Hey Elizabeth, To answer your second question first, I think if the atom name for water is "W", it is read as a density peak by shelxl. If you change "W" to "O", it will read it as water and refine it. I have some idea about your question about the B-factor. Arg and Met can often be seen in alternate conformations, so I would check to see if this is actually the case. When you model these in and refine with 50% occupancies for both conformations, B-factors might be more reasonable. Also make sure you have the atoms in the best possible place in the density in the difference map before you try the alternate conf. Might work. Arti
> Dear all, > > I am refining a perfectly twinned structure at 1.8 A using > Shelxl.Currently the Rfactors/Rfree are 20/28%. > > I have a problem with the B-values that I get after refinement. Within the > same residue I may get very low numbers or very high numbers as I show > below: > > ATOM 415 N ARG 1091 101.144 31.968 -4.016 1.00 14.74 > N > ATOM 416 CA ARG 1091 101.658 32.276 -2.683 1.00 14.88 > C > ATOM 417 CB ARG 1091 100.799 31.584 -1.644 1.00 3.05 > C > ATOM 418 CG ARG 1091 101.034 31.917 -0.187 1.00 7.64 > C > ATOM 419 CD ARG 1091 101.523 33.351 -0.044 1.00 18.07 > C > ATOM 420 NE ARG 1091 101.764 33.779 1.335 1.00 20.18 > N > ATOM 421 CZ ARG 1091 103.009 34.023 1.741 1.00 12.87 > C > ATOM 422 NH1 ARG 1091 103.939 33.836 0.817 1.00 5.48 > N > ATOM 423 NH2 ARG 1091 103.297 34.415 2.955 1.00 18.82 > N > ATOM 424 C ARG 1091 103.126 31.903 -2.528 1.00 26.11 > C > ATOM 425 O ARG 1091 103.894 32.580 -1.827 1.00 17.11 > > OR > > ATOM 986 N MET 1162 123.943 36.751 -5.048 1.00 34.77 > N > ATOM 987 CA MET 1162 124.217 35.582 -4.228 1.00 22.54 > C > ATOM 988 CB MET 1162 122.924 34.775 -4.090 1.00 13.02 > C > ATOM 989 CG MET 1162 122.563 34.285 -2.723 1.00 16.29 > C > ATOM 990 SD MET 1162 122.884 35.396 -1.350 1.00157.91 > S > ATOM 991 CE MET 1162 122.264 34.383 -0.003 1.00 29.22 > C > ATOM 992 C MET 1162 125.297 34.673 -4.810 1.00 36.57 > C > ATOM 993 O MET 1162 125.791 33.803 -4.091 1.00 25.97 > O > > My input file looks like this: > > LATT -7 > SYMM -X, -Y, 1/2+Z > SYMM -X, Y, 1/2-Z > SYMM X, -Y, -Z > SFAC C H N O S P > UNIT 37872 70560 9752 11176 192 64 > > DEFS 0.02 0.1 0.01 0.04 > CGLS 30 -1 > SHEL 30 0.1 > FMAP 2 > PLAN 200 2.3 > LIST 6 > WPDB 2 > > TWIN 0 1 0 1 0 0 0 0 -1 > BASF 0.48366 > STIR 2.2 0.05 > > DELU $C_* $N_* $O_* $S_* $P_* > SIMU 0.1 $C_* $N_* $O_* $S_* $P_* > REM ISOR and CONN 0 recommended on adding water > BUMP > SWAT > REM HOPE > > REM Remove MERG 4 instruction if Friedel opposites should not be merged > > MERG 4 > > > Could you please tell me if I am missing some important key word in my > input file? > > Also, once I add water molecules with Coot (for example), how do I tell > Shelxl to refine them? It seems that it refuses to do it! > ATOM 7500 W HOH 4401 101.180 33.600 9.444 1.000 50.00 > > Thank you!!!! > > Eli :o) > > -- > Elisabetta Sabini, Ph.D. > University of Illinois at Chicago > Department of Biochemistry and Molecular Genetics > Molecular Biology Research Building, Rm. 1108 > 900 South Ashland Avenue > Chicago, IL 60607 > U.S.A. > > Tel: (312) 996-6299 > Fax: (312) 355-4535 > E-mail: [EMAIL PROTECTED] > Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
