SCSB X-Ray Crystallography Center

SAINT Quick Users Guide

SAINT
INTEGRATION:
SCALE:
FILTER:
STATISTICS:
SORT:
APPENDIX

ASTRO: Data optimization
XPREP: Merging symmetry related reflections
SMART: Data collection and image viewer
DOS: Some useful dos commands
UNIX: Some useful unix commands

For additional help using any of the software packages please see the SOFTWARE help section of this center's HOMEPAGE.

SAINT { Top }

SAINT is a program for integrating frames, sorting refelection lists, scaling, filtering, sorting and merging of reflections. Although saint can be used to merge reflections it is recommended that XPRED is used to merge the symmetry related reflections after scaling and filtering the reflection list in SAINT. Several refinement contraints can only be entered on the command line:

SAINT is available in both DOS and UNIX versions. Only the UNIX version should be used.

saint [/k1:lattice_type] [/l1:constraint_mask] [/k2:lattice_type] [/l2:constraint_mask] [/bg:bgnd_scale] [/ls:lst_sqrs_profile] [/t:int_box] [/h:memory]

/k1: 0=none, 1=Triclinic, 2=C-Monoclinic, 3=B-Mono, 4=A-Mono, 5=Orthorhombic , 6=Tetragonal, 7=Hexagonal, 8=Rhombohedral, 9=Cubic
/k2: Lattice type for global refinement. This should be the same as k1
/l1: Constraintmask.

768 fixes crystal translations(512)+ goniometer axes (256) (this is not recommended)
771 fixes crystal translations(512)+ goniometer axes (256)+ restrains Ybeam (2) + Xbeam (1)

/l2: Constraintmask for global refinement: This should be 771
/ls: 1 {default value}
/bg: 5 {default value} -This may need to be lowered to 4 if the (diffuse) background is high
/t: 0.02 {default value}
/h: 11 {default value} -HASH memory allocation 2^11=2048 reflections/frame

Examples:
/data5/my_data>saint /k1:6 /k2:6 /l1:771 /l2:771 /bg:4 Staph. Nuclease (P41, high diffuse)
/data6/My_data>saint /k1:7 /k2:7 /l1:771 /l2:7 /h:12 Dps (P31, large unit cell)
/data4/my_data>saint /k1:5 /k2:5 /l1:771 /l2:771 CRP ( P212121, medium cell)

A typical SAINT data processing run will take many hours. The sequence of routines is as follows:

Integration: This is very slow
Scaling : Calculates inter and intra-frame scalefactors
Filtering: Remove outliers
Scaling: Calculates inter and intra-frame scalefactor
Filtering: Remove outliers, impose resolution limits
Statistics: Calculates full statistics on complete reflection list
SORT: Combine data from separate runs: repeat steps 2-5 before proceeding to XPREP
XPREP: Merging of reflections

Note: Do not run more that ONE (1) saint data processing in any directory. (Certain temporary files are created which will be scrambled if more than one copy of saint is run.)

INTEGRATION {Top}

This routine will integrate the BRUKER2K CCD images and create a reflection list. The integration method will be either Kapsch 3-D profiling or Rossman 2-D profiling depending on the ratio Spot_Z / Frame_width. Before integration can proceed, you will need to note the following

Filename of first frame.
Total number of frames.
Spot mosaicity (Spot_Z). Measure using the rocking curve's Full Width: SMART: GRAPH / ROCKING
Spot size (Spot(XY) in degrees.

Measure the FW width of the spot in pixels: SMART: GRAPH / VECTOR
Then measure the 2-theta width of the detector: SMART: CURSORS / PIXEL.
The spot size is given by: Spot_XY= spot_width (pixels) * detector 2-theta width (deg.) / 1024 (pixels)

Compute a new orientaion matrix using the first 30 frames of data. SMART: REFL_LIST / CLEAR / THRESHOLD / INDEX / BRAVAIS / LEAST_SQRS -Note the output filename {filename.p4p}

[T] Title: enter a descriptive title
[I] Input frame 1: {filename.001}
[N] Number of frames 670
[B] Batch# 1 -For later scaling of several batches or runs of data.
[M] Orientation Filename: {filename.p4p} -OM from first 30 frames of data
[Y] Refinement frequency: 40 -Number of frames to store in memory
[R] Output refl filename: {filename._rb}
[P] Point group: "4/m" -Laue point group. The quotes are required

"1-" , "2/m", "4/m", "3-", "6/m",, "m3-", "mmm", "4/mmm", "6/mmm", "3-m1", "3-1m", "3-m", "m3-m"

[U] Resolution: 2.0 -Maximum resolution of integration
[S] Spot parameters:

XY size(deg) 0.80 Z size(deg) 0.40 -These parameters are determined using SMART
I/sigma "strong" threshold 10.0 Suppress size refinement: Y

[Z] Option string d -Clean-up parameters D: delete temp files T: suppress time decay
[!] Go -- begin integration -START integration

SCALE {Top}

This routine will calculate the inter-frame scale factors and apply then to all the relections in the reflection list. Symmetry equivilent reflections are not merged nor are outliers removed from the reflection list. The image can be subdivided into (1, 5, or 9) regions for calculation of the scale-factors. These micro-regions will each have different scale factors. A large number of regions is useful for making absorption and resolution dependent decay corrections, but requires a high redundency (symmetry) of data. The time decay model is for small-molecule data and not recommended for macromolecular data.

[T] Title: enter a descriptive title
[I] Input reflection file: {filename._rb}

Min input I/sigma: 2.0
Rejection option: 0 -{do not reject reflections }

[O] Output reflection file: {filename._rb}
Min output I/sigma: 0 -{write all reflections to file}
[L] Output listing file: {filename._ls} -all output messages and statisitics are recorded here. Message is appended to file.
[M] Min, Max resolution: 9999.0 2.0 -scale all data to 2.0A.
[G] Grid: 9 -this determines how many micro-regions per frame are used for scaling (1, 5, 9).
[W] Wedge type: FIXED Wedge size: 15.0 (degrees) -3D profiling uses wedges of data stored in memmory. Low symmetry lattices require a larger wedge (cubic 10 -> triclinic 50 deg.)
[B] B-factor refinement cycles: 2,40 -0=Do not refine B-factor, ALL -refine on every cycle.
[!] GO -- begin scaling: -STARTS scaling process

FILTER {Top}

This routine is used to remove reflections from the reflection list based on input criteria.

[T] Title: a descriptive title
[I] Input file: {filename._rb} -This is automatically the output file of your last SAINT run
[O] Output file: {filename.hkl} - Specify hkl (ASCII) text format
[1] Operation 1: EXCLUDE BAD 4.0 6.0 -EXCLUDE outliers 4sigma in group, 6 sigma if equivalent.
[2] Operation 2: INCLUDE STL 0.001 0.250 -INCLUDE all reflections 500.0- 2.0 A resolution. {stl= 1/(2*d)}
[!] Go --begin filtering -START filtering

SORT {Top}

This routine will merge the reflection list into a set of unique reflections. It is recommended by the manufacturer that the external software package XPREP is used for merging of reflections. Use sort to combine data from 2 or more runs. It is a good idea to SCALE & FILTER each run before combining them.

STATISTICS {Top}

This routine will calculate statistics using the full reflection list. There are many different types of statistics calculated by this utility.

APPENDIX

ASTRO {Top}

ASTRO is a program for choosing optimal data collection parameters.

SMART {Top}

SMART is a program for collecting CCD data, indexing reflection lists, and viewing CCD images.

XPREP { Top }

Xprep is a small utility for merging of symmetry related reflections in a list. It is used after SAINT has integrated, scaled, and filtered the reflection list. The file name of your unmerged but scaled and filtered hkl file and the cell parameters are prompted for after starting xprep.

>ls *.hkl *._rb
>head my_data.p4p
>xprep

Input file name:

my_data.hkl

my_data._rb

[4] SHELX HKLF 4 format or SAINT ._rb file

Select option [4]:

Enter cell:

Lattice type [P, A, B, C, I, F O, R]

Select option [P]:

choose your lattice type

Select option [H]:

Determine or input SPACE GROUP

Select option [S]:

Select option [ ]:

triclinic

monoclinic

orthorhombic

tetragonal

trigonal/hexagonal

cubics

Select option [P]:

Select lattice type from systematic absences

Select option [A]:

Select the space group from the choices given

Select option [H]:

Read, modify or merge DATASETS

Select option [E]:

Sort-MERGE current data (no scaling)}

Select option [A]:

merge ALL equivalents

to keep anomalous pairs

Select option [E]:

WRITE dataset to file

DOS {Top}

The following DOS commands may be usefull.

copy {filenames} {path\filename}...........COPY
move {filenames} {path\filename}...........MOVE
dir {optional path}........................LIST files
cd {path}..................................Change Directory
cd {..}....................................Back up directory tree
c {enter} ................................ cd to the C:\ HD
m {enter} ................................ cd to the m:\ HD
pwd .......................................Print Working Directory
mkdir {dirname}............................Make a New Directory
type {filenames}...........................Print file to screen
edit {filename}............................GUI file editor

Note: The DOS format change directory commands:
m:
n:
o:
will also work on the SGI workstation to get you to these same directories. These call specific unix utilities and are not applicable to any other directories.
{ m: => /data4/bruker2k/, n: => /data5/, o: => /data6/ }

UNIX {Top}

The following UNIX commands may be usefull.

cp {filenames} {/path/filename}............COPY
mv {filenames} {/path/filename}............MOVE
ls [-ltr ]{optional path}..................LIST files -l:long, -t:time, -r: reverse
cd {path}..................................Change Directory
cd {../}...................................Back up directory tree
cd /data4{enter} ..........................cd to the /data4 HD
pwd .......................................Print Working Directory
mkdir {dirname}............................Make a New Directory
more {filenames}...........................Print file to screen, one page at a time
cat {filenames}............................Print file to screen
jot {filename}.............................GUI file editor