Regarding your script: change a couple of things: MODE HIST SOLV MULT AVER COMBINE PERT SCHEME RES FROM 3.0 (or from where you have FOM >70%, as your low res phases will be more reliable) NCYCLE 50 (since you have 12 molecules you should get a significant benefit from averaging.
Then the first Aver card does not require the REFI card as it should not be refined. For all the others I would change them to AVER REFI EVERY 3 to update the matrices while performing the averaging. You could also update the solvent mask with the command SOLMASK UPDATE 20 if you want. Good luck, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Aug 28, 2010, at 10:05 PM, Hailiang Zhang wrote: > Hi, > > I am using the following DM script to perform a NCS averaging. I have a > fundemental question: after NCS averaging, are the density distrubitions > of different NCS unit being averaged supposed to be the same? I found they > are different by checking FCDM/PHICDM, and maybe I am wrong somewhere... > > > dm NCSIN ${PDB}.msk HKLIN ${PDBALL}.mtz HKLOUT ${PDBALL}-dm.mtz \ > <<dmtest > mode AVER > ncycle 1 > combine PERT > scheme ALL > solc 0.6213 > #Identical > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 > TRAN 0.0 0.0 0.0 > #A>C > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX -0.22748 0.97259 0.04813 -0.97372 -0.22662 -0.02273 > -0.01120 -0.05203 0.99858 > TRAN 101.46837 81.74413 2.89341 > #A>D > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX -0.90337 0.42792 0.02831 -0.42883 -0.90066 -0.07011 > -0.00451 -0.07547 0.99714 > TRAN 158.03317 36.91842 3.25853 > #A>F > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX -0.21272 -0.97702 0.01352 0.97675 -0.21300 -0.02424 0.02657 > 0.00805 0.99961 > TRAN 100.69797 -81.01860 -1.71365 > #A>G > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX 0.61704 -0.78687 -0.01005 0.78590 0.61553 0.05899 -0.04023 > -0.04429 0.99821 > TRAN 32.50667 -65.76570 7.05504 > #A>H > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX -0.85814 -0.51116 -0.04813 -0.51290 0.85771 0.03558 > 0.02310 0.05522 -0.99821 > TRAN 156.14981 42.23873 48.93406 > #A>I > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX -0.13703 -0.98975 -0.04032 -0.99048 0.13635 0.01902 > -0.01332 0.04254 -0.99901 > TRAN 95.97630 82.30948 52.82510 > #A>J > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX 0.69662 -0.71695 -0.02645 -0.71716 -0.69691 0.00230 > -0.02008 0.01737 -0.99965 > TRAN 25.84588 59.76286 53.68224 > #A>K > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX 0.99467 0.10258 -0.01072 0.10259 -0.99472 0.00088 -0.01057 > -0.00197 -0.99994 > TRAN 0.47215 -8.86082 52.78315 > #A>L > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX 0.55782 0.82946 0.02875 0.82987 -0.55793 -0.00466 0.01218 > 0.02646 -0.99958 > TRAN 36.68436 -68.63833 49.21587 > #A>M > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX -0.30892 0.95102 -0.01113 0.95109 0.30890 -0.00370 > -0.00008 -0.01173 -0.99993 > TRAN 109.48987 -79.05550 52.39334 > #A>N > AVER REFI > NCSMASK NMER 1 > ROTA MATRIX -0.93676 0.34855 -0.03147 0.34600 0.93589 0.06627 0.05255 > 0.05119 -0.99731 > TRAN 162.32979 -29.26800 45.41564 > LABIN FP = FWT PHIO = PHIC FOMO = WCMB > LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM > END > dmtest
