REFMAC (CCP4: Supported Program)
User's manual for the program refmac_5.0.36
Keyworded input - Other Xray keywords
Anything input on a line after "!" or "#" is ignored and lines can be continued by using a minus (-) sign. The program only checks the first 4 characters of each keyword. The order of the cards is not important except that an END card must be last. Some keywords have various subsidiary keywords. The available keywords in this section are:
BINS | RANGE <nbins> | <range>
Number of resolution bins <nbins>. Default 20, maximum allowed 100. For least-square refinements it is useful only for monitoring statistics on resolution ranges. For maximum likelhood it is used for normalisation to convert Fs to Es (i.e. normalisation coefficients are calculated in these resolution bins).
Or <range>. If the value after BINS/RANGE is less than 1.0 this is assumed to define the bin width in units of 4*sin**2/Lambda**2.
BLIM <Bmin> <Bmax>
[Default 2.0 500.0]
CELL <a> <b> <c> [ <alpha> <beta> <gamma> ]
Defines parameters of the cell. If this keyword is specified then cell parameters from MTZ and coordinate files will be overridden. This keyword could be important when cell dimensions are suspect and the user wants to change them. This keyword is generally not recommended.
DAMP <Pdamp> <Bdamp>
[Default 1.0 1.0 for resolution > 2.5Å, 0.5 0.5 for
resolutions < 2.5Å]
LABOUT <program label>=<file label> ...
This keyword tells the program that in output MTZ file calculated structure factors, their phases, coefficients for map calculations should have given labels.
# Output labels for calculated structure factors and # coefficients for weighted "difference" and "2Fo-Fc" # maps. Corresponding phases will have labels PHWT, DELFWT # figure of merit of phases will be FOM # LABOUT FC=FC PHIC=PHIC FWT=2FOFCWT DELFWT=FOFCWT # Another example when all labels are given explicitly # LABOUT FC=FC PHIC=PHIC FWT=2FOFCWT PHWT=PH2FOFCWT DELFWT=FOFCW - PHDELWT=PH_fofc FOM=FOM_refmac
FP SIGFP (and FREE if available) plus the following additional columns are written to the output MTZ file. Labels can be assigned for:
FP SIGFP FREE FC PHIC FWT PHWT DELFWT PHDELWT FOM [PHCOMB]
For the FWT and DELFWT terms, FP is scaled to be at the same scale as Fcalc,
Missing Data: For those reflections where the FP are missing, mFo is set equal to dFc. Hence the terms become FWT=dFC and DELFWT=0.0. The m and D are based on the program's estimate of SigmaA.
Rebuilding into these 2mFo-DFcalc and mFo-DFcalc maps seems to be easier than using classic nFO-(n-1)FC and difference maps, consistent with the established technique for SigmaA style maps. One advantage here is that since the m and D values are based on the Free set of reflections they are less biased than the values obtained by the CCP4 version of SIGMAA after refinement.
MODE [HKRF | RIGID | TLSR]
MONI <subkeyword 1> [<subkeyword i> <value>]
This keyword controls level of monitoring statistics during refinement.
MONItor MEDIim MONItor DISTances 10.0 MONItor TORSions 10.0 MONItor ANGLes 10.0 MONItor CHIRals 10.0 MONItor PLANes 10.0 MONItor BFACtors 10.0 MONItor BSHPere 10.0 MONItor VDWrest 3.0 MONItor RBONd 10.0 MONItor NCSR 10.0
<subkeyword 1> can be one of:
The subsequent <subkeyword i> are:
PHASe SCBL <scblur> | BBLUr <bblur>
This keyword tells the program that probability distribution of given phase information should be altered (this can also be done through REFI PHAS). For example:
PHASe SCBLur 0.7 BBLUr 20.0
Program will apply blurring as follows:
HLAnew = HLA*scblur*exp(-(sin(theta)/lambda)**2*bblur) HLBnew = HLB*scblur*exp(-(sin(theta)/lambda)**2*bblur) HLCnew = HLC*scblur*exp(-(sin(theta)/lambda)**2*bblur) HLDnew = HLD*scblur*exp(-(sin(theta)/lambda)**2*bblur)
or if PHASE and FOM are given: the program first generates HLA and HLB using the formula:
HLA = Func(FOM)*COS(DEGTOR*PHASE), HLB = Func(FOM)*SIN(DEGTOR*PHASE), HLC = HLD = 0.
i.e. the Phase probability distribution is unimodal.
RIGIDbody GROUP | PRINT | NCYCLE
This keyword controls parameters of the rigid body refinement.
RIGIDbody NCYCle 10 RIGIDbody GROUp 1 FROM 1 A TO 100 A RIGIDbody GROUp 1 FROM 200 A TO 300 A RIGIDbody GROUp 2 FROM 101 A TO 199 A RIGIDbody GROUp 3 FROM 1 B TO 500 B
SCPArt < nsc1> <nsc2> <nsc3> ...
If NSCi are set, the FPARTnsci is scaled relative of the FC FC_tot = FC_calc(PHIcalc) + sc1*FPART1(PHIP1) + sc2*FPART2(PHI2) + ....
If NSCi set - that partial structure factor will be scaled
# # Scale only partial 1st, 3rd and 4th structure factors. # All others should be added to Fcalc without scaling # SCPArt 1 3 4
Defines space group symmetry name or number. If MTZ or coordinate files have symmetry then they will be used. It is good idea to have symmetry in the MTZ and coordinate files. This keyword is not recommended.
It defines number of TLS refinement cycles. If this keyword is specified then program will do TLS refinement only. It is useful if one is interested in TLS parameters only. If TLS refinement is considered as precursor of individual atomic refinement then
should be used. In any case it seems to be better if B values of all atoms are set to some predefined value before tls refinement using
BFACtor SET <value>
Number of cycles for idealisation or restrained or unrestrained refinement.
This keywords tells the program to change grid spacing by a given factor.
If this keyword is given then grid spacing for structure factor, gradient and second derivative calculation will change accordingly. According to Niquist for a given resolution if grid spacing is equal to grid_spacing_min=0.5 d_max, where d_max is maximum resolution in angstroms, then a discrete Fourier transform will not lose any information. It is true when structure factors are calculated from the map and vice versa. When maps are calculated from atomic model (or gradients and second derivatives are calculated using convolution of derivatives of atom with difference and "Hessian" maps), then finer grid might be needed. The reason is for example if grid spacing is coarse and atoms have small B values, then values of electron density at the grid points may not approximate atoms correctly. Default (1.5) is good compromise. But if desired it could be changed. Shannon factor tells the program that actual grid spacing should be equal to grid_spacing_min/shannon_factor. If <shannon_factor> is increased then calculation will require larger memory and more time. If it is too small then approximation will not be correct and the program might become unstable.
END | GO | QUIT | STOP
End of keywords. Time to do work.