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Re: [ccp4bb]: RS au.s again
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Bernhard Rupp wrote:
>
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> Dear All :
>
> recently someone (I think Clemens) sent me kindly an immensely useful
> list regarding grid settings in several ccp4 programs.
>
> It appears though that at least for #20 SFALL does well using the FFT
> grid and does not need P1 expansion - am I interpreting this list wrong?
>
Here is the extract for SFALL limits from the documentation.
X1 and X2 are always set to 0 to NX1-1; 0 to NX2-1;
BUT by far the best way to run sfall is to precede it with MAPMASK to
generate a "whole cell" map and use the inverse FFT in P1.
The other cells are archaic remnants of the days when we were seriously
short of memory and it mad sense to work with the smallest possible map
volume.
MAPMASK mapin asymm_unit.map mapout whole-cell.map
XYZLIM 0 0.999 0.999 0 0.999
AXIS Z X Y
END
then sfall hklin asymm_unit.mtz hklout asymm_unit+FC.mtz mapin
whole-cell.map
SFSG P1
MODE SFCALC MAPIN HKLIN
LABI FP=... SIGFP=...
LABO FC=FC_map PHIC=PHIC_map
END
sfall checks symmetry from the mtz file and outputs a list
of h k l FP SIGFP ... FC PHIC for the asymm unit only
If you have no HKLIN you must also give SYMM and RESO
but otherwise resist the temptation to add any key words - the programs
are meant to be able to sort themselves out..
Here is the extract from the sfall document
Limits for axes for the various space groups (these are the same as
those used as defaults in FFT):
In space group P1, P21 and P21212a, 'b' is taken as the unique
axis.
In space group P21212a, 1/4 is subtracted from the X and Y values
of the equivalent positions given in International Tables.
X1 X2 X3 Range of X3 Axis order
P1 Z X Y 0 to Y Z X Y
P21 Z X Y 0 to Y/2-1 Z X Y
P21212a Z X Y 0 to Y/4 Z X Y
P212121 X Y Z 0 to Z/4 Y X Z
P4122 X Y Z 0 to Z/8 Y X Z
P41212 X Y Z 0 to Z/8 Y X Z
P4322 X Y Z 0 to Z/8 Y X Z
P43212 X Y Z 0 to Z/8 Y X Z
P31 X Y Z 0 to Z/3-1 Y X Z
P32 X Y Z 0 to Z/3-1 Y X Z
P3 X Y Z 0 to Z-1 Y X Z
R3 X Y Z 0 to Z/3-1 Y X Z
P3121 X Y Z 0 to Z/6 Y X Z
P3221 X Y Z 0 to Z/6 Y X Z
P61 X Y Z 0 to Z/6-1 Y X Z
P65 X Y Z 0 to Z/6-1 Y X Z
Limits for arp are embodied in this code: I guess someone should
tabulate it nicely - maybe Clemens has?
PARAMETER (ROUND=0.00001, ROUND2=2.0*ROUND)
PARAMETER (ONE=1.0+ROUND,HALF=0.5+ROUND,THRD=1./3.+ROUND,
$ TWTD=2./3.+ROUND,SIXT=1./6.+ROUND,THRQ=0.75+ROUND,
$ QUAR=0.25+ROUND,EIGH=0.125+ROUND,TWLT=1./12.+ROUND)
PARAMETER (ONEL=ONE-ROUND2,HALFL=HALF-ROUND2,THRDL=THRD-ROUND2,
$ SIXTL=SIXT-ROUND2,QUARL=QUAR-ROUND2)
C asulim contains maximum limit on x,y,z: the box is always assumed to
C start at 0,0,0
C
C Space group numbers
DATA NSPGRP/
$ 1, 2, 3, 4, 5, 10, 16, 17, 18,1018, 19, 20,
$ 21, 22, 23, 24, 47, 65, 69, 71, 75, 76, 77, 78,
$ 79, 80, 83, 87, 89, 90, 91, 92, 93, 94, 95, 96,
$ 97, 98, 123, 139, 143, 144, 145, 146, 147, 148, 149, 150,
$ 151, 152, 153, 154, 155, 162, 164, 166, 168, 169, 170, 171,
$ 172, 173, 175, 177, 178, 179, 180, 181, 182, 191, 195, 196,
$ 197, 198, 199, 200, 202, 204, 207, 208, 209, 210, 211, 212,
$ 213, 214, 221, 225, 229/
C
DATA ((ASULIM(II,JJ),II=1,3),JJ=1,73)/
C 1: P1 2: P-1 3: P2 4: P21
$ ONE,ONE,ONE, ONE,ONE,HALF, ONE,ONE,HALF, ONE,HALF,ONE,
CCP4 $ ONEL,ONEL,ONEL, ONEL,HALF,ONEL, HALF,ONEL,ONEL, ONEL,HALFL,ONEL,
C 5: C2 10: P2/m 16: P222 17: P2221
$ HALF,ONE,HALF, half,half,onel,HALF,ONE,HALF, HALF,ONE,HALF,
CCP4 $ HALF,HALFL,ONEL, HALF,HALF,ONEL,HALF,HALF,ONEL, HALF,HALF,ONEL,
C 18: P21212 1018: P21212 19: P212121 20:C2221
$ ONE,QUAR,ONE, onel,quar,onel, ONE,ONE,QUAR, HALF,HALF,HALF,
CCP4 $ ONEL,QUAR,ONEL, ONEL,QUAR,ONEL, ONEL,ONEL,QUAR, HALF,QUAR,ONEL,
C 21: C222 22: F222 23: I222 24: I212121
$ QUAR,HALF,ONE, ONE,QUAR,QUAR, HALF,HALF,HALF, HALF,HALF,HALF,
CCP4 $ HALF,QUAR,ONEL, QUAR,QUAR,ONEL, HALF,QUAR,ONE, HALF,QUAR,ONEL,
C 47: Pmmm 65: Cmmm 69: Fmmm 71: Immm
$ half,half,half, half,quar,half, quar,quar,half, half,quar,half,
CCP4 $ HALF,HALF,HALF, HALF,QUAR,HALF, QUAR,QUAR,HALF, HALF,QUAR,HALF,
C 75: P4 76: P41 77: P42 78: P43
$ HALF,HALF,ONE, HALF,HALF,ONE, HALF,HALF,ONE, HALF,HALF,ONE,
CCP4 $ HALF,HALF,ONEL,ONEL,ONEL,QUARL, HALF,ONEL,HALFL,ONEL,ONEL,QUARL,
C 79: I4 80: I41 83: P4/m 87: I4/m
$ HALF,HALF,HALF, ONE,HALF,QUAR, half,half,half, half,half,quar,
CCP4 $ HALF,HALF,HALF,HALF,ONEL,QUARL, HALF,HALF,HALF, HALF,HALF,QUAR,
C 89: P422 90: P4212 91: P4122 92: P41212
$ HALF,HALF,HALF, HALF,HALF,HALF, ONE,ONE,EIGH, HALF,HALF,HALF,
CCP4 $ HALF,HALF,HALF, HALF,HALF,HALF, ONEL,ONEL,EIGH, ONEL,ONEL,EIGH,
C 93: P4222 94: P42212 95: P4322 96: P43212
$ ONE,HALF,QUAR, HALF,HALF,HALF, ONE,ONE,EIGH, HALF,HALF,HALF,
CCP4 $ HALF,ONEL,QUAR, HALF,HALF,HALF, ONEL,ONEL,EIGH, ONEL,ONEL,EIGH,
C 97: I422 98: I4122 123: P4/mmm 139: I4/mmm
$ HALF,HALF,QUAR, ONE,QUAR,QUAR, half,half,half, half,half,quar,
CCP4 $ HALF,HALF,QUAR, HALF,ONEL,EIGH, HALF,HALF,HALF, HALF,HALF,QUAR,
C 143: P3 144: P31 145: P32 146: R3
$ ONE,ONE,ONE, ONE,ONE,THRD, ONE,ONE,THRD, THRD,THRD,ONE,
CCP4 $ TWTD,TWTD,ONEL,ONEL,ONEL,THRDL,ONEL,ONEL,THRDL, TWTD,TWTD,THRDL,
C 147: P-3 148: R-3 149: P312 150: P321
$ twtd,twtd,half, twtd,twtd,sixt, ONE,ONE,HALF, ONE,ONE,HALF,
CCP4 $ TWTD,TWTD,HALF, TWTD,TWTD,SIXT, TWTD,TWTD,HALF, TWTD,TWTD,HALF,
C 151: P3112 152: P3121 153: P3212 154: P3221
$ ONE,ONE,SIXT, ONE,ONE,SIXT, ONE,ONE,SIXT, ONE,ONE,SIXT,
CCP4 $ ONEL, ONEL,SIXT, ONEL,ONEL,SIXT, ONEL,ONEL,SIXT, ONEL,ONEL,SIXT,
C 155: R32 162: P-31m 164: P-3m1
$ THRD,THRD,HALF, twtd,half,half, twtd,thrd, one,
CCP4 $ TWTD,TWTD,SIXT, TWTD,HALF,HALF, TWTD,THRD, ONE,
C 166: R-3m 168: P6
$ twtd,twtd,sixt, ONE,HALF,ONE,
CCP4 $ TWTD,TWTD,SIXT, TWTD,HALF,ONEL,
C 169: P61 170: P65 171: P62 172: P64
$ ONE,ONE,SIXT, ONE,ONE,SIXT, ONE,HALF,THRD, ONE,HALF,THRD,
CCP4 $ ONEL,ONEL,SIXTL,ONEL,ONEL,SIXTL,ONEL,ONEL,THRDL,ONEL,ONEL,THRDL,
C 173: P63 175: P6/m 177: P622 178: P6122
$ ONE,ONE,HALF, twtd,twtd,half, ONE,HALF,HALF, ONE,ONE,TWLT,
CCP4 $ TWTD,TWTD,HALFL, TWTD,TWTD,HALF,TWTD,HALF,HALF, ONEL,ONEL,TWLT,
C 179: P6522 180: P6222 181: P6422 182: P6322
$ ONE,ONE,TWLT, ONE,HALF,SIXT, ONE,HALF,SIXT, ONE,ONE,QUAR,
CCP4 $ ONEL,ONEL,TWLT, ONEL,ONEL,SIXT, ONEL,ONEL,SIXT, TWTD,TWTD,QUAR,
C 191: P6/mmm 195: P23 196: F23 197: I23
$ twtd,thrd,half, ONE,ONE,HALF, ONE,HALF,HALF, HALF,HALF,ONE/
CCP4 $ TWTD,THRD,HALF, ONEL,ONEL,HALF, QUAR,QUAR,ONEL, ONEL,ONEL,HALF/
DATA ((ASULIM(II,JJ),II=1,3),JJ=74,NUMSGP)/
C 198: P213 199: I213 200: Pm-3 202: Fm-3
$ HALF,HALF,ONE, HALF,HALF,ONE, half,half,half, half,half,quar,
CCP4 $ HALF,HALF,ONEL, HALF,HALF,HALF, HALF,HALF,HALF, HALF,HALF,QUAR,
C 204: Im-3 207: P432 208: P4232 209: F432
$ half,half,half, HALF,HALF,ONE, ONE,HALF,HALF, HALF,HALF,HALF,
CCP4 $ HALF,HALF,HALF, ONEL,HALF,HALF, HALF,ONEL,QUAR, HALF,HALF,HALF,
C 210: F4132 211: I432 212: P4332 213: P4132
$ HALF,THRQ,TWTD, QUAR,THRQ,TWTD, ONE,ONE,ONE, ONE,ONE,ONE,
CCP4 $ HALF,ONEL,EIGH, HALF,HALF,QUAR, ONEL,ONEL,EIGH, ONEL,ONEL,EIGH,
C 214: I4132 221: Pm-3m 225: Fm-3m 229: Im-3m
$ half,onel,eigh, half,half,half, half,quar,quar, half,half,quar/
CCP4 $ HALF,ONEL,EIGH, HALF,HALF,HALF, HALF,QUAR,QUAR, HALF,HALF,QUAR/
C
O
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