Thanks. I will try the comprehensive script. Originally I just wanted to see what happens if I do NCS averaging only without solvent flattening or histogram match, to see whether all NCS units are the same. Anyway, it is always better to use more of them.
Also thanks for pointing out that the REFI is not necessary for the identity op. Best Regards, Hailiang > 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 > >
