file with a text editor one-by-one for each water molecule. Is there a faster and smarter solution? Thank you in anticipation for your kind help. Best regards, Ida Noemi Simon ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
