overview of mr in ccp4 ii. roadmap
TRANSCRIPT
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Overview of MR in CCP4 II
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Roadmap
http://www.ccp4.ac.uk/dist/ccp4i/help/roadmaps/
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Information On Molecular Replacement
CCP4 Study Weekend Proceedings 2001Acta D57 October 2001 Part 10
http://www.ccp4.ac.uk/dist/examples/tutorial2000/html/
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CCP4 Programs Used In MRalmn - calculates rotation function overlap values using FFT techniques (alternative to AMORE) amore - Jorge Navaza's state-of-the-art molecular replacement package beast - Likelihood-based molecular replacement ecalc - calculate normalised structure amplitudes fsearch - 6-d molecular replacement (envelope) search getax - real space correlation search molrep - automated program for molecular replacement polarrfn - fast rotation function which works in polar angles rfcorr - Analysis of correlations between cross- and self-Rotation functions rotmat - interconverts CCP4/MERLOT/X-PLOR rotation angles rsearch - R-factor and correlation coefficient between Fcalc and Fobs tffc - Translation Function Fourier Coefficients
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Estimating The NO of Molecules in ASU
Most protein crystals contain about 50% water. The number of protein molecules in the asymmetric unit of a crystal can be estimated with Matthews_coef. Biochemical data is also important.
Vm = cell volume ( cubic As) V ----------------------- = --- M*nasymu*nmols_asu M*Z
M = molecular weight of protein in daltons V = volume of unit cell. Z = no. of molecules in unit cell. = nasymu*nmols_asu nasymu = number of asymm. units nmols_asu = number of molecules in asym unit.
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Matthews_coef
1.2.
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Analyse Data For MRLook at the Experimental Data
You should do two things:
a) Create a Patterson map and search it for peaks. We expect a big peak at the origin (position 0,0,0) but if there is another big peak (perhaps about 0.25 the size of the origin peak) then perhaps there is translation between the molecules in the asymmetric unit and it will be more difficult to solve.
(The theory behind this is explained on the web site of Bernhard Rupp:
http://www-structure.llnl.gov/xray/101index.html
For more information, go to the section on Phasing Techniques on this website, and click on NCS with native Patterson maps)
b) Create a Wilson plot which is an indication of the self consistency of the data. Also find the average B-value of the data - this can be used to help the molecular replacement program.
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Analyse Data for MR II
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Analyse Data For MR III
Wilson Plot
Compare Model and Data Bfactors
If they differ greatly youwill need correcting BADD value in amore
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Main Molecular Replacement Programs
AMoRe: Jorge Navaza's state-of-the-art molecular replacement package ActaD D57 p1367
MOLREP: automated program for molecular replacement ActaD D57 p1451
BEAST: Likelihood-based molecular replacement ActaD D57 p1373
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AMoRe : Model Database
Currently only AMoRe has this functionality.
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AMoRe : Main Window
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AMoRe : Choosing a procedure
Choose the procedureyou want to follow
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AMoRe: ParametersChoose the model to use
MTZ file (line beneath is equivalent to LABIN)
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AMoRe : Key Parameters
Resolution Range Space Group Choice
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AMoRe: Output Files
Http://www.ccp4.ac.uk/dist/ccp4i/help/modules/molrepl.html#solution_files
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AMoRe: Output Files IIEuler Angles Fractional
Shift
RFactor
CC between Fs and Is
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AMoRe: Memory?
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AMoRe: Other Utils
Amore Model Database
Amore Main Window
Edit Amore Solution File
Build Amore Output Model
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MOLREP: Main Window
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MOLREP: Main Widow II
Values for Translational NCS automaticallyput in if XML enabled from Preferences.
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BEAST
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BEAST : Main Window II
BEAST is a slow procedure but has proven successful insome difficult cases.
Fraction of target represented by model
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Comparative Times
Amore 30 seconds
MOLREP 3 min
Beast