DEF 0.0.4 crank2 17:03 29/Jul/14 CObsDataFile Input Friedel pairs I+/I- or F+/F- for SAD, SIRAS or MAD phasing True 1,2 CObsDataFile Input Friedel pairs I+/I- or F+/F- for MAD phasing True 1,2 CObsDataFile Input Friedel pairs I+/I- or F+/F- for MAD phasing True 1,2 CObsDataFile Input Friedel pairs I+/I- or F+/F- for MAD phasing True 1,2 CBoolean Select this option if you wish to input HKL or SCA file(s) (both unmerged and merged data will be accepted) False CUnmergedDataFile Input unmerged or merged hkl/sca with anomalous signal for SAD, SIRAS or MAD phasing True 1,2 Reflections CUnmergedDataFile Input unmerged or merged hkl/sca with anomalous signal for MAD phasing True 1,2 Reflections CUnmergedDataFile Input unmerged or merged hkl/sca with anomalous signal for MAD phasing True 1,2 Reflections CUnmergedDataFile Input unmerged or merged hkl/sca with anomalous signal for MAD phasing True 1,2 Reflections CString Substructure (heavy atom) element type (periodic table symbol) 3 Se CObsDataFile Input intensities or structure factors for the "native" crystal CUnmergedDataFile Input intensities or structure factors in sca/hkl for the "native" crystal True Reflections CFloat Wavelength at which the dataset was measured. Used for estimation of f',f'' if they were not specified by user, otherwise ignored 7 0.0 CFloat Wavelength at which the dataset was measured. Used for estimation of f',f'' if they were not specified by user, otherwise ignored 7 0.0 CFloat Wavelength at which the dataset was measured. Used for estimation of f',f'' if they were not specified by user, otherwise ignored 7 0.0 CFloat Wavelength at which the dataset was measured. Used for estimation of f',f'' if they were not specified by user, otherwise ignored 7 0.0 CBoolean CBoolean CBoolean CBoolean CFloat 5 Anomalous scattering coefficient f' for the dataset #1 and substructure atom type. A good estimate can be obtained from a fluorescence scan. CFloat Anomalous scattering coefficient f'' for the dataset #1 and substructure atom type. A good estimate can be obtained from a fluorescence scan. 5 CFloat Anomalous scattering coefficient f' for the dataset #2 and substructure atom type. A good estimate can be obtained from a fluorescence scan. 5 CFloat Anomalous scattering coefficient f'' for the dataset #2 and substructure atom type. A good estimate can be obtained from a fluorescence scan. 5 CFloat Anomalous scattering coefficient f' for the dataset #3 and substructure atom type. A good estimate can be obtained from a fluorescence scan. 5 CFloat Anomalous scattering coefficient f'' for the dataset #3 and substructure atom type. A good estimate can be obtained from a fluorescence scan. 5 CFloat Anomalous scattering coefficient f' for the dataset #4 and substructure atom type. A good estimate can be obtained from a fluorescence scan. 5 CFloat Anomalous scattering coefficient f'' for the dataset #4 and substructure atom type. A good estimate can be obtained from a fluorescence scan. 5 CBoolean CBoolean CBoolean CBoolean CBoolean CBoolean CBoolean CBoolean CFloat Cell dimension "a" (in A) 6 CFloat Cell dimension "b" (in A) 6 0.0 CFloat Cell dimension "c" (in A) 6 0.0 CFloat Cell angle alpha (in deg) 6 0.0 CFloat Cell angle beta (in deg) 6 0.0 CFloat Cell angle gamma (in deg) 6 0.0 CString Spacegroup (CCP4 style; for example P212121) 8 CBoolean CBoolean CBoolean CBoolean CBoolean CBoolean CBoolean CInt Expected total number of substructure atoms in the asymmetric unit 1 3 CInt Number of disulphides in the asymmetric unit that substructure detection should search for as single atoms and then model as disulfides 0 2 CBoolean CBoolean CSeqDataFile Protein sequence (will be used for parameter estimation and model building) True True ['pir','seq','fas'] CPdbDataFile Input (partial) model {'subType': '1'} 1,0 True True unknown,model,homolog,fragment 0,1,2,3 1 CPdbDataFile Input substructure model (for phasing purposes) {'subType': '1'} 1,0 True unknown,model,homolog,fragment 0,1,2,3 1 CString CPhsDataFile 1 Input phase distribution True True CBoolean Select this option if you have initial phases for input False CString SAD,SIRAS,MAD True SAD,SIRAS,MAD False SAD CBoolean CBoolean Select this option if you wish to replace methionines by selenomethionines in the input partial model False CString The pipeline will start with this process (the actual pipeline and parameters can be found in Advanced Options) True refatompick,substrdet,phdmmb,phas,handdet,dmfull,building,ref Substructure improvement,Substructure detection,Den.mod. + poly-Ala tracing,Substructure phasing,Hand determination,Density modification,Model building,Refinement substrdet False CString The pipeline will end with this process (the actual pipeline and parameters an be found in Advanced Options) True substrdet,phdmmb,phas,refatompick,handdet,dmfull,building,ref Substructure detection,Den.mod. + poly-Ala tracing,Substructure phasing,Substructure improvement,Hand determination,Density modification,Model building,Refinement ref False CBoolean Select this option if you wish to use SHELXC->SHELXD->SHELXE in the pipeline (the actual pipeline and parameters can be found in Advanced Options) False CBoolean CBoolean False CBoolean Select this option if the substructure from the crystal #1 is also present in the "native" crystal False CBoolean CBoolean Select this option if data from a "native" crystal is available (will be used for model building and refinement as well as phasing) False CBoolean Select this option if you have another anomalously scattering dataset collected at a different wavelength (will be used for MAD phasing) False CBoolean Select this option if you have another anomalously scattering dataset collected at a different wavelength (will be used for MAD phasing) False CBoolean Select this option if you have another anomalously scattering dataset collected at a different wavelength (will be used for MAD phasing) False CString Specify whether the dataset #1 was collected at peak, inflection point, high or low remote of the anomalous scattering curve (may be often omitted for SAD,SIRAS) False peak,infl,hrem,lrem peak,infl,hrem,lrem True CString Specify whether the dataset #2 was collected at peak, inflection point, high or low remote of the anomalous scattering curve False peak,infl,hrem,lrem peak,infl,hrem,lrem True CString Specify whether the dataset #3 was collected at peak, inflection point, high or low remote of the anomalous scattering curve False peak,infl,hrem,lrem peak,infl,hrem,lrem True CString Specify whether the dataset #4 was collected at peak, inflection point, high or low remote of the anomalous scattering curve False peak,infl,hrem,lrem peak,infl,hrem,lrem True CBoolean CBoolean CBoolean CBoolean CBoolean Select this option if you have a partial model (for example from molecular replacement) that needs to be rebuilt False CBoolean Select this option if you wish to remove all protein atoms from the inputted partial model and start phasing only from the anomalous substucture atoms present in the model False CBoolean True CString Specify whether free set of reflections should be excluded in refinement to calculate Rfree. Either an existing free set of reflections can be inputted or a new free set can be generated. True new,existing,no new set,existing set,no new CInt Number of monomers in the asymmetric unit (expected) 1 True 3 CBoolean CFloat Solvent content in the crystal (expected) 0.0 1.0 True 7 CBoolean CInt Number of residues per monomer 0 CBoolean CInt Input the (expected) number of residues per monomer. 0 5 CString CInt 0 CBoolean Select this option if sequence for the protein is available (recommended) True CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CString CFreeRDataFile Specify the existing 'free' set of reflections to be used True CFloat Specify the ratio of reflections tagged as 'free' and used for validation purposes 5 3 CPdbDataFile {'subType': '1'} CMapCoeffsDataFile 1 True CMapCoeffsDataFile 1 True CPdbDataFile {'subType': '1'} CString CPhsDataFile True CMapCoeffsDataFile 2 True CMapCoeffsDataFile 1 2 True CPdbDataFile {'subType': '1'} CMapCoeffsDataFile 1 True CPhsDataFile True CFreeRDataFile CExpPhasPerformance CString The program that will be used in the process of substructure improvement True REFMAC5 refmac True CFloat Atoms above the specified RMS threshold in the anomalous difference map will be added to the substructure True 0.0 CBoolean CInt Number of iterations of new substructure atoms picking True 0 3 CBoolean CInt Number of refinement cycles in each picking iteration True 0 3 CBoolean CList Additional keywords for substructure improvement True CString Program used for FA estimation SHELXC,AFRO,ECALC True shelxc,afro,ecalc True CString Program used for substructure determination True SHELXD,CRUNCH2,PRASA shelxd,crunch2,prasa True CFloat High resolution cutoff used in substructure determination. A starting point rule of thumb for SAD data is resolution + 0.5A. 0.0 5 CBoolean CFloat Substructure determination high resolution cutoff radius: cutoffs will be tested in this radius around the specified initial cutoff. A radius of 0.5A around data resolution+0.5A is typically sufficient. 0.0 5 CBoolean CFloat In the specified substructure determination high resolution cutoff radius, the testing cutoff values will be derived by increasing/decreasing by the step value. A step of 0.25A is typically sufficient. 0.0 5 CBoolean CFloat If this threshold is reached, substructure determination will stop early, assuming a solution that will be used for phasing (saving some time for the "easy" datasets). CFOM is defined as CC+CCweak for SHELXD, CC*FOM*CLD for PRASA 0.0 5 CBoolean CFloat If CFOM from SHELXD is smaller than this threshold, thorough building will be used: more cycles, search for helices, increased search time factor. Set to 0 to disable, set to 1000 to always use thorough building. 5 CBoolean CInt Number of substructure detection trials performed if CFOM threshold is not reached. 0 5 CBoolean CFloat The (expected) minimal distance between substructure atoms 4 CBoolean CBoolean Select this option if you expect that (some) substucture atoms can be in special positions in the cell CBoolean CBoolean Restrain to the estimated number of substructure atoms in the asymmetric unit False CString Specify any additional program keywords (separate multiple keywords by a comma). Keywords specified here will always take preference over defaults or other settings. True 25 CString Program used for substructure phasing and refinement True REFMAC5,BP3 refmac,bp3 True CInt Number of substructure refinement cycles CBoolean CString Specify any additional program keywords True CBoolean If selected, hand determination will be performed. If not selected, the input hand will be assumed correct. True CInt Number of density modification cycles in hand determination CString Program used for density modification in hand determination True Solomon solomon True CString True CString Program used for phase combination in hand determination Multicomb True multicomb True CString True CInt Number of density modification cycles 4 CBoolean CFloat If this threshold is reached, density modification will stop early, assuming a good map that can be used for building (saving some time for the "easy" datasets) 0.0 5 CBoolean CString Program used for density modification True Parrot,Solomon parrot,solomon True CString Program used for phase combination in density modification REFMAC5,Multicomb True refmac,multicomb True CString Specify any custom phase combination program options (separate multiple options by a comma) True 30 CString Specify any custom density modification program options (separate multiple options by a comma) True 30 CInt Number of density modification cycles per each model building iteration True 4 CBoolean CInt Number of model building cycles True 4 CBoolean CFloat If this threshold is reached, poly-Ala tracing will stop early, assuming a good quality model has been obtained (saving time for the "easy" datasets) 0.0 5 CBoolean CFloat If this correlation coefficient threshold is reached, hand is considered determined and poly-Ala tracing for the other hand will stop 0.0 5 CBoolean CBoolean Use "thorough" SHELXE building (more cycles, search for helices, increased search time factor) CBoolean CString Specify any additional SHELXE arguments, separate multiple arguments by a comma (example: -z for substructure optimization). Arguments specified here will always take preference over defaults or other settings. True 25 CBoolean Use the "combined" Crank2 building algorithm - a multivariate SAD function combining information from anomalous and non-anomalous signal from data, density modification and model building True CInt Minimal number of model building iterations 4 CBoolean CInt Maximal number of model building iterations 4 CBoolean CBoolean Select this option to estimate NCS (can be time consuming with large number of atoms) CBoolean CBoolean Select this option to estimate NCS from the partial model CBoolean CBoolean Skip the first model building iteration (the initial phase and DM restrained refinement cycles are performed with the model inputted to this step) CBoolean CBoolean Select this option if the actual model should be inputted to each building cycle (if not selected then alternate building from phases only and from phases+model) CBoolean CBoolean Option to start building using ShelxE backbone tracing and later switch to Buccaneer. May improve the building at higher resolutions. CBoolean CString Program used for real space density modification within the "combined" model building True Parrot,Solomon parrot,solomon True CString Specify any custom density modification program options (separate multiple options by a comma) True 30 CString Specify any custom SHELXE program options (separate multiple options by a comma) True 15 CBoolean CString Program used for data and density modification phase restrained refinement True REFMAC5 refmac True CString Program used for automatic real space model building True Buccaneer,ARP/wARP buccaneer,arpwarp True CString Specify any custom model building program options (separate multiple options by a comma) True 30 CString Program used for model refinement between the model building iterations True REFMAC5 refmac True CInt Number of model building iterations 4 CString True CString Program used for refinement True REFMAC5 refmac True CString True CInt Number of refinement cycles 4 CBoolean CBoolean Select this option to exclude the "free" reflections in refinement True CBoolean Select this option to exclude the "free" reflections in model building and refinement True CString Specify when the "free" reflections will be excluded in the "combined" model building True never,in the last cycles,always never,last,always False always CString True tree in presentation,tree in i2 panel,rvapi folding page,native i2 folding page rvapi_tree,i2_tree,bigpage,i2_bigpage False i2_bigpage CBoolean False