If coordinates are input, it builds an `atom map' on a suitable grid over the asymmetric unit of the spacegroup. Atomic density is distributed as a Gaussian centred on the atom position. The value of the Gaussian depends on the distance from the atom centre, the atom type, and temperature factor. Its value is calculated at each grid point within a given radius for each atom, and the values are summed to give an `atom map'. This `map' can then be used for an inverse fast Fourier transform, which gives the structure factor. It is important that the grid is fine enough to sample the atomic Gaussians accurately - the accuracy of the structure factor estimates depends on this. I recommend using a grid which gives a sampling of ~0.5Å.
X-ray gradients are estimated by `differential synthesis'. A difference map is calculated, and this is convoluted with the atomic density.
By default, SFALL scales Fobs to Fcalc. This then lets you do maps on (or close to) an absolute scale if the map comes from coordinates. If you are back-transforming a map, e.g. in solvent-flattening or averaging, then the map isn't on an absolute scale anyway, and so this scaling is not particularly sensible (although not usually harmful). Note that in iterative procedures, the Fobs you bring in to SFALL on each cycle should be the original Fobs, not the one carried through from the previous cycle (which may have been scaled, selected, or otherwise corrupted). In this case, it is probably more sensible to use the NOSCALE option in SFALL, then either (i) use SIGMAA to generate Partial or Combined Fourier coefficients for the next map (if you want to weight them); or (ii) use RSTATS to scale Fcalc to Fobs.
For a description of the original method see [1]. A modification in calculating the gradients suggested by Alain Lifchitz is used.
A list of common problems (with possible solutions) can now be found below.
Input:
i) XYZIN
Output:
i) MAPOUT
- a)
- The `solvent' map. This map has zero at all points where there is atomic density, and a constant value for all points where there was no atomic density. It is used for calculating structure factors for `bulk solvent' (see ICOEFL for ideas on using this); or for use as a mask.
- b)
- A tagged `atom map' where each grid point is tagged with a flag to say which residue, or which atom number, contributed most to it. This is used for analysing map correlations, and real space R-factors.
By default a scale factor is calculated between Fobs and Fc and is applied to the output Fobs. If this is not wanted then the keyword NOSCALE must be used.
Input:
i) either coordinates or a map (compulsory)
Output:
i) HKLOUT containing: H K L ... FC PHIC (WANGWT)
ii) MAPOUT - The atom `map' (optional).
These are used for minimisation of X-ray differences between FP and FC. This calculation uses the forward FFT.
Input:
i) XYZIN
ii) HKLIN
Output:
i) XYZOUT
ii) GRADMAT
Further details of the specification of input and output files is given in section INPUT AND OUTPUT FILES.
See description of keyword MODE and examples for uses for the various options.
P1 P21(4) P21212(1018 - alt. origin) P212121(19) P4122/P4322(91/95) P41212/P43212 (92/96) P31/P32(144/145) P3/R3(143/146) P3121/P3221(152/154) P61/P65 (169/170)It is possible to use the P1 version (or any suitable lower symmetry) for the calculations. In particular, any non-primitive spacegroup can be run in the appropriate primitive one. See keyword SFSGROUP for details.
BUT BEWARE: To use SFSG P1 you must have your reflections sorted with l>=0. This is NOT the default for P3121/P3221 or P6i22. You would be sensible to run CAD with the keyword: `OUTLIM SPACEGROUP P1' before calculating structure factors.
The crystal symmetry will be used to generate atom positions from a unique molecule. See NOTES ON HKLIN for special requirements for the HKLIN file when using a lower symmetry version.
Anything on a line after an ! or # is ignored and lines can be continued by using a minus sign.
The possible keywords are:
MODE
AVMODE, BADD, BINS, BRESET, CELL, CHAIN, EDEN, END, FORMFACTOR, FREERFLAG, GRID, H2OBG, LABIN, LABOUT, NAME, NOSCALE, OMIT, RATIO, RESOLUTION, RMSSHIFT, RSCB, SCALE, SFSGROUP, SIGMA, STEPSIZE, SYMMETRY, TITLE, TRUNCATE, VDWR, VERBOSE, WEIGHT.
N.B. Some of these are compulsory for some MODEs.
- RESMOD
- output `atom map' values tagged by a residue number flag.
- ATMMOD
- output `atom map' values tagged by a atom number flag.
- SOLVMAP
- output `solvent map' with value specified by the H2OBG keyword (default=0.03) at all points not occupied by atom density. All points occupied by atom density set to 0.0.
- XYZIN or MAPIN (one essential)
- Define input type, either coordinates or a map. N.B. XYZIN or MAPIN must be assigned.
- followed by:
- HKLIN (optional)
- Only reflections which exist in the HKLIN file are output to HKLOUT. The output FC PHIC are appended to input H K L FP SIGFP... See keywords LABIN and LABOUT for further details.
N.B. HKLIN and HKLOUT must be assigned. See NOTES ON HKLIN for the requirements placed on the HKLIN file.- ATMMAP or SOLVMAP (optional)
- Either an `atom map' or a `solvent map' is output. The map extends over the asymmetric unit of the space group used in the structure factor calculation (see keyword SFSGROUP). Note that for non-primitive space groups, only density for symmetry mates corresponding to primitive symmetry operations is output; use MODE ATMMAP to obtain a complete map. N.B. MAPOUT must be assigned.
- MAPIN
- (This option is exceedingly unlikely to be needed.) Gradients will be taken from an input difference map. Usually this difference map is generated internally from the structure factors calculated from the atomic coordinates. However, in some special situations, e.g. if you had averaged a difference map earlier, you may want to input it rather than use the internally generated one.
- RESTRAINED
- Atom parameter gradients calculated from the fit of the X-ray data are output to GRADMAT, to be combined with geometric restraints calculated by PROTIN and PROLSQ (no longer available in the CCP4 Suite).
- UNRESTRAINED
- Parameter shifts to be applied without restraints; a file will be written to XYZOUT.
- If followed by:
- XYZ
- refinement of the X Y and Z parameters will be done.
- XYZB
- refinement of the XYZ and B parameters will be done.
- B
- refinement of the B parameters will be done.
N.B. - This IS NOT NECESSARILY the spacegroup of your structure. E.g., you may well be calculating structure factors in P1 for a structure with spacegroup F43212. The program will check whether the requested <sfsgroup> is compatible with your data.
The possibilities for <sfsgroup> are: P1, P21 (4), P21212 (1018 - alternative origin), P212121 (19), P4122/P4322 (91/95), P41212/P43212 (92/96), P31/P32 (144/145), P3/R3 (143/146), P3121/P3221 (152/154), P61/P65 (169/170).
Any spacegroup can be run in an appropriate one whose symmetry operators are a subset of the one of interest (P1 can always be used as long as the hkl data are sorted with l>=0). By judiciously shifting origins many spacegroups become supergroups. $CLIBD/symop.lib contains the modified symmetry operators for some spacegroups. You may move the origin of your coordinates with PDBSET. For example:
The following labels can be assigned.
H K L FP SIGFP FREE FPART PHIP
PHIP F0 F1 F2 F3 F4 F5 F6
F7 F8 F9 F10 F11 F12 F13 F14
F15 F16 F17 F18 F19
Assignments for FP and SIGFP are always required.
If the free R flag is assigned to FREE, a subset of
reflections can be excluded from the calculation or refinement. See the
keyword FREERFLAG.
If you wish to add a known FPART to the structure factors, assign FPART
and PHIP. This is useful if you want to calculate hydrogen contributions,
add in an anisotropic heavy atom, add in a bulk solvent correction, which
has been calculated somewhere else.
The FPART can be scaled relative to the FC by inputting a SCALE.
If you wish to copy some but not all the other columns from your input to your output file, you may assign F0 F1 ... F19. These will be transcribed to the output file. If you want to copy everything over, use ALLIN on the LABOUT line.
Subsidiary keywords:
- <modewt> = 1
- Use weighting scheme w=1-(r/R) (Wang's method)
- <modewt> = 2
- Use weighting scheme w=1-(r/R)**2
if density(x,y,z)<0
density(x,y,z)=xscal*cmn*tanh(density(x,y,z)/cmn))
if density(x,y,z)>0
density(x,y,z)=xscal*cmp*tanh(density(x,y,z)/cmp))
SFALL has hardcoded X-ray and neutron formfactors available for atom types H C N O S. (Default CuKa X-ray formfactors.) Other atom types are tabulated in $CLIBD/atomsf.lib (X-ray) and $CLIBD/atomsf_neutron.lib (neutron). If your atom identifier is not recognised (i.e. it is not C, N, O, or S) the program will read atomsf.lib and take the FIRST table which matches your atom ID. This may not be satisfactory if your atom type is Fe+3, say, and you may wish to specify the formfactor yourself.
Subsidiary keywords:
or
Example:
FORM NEUTRON P Co+3 D FORM NGAUSS 5 Fe+3
The following general restrictions must be observed:
<nx> >= 2 * HMAX + 1
<ny> >= 2 * KMAX + 1
<nz> >= 2 * LMAX + 1
In addition there are further space group dependent
conditions as follows (where `n' is an integer, i.e. <nz> must be
even, for instance):
<nx> <ny> <nz>
P1 - 2n 2n
P21 2n 4n 2n
P21212 4n 4n 4n
P21212a '' '' ''
P212121 '' '' ''
P4122/P4322 4n 4n 8n
P41212/P43212 '' '' ''
P31/P32 6n 6n 6n
P3/R3 '' '' ''
P3121/p3221 '' '' ''
P61/P65 6n 6n 12n
At the beginning of a refinement, the value of ratio should be kept fairly low (1.5 - 2.0) as shifts tend to be large when the errors in the parameters are large. When most atoms are well refined, then the ratio may be increased to 3 or 4, to allow for the refinement of these atoms which are poorly placed.
Default values are overwritten from HKLIN to include all reflections.
If appropriate the program refines the value of the scale and overall B value to fit <Fo**2> to <Fc**2> using reflections within this resolution range. The default resolution range is chosen to use only those reflections where the <Fo**2> distribution fit Wilson statistics reasonably well. A standard protein distribution shows a sharp 5Å dip, which can distort the scale factors. <Fc**2> is often unrealistically high for low resolution data, until the solvent is adequately modelled. The lack of `solvent contrast' causes this.
Users are often worried because they get lower R-Factors if this scale is fitted for all data. This does not necessarily mean such a scale is more correct!
The default HKLOUT will have:
If NOSCALE is specified HKLOUT will have:
After the end of each structure factor calculation a new scale factor is calculated from the following expression, where SCNEW is the new scale factor and SCALE is the previous scale factor.
Sum {(SCALE * Fcalc) * (Fobs)}
SCNEW = SCALE * --------------------------------------
Sum {(SCALE * Fcalc) * (SCALE * Fcalc)}
Some structure factor outputs (notably SHELX) include an Fcalc scaled
as 10*absolute.
SFALL calculates FC on the absolute scale. If you wanted to combine these
values you would need
SCALE FPART 0.1
The program tries to estimate these using an algorithm of R. Agarwal's. See NOTES ON STEPSIZE.
If you are doing unrestrained refinement, structure factor calculation will be repeated if abs(initial step - optimum step)/(initial step).
The speed and accuracy of the calculation depend to some extent on the values chosen. For 1.5Å data a value of 2.5 is sufficient (a maximum value of 3.0 is allowed). For neutron data, or for atoms with low B values, it could safely be reset to 1Å.
Input Files:
Output Files:
The files used in a single run of the program depend on the options requested via the data control keywords.
a1*exp(-b1*s*s) + a2*exp(-b2*s*s) - 2 Gaussian approximation
(Agarwal, 1978)
or as:
a1*exp(-b1*s*s) + a2*exp(-b2*s*s) + a3*exp(-b3*s*s)
+ a4*exp(-b4*s*s) + c
- 5 Gaussian approximation
See [2] pp. 99-101 (Table 2.2B) or
[5] p. 500ff, table 6.1.1.4 for values a1-a4, b1-b4, c for X-rays.
For neutron scattering see [2] pp. 99-101 (Table 2.2B).
The atom name can be used to assign a formfactor to it.
0 1
e.g. column 1 5 0 34
ATOM ... ZN is Zinc
ATOM ... U is Uranium
For the common atom types the program includes tables for form factors for the required value of NGAUSS. They are C N O H and S. All others must be read from the library files atomsf.lib or atomsf_neutron.lib which are automatically assigned. These contain tables of formfactors for every known atom (Kim Henrick monument).
atomsf.lib contains the five Gaussian form for X-ray data and the two Gaussian form for atoms H C N O and S. Unless you are working at very high resolution (>1.5Å) the two Gaussian approximations are adequate and speed up the calculations somewhat.
atomsf_neutron.lib has the constant value needed for neutron scattering.
The CRYST1 card (which gives the cell dimensions) and the SCALEi cards (which give the required transform for turning the coordinates into fractional ones) should be included in XYZIN.
Cell parameters from the HKLIN file or CELL keyword (if either are present) will be used in the absence of CRYST1 and SCALEi cards, but otherwise the results of omitting the cards are somewhat unpredictable - in some cases the program may fail, in others it may proceed but using random or inappropriate values for the cell parameters.
If an atom has occupancy set =0.0 it will be copied to the output file if appropriate, but not used in the calculation. This means it is easy to exclude suspect atoms from any calculation without deleting them from the file.
The program does not make use of anisotropic U factors in the calculation of electron density and structure factors, and so ANISOU records are ignored.
Example of part of XYZIN:
REMARK 2ZN refined coordinates CRYST1 82.500 82.500 34.000 90.00 90.00 120.0 1 R3 SCALE1 0.01212 0.00700 0.00000 0.00000 SCALE2 0.00000 0.01400 0.00000 0.00000 SCALE3 0.00000 0.00000 0.02941 0.00000 ATOM 1 N GLY A 201 1 -8.863 16.944 14.289 1.00 21.88 ................................. ATOM 826 CA ALA D 130 4 -5.022 21.709 -11.876 1.00 15.58 ATOM 830 CA WAT A 249 1 -0.002 -0.004 7.891 0.33 10.40 ATOM 831 ZN2 WAT A 249 1 0.000 0.000 -8.039 0.33 11.00 ATOM 832 OW1 WAT A 249 1 0.000 0.000 -8.039 0.00 11.00 ................................. Atom 1 is Nitrogen, 826 is Carbon, 830 is Calcium, 831 is Zinc and 832 is Oxygen.
An MTZ file with column labels corresponding to H K L .. FP SIGFP [FREE FPART PHIP F0 .. F19]. The header will contain the cell dimensions and spacegroup of the structure (if you want to change these, use MTZUTILS).
For SFCALC this file MUST BE SORTED on h k l (i.e. so h is the slowest varying index, then k and l is the fastest), and be within the asymmetric unit expected by the program; see below for expected limits (CAD will reorder your file if necessary). It is sensible to do this if your data has not been processed by CCP4 programs. XDS, MADNESS etc. sometimes have different default asymmetric units to the CCP4 suite.
# an example of sorting native data and checking for correct # asymmetric unit cad HKLIN1 $CEXAM/toxd/toxd HKLOUT toxd_sorted <<EOF TITLE Toxd data sorted - default symmetry P212121 LABIN FILE 1 E1=FTOXD3 E2=SIGFTOXD3 CTYPE FILE 1 E1=F E2=Q EOF
For SFREF this file MUST BE SORTED on h k l (i.e. so h is the slowest varying index, then k and l is the fastest), and be extended if necessary to cover the whole asymmetric unit expected by the program for the SF spacegroup; see below for expected limits. If you are working at a lower symmetry than optimal the data must have been extended and sorted (CAD will do this too). There is a reason - sorting data is quite slow, and you will probably use this file many times during the course of a refinement.
# an example of extending and sorting native data to P1 +-h,+-k,+l cad HKLIN1 $CEXAM/toxd/toxd HKLOUT toxd_p1 << EOF OUTLIM SPACEGROUP P1 TITLE Toxd data extended to P1 cell LABIN FILE 1 E1=FTOXD3 E2=SIGFTOXD3 CTYPE FILE 1 E1=F E2=Q EOF
The agreement factor analysis is carried out against the values of FP. Sigma values are assumed to be in column SIGFP.
IF FPART and PHIP have been defined, the FC vector equals the FPART vector plus the FC contribution calculated from the input. FPART can be scaled by entering a suitable value on the SCALE input.
Other columns in the input file can be copied to the output file by assigning
them to F0= F1= ... Or all columns can be copied over if the ALLIN subkeyword
is given in LABOUT.
Note however that if the input file contains columns with labels that match the
program labels then SFALL will stop with a fatal error.
Limits for Indices for the various space groups (these are the same as those used in the data reduction programs and FFT):
P1 h k l : l >= 0
h k 0 : h >= 0
0 k 0 : k >= 0
P21 h k l : k >= 0, l >= 0
h k 0 : h >= 0
P21212 h k l : h >= 0, k >= 0, l >= 0
P212121 h k l : h >= 0, k >= 0, l >= 0
P41212 h k l : h >= 0, k >= 0, l >= 0, h >= k
(+ other tetragonal)
P31/P32 h k l : h >= 0, k > 0
0 0 l : l > 0
P3/R3 h k l : h >= 0, k > 0
0 0 l : l > 0
P3121/P3221 h k l : h >= 0, k >= 0, k <= h (all l)
h h l : l >= 0
P61/P65 h k l : h >= 0, k >= 0, k <= h (all l)
h h l : l >= 0
If you wish to generate structure factors from a input map it is essential that the map is in an appropriate format for the SFALL spacegroup you request.
Common errors are:
1) using a different grid for the FFT calculation and the SFALL calculation. FATAL!
2) Changing the axis order in the FFT calculation - both have the same defaults for the same spacegroup! FATAL!
3) Choosing a different asymmetric unit for the FFT and the SFALL calculation. You must make sure your map has the one which covers the SFALL requirements. There is no flexibility here.
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
The proportion of the shift to be applied can be modified (see the description of keyword STEPSIZE).
If an input atom has occupancy of 0.0 it will be copied to the output file.
If no HKLIN has been assigned the program outputs a list of H K L FC PHIC for all possible reflections within the reciprocal asymmetric unit for the SFSGROUP that are within the requested resolution limits.
FC and PHIC can be modified for use in solvent flattening (see keyword AVMODE).
Solution: This may not crash the program (sometimes it does) but even so some of the output may be unreliable if the reflections in HKLIN have not been sorted with h as the slowest, k as the intermediate, and l as the fastest varying index. See NOTES ON HKLIN above for the requirements placed on HKLIN.
Solution: SFALL should warn you before stopping, which labels are duplicated, e.g.:
Warning: this may fail! This column label FC is also a program labelThe suggested workaround at present is to rename the offending file labels, for example using a utility program such as SFTOOLS, before rerunning the program.
or
Problem: Program stops with the message:
**** No Cell Input to subroutine rbfro1?? ****
after reading in XYZIN.
Solution: Check that CRYST1 and SCALE cards are present in the input co-ordinate file XYZIN.(See NOTES ON XYZIN above).
Solution: Check that the input reflection file has the correct asymmetric unit and that the reflections have been sorted so that h is the slowest changing index, k is the next, and l varies the fastest. (See NOTES ON HKLIN above). Nb: the program should now generate an explicit error message suggesting that this is the problem.
Solution: You may have to increase the value of MEMSIZE (see MEMORY ALLOCATION above). N.B.: the program should now generate an explicit error message suggesting that this is the problem.
sfall XYZIN /f/scratch/swift/pa_model1_2.pdb XYZOUT $SCRATCH/junk.pdb MAPOUT $SCRATCH/junk.map << END-sfall TITL Phasing on initial PA structure (refined twice) GRID 52 64 76 MODE ATMMAP RESO 30 2.1 BINS 60 RSCB 5.0 2.1 SFSG 1 END END-sfall
sfall HKLIN $SCRATCH/pt2_pt4_shhg2_os2_nat.mtz HKLOUT $SCRATCH/pa_model1_2_phase.mtz XYZIN /f/scratch/swift/pa_model1_2.pdb << END-sfall TITL Phasing on initial PA structure (refined twice) GRID 52 64 76 MODE SFCALC XYZIN HKLIN RESO 30 2.1 BINS 60 RSCB 5.0 2.1 SFSG 1 LABI FP=F_V4 SIGFP=SIGF_V4 FREE=FreeRflag LABO FC=FC PHIC=AC END END-sfall
sfall HKLIN $SCRATCH/pt2_pt4_shhg2_os2_nat.mtz HKLOUT $SCRATCH/pa_model1_2_phase.mtz MAPIN $SCRATCH/junk.map << END-sfall TITL Phasing on initial PA structure (refined twice) GRID 52 64 76 MODE SFCALC MAPIN HKLIN RESO 30 2.1 BINS 60 RSCB 8.0 2.1 SFSG 1 LABI FP=F_V4 SIGFP=SIGF_V4 LABO FC=FC PHIC=AC END END-sfall
# - back-transform map with sfall to obtain Fcs and phases, scale
# and calculate R-factor
# - combine the phases with sigmaa
# - run fft to calculate a new map with Fobs and combined phases as
# input to flatmap
#
sfall HKLIN ../mtz/fvb18_sigmaa.mtz
HKLOUT fvb_flat_14.mtz
MAPIN fvb_flattened_14.map
<< EOF-sfall
titl back transformation for cyc 14
mode SFCALC MAPIN HKLIN
grid 104 128 160
reso 200.0 3.0
BINS 40
rscb 10.0 3.0
sfsg 19
AVMODE RADIUS 8
badd 0
FORM NGAUSS 5 C H N O S
LABI FP=fvb_Fnp SIGFP=fvb_SIGFnp -
F0=PHIB_I3 F1=FOM_I3 -
F2=A F3=B F4=C F5=D
LABO FC=FCWANG PHIC=PHICWANG WANGWT=WC8
END
EOF-sfall
sfall HKLIN ../data/taka_fx_trunc.mtz XYZIN ../data/takaxp_model8_b.pdb XYZOUT $SCRATCH/junk.pdb << END-sfall TITL TAKAXP_MODEL8_9 SFS GRID 104 136 264 MODE SFREF XYZ UNRESTRAINED FREE 3.0 RESO 20 2.1 60 RSCB 8.0 2.1 SFSG 19 FORM NGAU 2 Ca Cr Fe+2 P LABI FP=FP SIG=SIGFP FREE=FreeRflag END-sfall
#!/bin/csh -f
#
# REFINE consists of sfall, protin and prolsq
#
set LastCycle=146
set Number_of_Cycles=8
set CycleCounter=0
#
Begin:
#
@ CurrentCycle=$LastCycle + 1
#
# ========== SFALL ==========
#
set DATE=`date`
echo ' *************************** '$CurrentCycle' **************'
echo ' '
echo ' Running SFALL for Cycle Number :' $CurrentCycle' on '$DATE
echo ' '
echo ' *************************** '$CurrentCycle' **************'
#
sfall HKLIN s91a.mtz
XYZIN s91a_cyc${LastCycle}.brk
GRADMAT s91a_GRADMAT${CurrentCycle}.tmp
<< END-sfall
TITL Barnase s91a Mutant
MODE SFREF XYZB RESTRAINED ! for prolsq
GRID 90 90 120 !div CELL by these should give .=. 0.7 A
BINS 60
RESO 10 2.2 !last no. is nstep
RATI 3 !truncate xyz and B shrifts to RATI*RMS
BADD 0 !smear the gaussians to gen atomic density [10.0]
RSCB 4 1.5 !limits for refining scale and B, same as RESO ?
SFSG 145 ! fft space group
LABIN FP=S91A_F SIGFP=S91A_SIGF FREE=FreeRflag
END
END-sfall
#
/bin/rm ${SCRATCH}s91a_junk.brk ${SCRATCH}sfall*
#
# ========== PROTIN ==========
#
set DATE=`date`
echo ' *************************** '$CurrentCycle' **************'
echo ' '
echo ' Running PROTIN for Cycle Number :' $CurrentCycle' on '$DATE
echo ' Running PROTIN for Cycle Number :' $CurrentCycle' on '$DATE
echo ' '
echo ' *************************** '$CurrentCycle' **************'
#
protin XYZIN s91a_cyc${LastCycle}.brk
PROTOUT s91a_protout.out
PROTCOUNTS s91a_protcounts.out
DICTPROTN ${LIBD}protin.dict
<< END-protin
TITLE Barnase Ser91 -> Ala
SYMMETRY 145
!
CHNNAME ID A CHNTYP 1 ROFFSET 0
CHNNAME ID B CHNTYP 2 ROFFSET 0
CHNNAME ID C CHNTYP 3 ROFFSET 0
chnname id E chntyp 4 roffset 0
!
CHNTYP 1 NTER 3 VAL 3 CTER 110 ARG 2
CHNTYP 2 NTER 3 VAL 3 CTER 110 ARG 2
CHNTYP 3 NTER 2 GLN 3 CTER 110 ARG 2
chntyp 4 wat
!
LIST FEW ![few]/some (for >20A)/all
PEPP 5 !no. of atoms restrained to be in a plane [5]
VDWR 1 CPR 8 3.4
END
END-protin
#
# ========== PROLSQ ==========
#
set DATE=`date`
echo ' *************************** '$CurrentCycle' **************'
echo ' '
echo ' Running PROLSQ for Cycle Number :' $CurrentCycle' on '$DATE
echo ' '
echo ' *************************** '$CurrentCycle' **************'
#
prolsq XYZIN s91a_cyc${LastCycle}.brk
PROTOUT s91a_protout.out
PROTCOUNTS s91a_protcounts.out
GRADMAT s91a_GRADMAT${CurrentCycle}.tmp
XYZOUT s91a_cyc${CurrentCycle}.brk
<< END-prol
TITLE Barnase s91a Mutant
CGCYCLES 20 100 1 !max no. cyc for conjugate gradient soln [50]
ORIGIN 0 0 0 !origin constraint flags
RESOLUTION 10 2.2 !select Fobs
OUTPUT XYZ !o/p XYZ(.brk)/SF(.mtz)/SHIFTS(shifts file)
RTEST -1 1 1 1 1 1 1 1 !-1 -> +1 when R factor .=25%
NOUPDATE !not update atomic coord in PROTIN o/p file
MATRIX .30 .85 .85 !1st param adjusts SF/geom contribution
!start=.08;.12;.2;.25;.3;.35; final=.08
!2nd&3rd:shift factors for position and B
BATOM !(+) when refining indiv B
!
! ***** Restraints *****
DISTANCE 1 0.02 0.04 0.05 0.01 0.1
PLANE 1 0.02
CHIRAL 1 0.12
TEMPERATURE 1.0 1.0 1.5 1.5 2.0 0.1 !start
!TEMPERATURE 1.0 1.5 2.0 2.0 2.5 3.0 !when R factor <25%
HOLD 0.1 1.0 0.1
!TORSION 1 20 20 30 50 !when R factor >25%
TORSION 1 10 10 15 45 !when R factor <25%
VANDERWAAL 1 0.2 -0.3 0.0 -0.2 0.0
!
! ***** Monitor *****
MONITOR DISTAN 3. VANDERWAAL .5 TORSION 3
MONITOR PLANE 3 CHIRAL 3 !for R factor<25%
END
END-prol
#
Cleanup:
#
/bin/rm s91a_protout.out s91a_protcounts.out s91a_GRADMAT${CurrentCycle}.tmp
#
@ CycleCounter=$CycleCounter + 1
@ LastCycle=$LastCycle + 1
#
# Test to see whether Number_of_cycles done
#
if ($CycleCounter<$Number_of_Cycles) goto Begin
#
The program may be used for
Tables of coefficients for a five term Gaussian approximation to the atomic form factors are given in the International Tables for X-ray Crystallography Vol.IV [2]. Some values for two and one term Gaussian approximations are given in the Agarwal paper.
The radius of the atoms (beyond which the electron density is considered to be negligible) is also required in the calculation. The value for this radius must be chosen to balance the requirements of accuracy (large radius) and speed (small radius). The tables below indicate the radii required for carbon atoms, for different temperature factors (Bm), to give a given fractional loss of electron density (DeltaZm/Zm).
DeltaZm/Zm 0.02 0.01 0.005
Two term Gaussian Bm
5 1.89 2.06 2.22
10 2.02 2.21 2.38
20 2.26 2.47 2.68
More values are given in the Agarwal paper.
The electron density map is built up using the contributions from each atom within, or near (within the atom radius) to, the part of the map being calculated. A three dimensional FFT of the electron density map is used to calculate the structure factors. In this calculation the space group symmetries are used whenever possible.
If the sampling grid is too coarse, significant errors may occur in the calculation of the structure factors. These errors may be reduced [3] either by using a finer grid for the calculation or by adding an artificial extra temperature factor to all the atoms when modelling the density (not recommended). This factor has also to be taken into account when the calculated structure factors are compared with the observed structure factors.
A set of terms, H, is only calculated for one parameter as the other diagonal terms may be calculated to a good degree of accuracy from this initial set. An inverse matrix is set up for calculating the orthogonalised contributions of the gradient.
RATIO * r.m.s. value of the shifts
At the beginning of a refinement, the value of RATIO should be kept fairly low
(1.5-2.0) as shifts tend to be large when the errors in the parameters are
large. When most atoms are well refined, then the ratio may be increased to 3
or 4, to allow for the refinement of these atoms which are poorly placed.
Even these truncated shifts may not be the optimum shifts to be applied. A displacement of the form alphaDelta(u), which minimises the minimisation function of the least squares P(u + alphaDelta(u)), will be the optimum where alpha is the optimum step size. As P as a function of alpha approximates to a quadratic function, it is possible to calculate the optimum step size, alphaopt, from the values of P(alpha) at alpha = 0 and alpha = alpha1 and from the slope of P(alpha) at alpha = 0. The initial step size alpha1 used in the calculation is chosen as 1.0 or the value input in the control data. If the fractional change in step size is greater than SZFRC (by default 0.3) then a second calculation is done with alpha1 taken as the optimum step size just calculated.