Hi Helena, from the symptoms you are describing I am guessing that your definition of alternate conformations is somehow not correct. How did you generate the alternate conformations, in COOT, by hand, or by some other means? In my hands I only see the problem of bumping residues out of density when the alternate conformations are ill defined. This example (not tested) should work. The alternate location indicator is in column 17 (http://www.ccp4.ac.uk/html/pdbformat.html) 1 10 20 30 40 50 60 70 80 |........|.........|.........|.........|.........|.........|.........|.........| ATOM 2133 N AARG B 5 -8.859 76.908 -23.554 0.50 62.53 N ATOM 2134 CA AARG B 5 -7.595 77.592 -23.916 0.50 73.84 C ATOM 2135 CB AARG B 5 -6.685 77.736 -22.691 0.50 68.34 C ATOM 2136 CG AARG B 5 -7.156 78.775 -21.687 0.50 64.25 C ATOM 2137 CD AARG B 5 -6.073 79.165 -20.698 0.00 65.04 C ATOM 2138 NE AARG B 5 -6.494 80.270 -19.841 0.00 63.73 N ATOM 2139 CZ AARG B 5 -5.692 80.907 -18.995 0.00 62.76 C ATOM 2140 NH1AARG B 5 -4.419 80.552 -18.890 0.00 62.59 N ATOM 2141 NH2AARG B 5 -6.161 81.902 -18.255 0.00 62.33 N ATOM 2142 C AARG B 5 -6.823 76.908 -25.061 0.50 90.43 C ATOM 2143 O AARG B 5 -6.316 77.579 -25.965 0.50 84.57 O ATOM 2144 N BARG B 5 -8.759 76.908 -23.554 0.50 62.53 N ATOM 2145 CA BARG B 5 -7.495 77.592 -23.916 0.50 73.84 C ATOM 2146 CB BARG B 5 -6.585 77.736 -22.691 0.50 68.34 C ATOM 2147 CG BARG B 5 -7.124 78.675 -21.625 0.50 64.25 C ATOM 2148 CD BARG B 5 -6.176 78.831 -20.450 0.50 65.04 C ATOM 2149 NE BARG B 5 -6.742 79.680 -19.405 0.50 63.73 N ATOM 2150 CZ BARG B 5 -6.175 79.889 -18.223 0.50 62.76 C ATOM 2151 NH1BARG B 5 -5.018 79.312 -17.929 0.50 62.59 N ATOM 2152 NH2BARG B 5 -6.761 80.679 -17.334 0.50 62.33 N ATOM 2153 C BARG B 5 -6.723 76.908 -25.061 0.50 90.43 C ATOM 2154 O BARG B 5 -6.216 77.579 -25.965 0.50 84.57 O HTH Carsten From: [email protected] [mailto:[email protected]] On Behalf Of Helena Taberman Sent: Monday, January 11, 2016 6:55 AM To: [email protected] Subject: [phenixbb] Additional conformations and partially occupied waters Hi, I’m trying to refine a structure determined to 1.6 Å resolution. There’s several residues with additional conformations and waters with partial occupancies stating that they would be there when the conformation of the residues allows it. When I try to refine these conformations and partially occupied waters together the refinement kicks the second conformations and water molecules out of their densities, since they are obviously too close to the other additional conformations of the residues or the following residues. What could I do? Should I somehow group them together or what? Best regards, Helena Helena Taberman, Ph.D. University of Eastern Finland Department of Chemistry Joensuu Campus P.O. Box 111 FI-80101 Joensuu, FINLAND Mobile: +358 50 337 2488