STANDARD TEST RUNS FOR THE LAUE PROGRAMS

INTRODUCTION

Some standard test data files are supplied to enable some basic testing of the Laue programs to be carried out (in $CCP4_MASTER/laue/testdata or on VMS CCP4_ROOT:[XTAL.LAUE.TESTDATA]). They may be used in two ways, either as test data sets just to check that the programs seem to be running OK or as part of a learning process about the programs.

The data sets come from three sources:

  1. Proflavin hemisulphate (smallish molecule) - film (pf...)

  2. Tetragonal HEWL Lysozyme (protein) - image-plate (lys...)

  3. 4 Zinc Insulin (protein) - film (zn...)

List of sections:

Setting Up the Tests
Some Notes on the Supplied Data Files
LAUEGEN Tests
NEWLAUE Tests
GENLAUE Tests
INTLAUE Tests
INTLDM Tests
AFSCALE Tests
LSCALE Tests
LAUENORM Tests
LAUESCALE Tests
DIFFLAUE Tests
LAUEDIFF Tests
UNSCRAM Tests
DECONV Tests
LCHK Tests
INTANAL Tests
SPOTIN Tests

SETTING UP THE TESTS

The user should set up a directory/sub-directory for performing the required tests. Apart from the film and image-plate image files, all other files required should be copied to the user's area from the supplied test data area. The command 'lget' has been set up to facilitate such copying. The command is followed by the names of one or more files which are to be copied (maximum of 8 names under VMS). These filename specifications may contain wild cards (will need to be enclosed in " " if under Unix). Some of the files used by the Laue programs are in machine dependent binary format and such files are supplied in ascii format and will be translated by the 'lget' command to the corrsponding binary files (more details below).

e.g. (for testing the program Lauescale)

lget lys_ls.ctl lys_ls.geasc lys_ls.mtzasc

This will copy the three named files to the user's area and will translate the file lys_ls.geasc to lys_ls.ge1 and lys_ls.ge2 and also translate the file lys_ls.mtzasc to lys_ls.mtz.

The film and image-plate files need not be copied but are handled as follows:

Under Unix

Soft links are made to the image files from the user's area. The files may then be referenced from the user's area as if they were present in that area.

This may be accomplished by using the supplied command 'linkimages'. This will make links to all the available image files.

Under VMS

The logical name 'lfilm' has been set up to point to the directory containing the test data image files. This is used when accessing a required image file.

e.g.

lfilm:pf1a.dat

SOME NOTES ON THE SUPPLIED DATA FILES

  1. Film/Image-plate^images

    The images supplied are as follows:

    1. Proflavin: The 'a' and 'b' films of a 6 film pack pf1a.dat and pf1b.dat.

    2. Lysozyme: A single MAR image-plate image lys.i2 (lys_swap.i2)

    Note:

    For the image-plate data, the data items are unsigned two byte integers. Most Unix based machines are big-endian. For a little-endian Unix machine, the byte swapped image lys_swap.i2 should be used instead of lys.i2. (Under VMS, lys.i2 has the correct byte order for the VMS, being the opposite of that in lys.i2 supplied on a Unix system)

  2. Laue.ge1/.ge2 files

    These are the files which contain the lists of the predicted reflections and store the integrated intensities. As used by the Laue program they are in a binary format. As such binary data is machine dependent, the files are supplied in an ascii format which needs to be translated to the required binary format using the supplied program 'exchge' with the option 'translate from ascii (f)'. If the supplied ascii files required for a test are copied to the user's directory using the supplied 'lget' command then the .geasc files will be automatically translated to the corresponding .ge1/.ge2 files.

  3. MTZ files

    These are also files which contain binary data. Again they are supplied in an ascii format which needs to be converted to the binary MTZ format for use using the supplied program 'na4tomtz'. The program is run by typing the command 'laue na4tomtz'. If the supplied ascii files required for a test are copied to the user's directory using the supplied 'lget' command then the .mtzasc files will be automatically translated to the corresponding .mtz files.

LAUEGEN TESTS

Prerequisites

Test 1: pf_lg.ldm (pf_lg_vms.ldm for VMS), pf_lg.spots

Test 2: lys_lg.ldm (lys_lg_vms.ldm for VMS), lys_lg.spots

Test 1

Run the program using the command 'laue lauegen'

Log file: pf_lg.log

Select <Read Parameters File>

input file name pf_lg (VMS: pf_lg_vms )

Select <Laue Simulations>

Select <Colour Coded Display> cf the postscript file pf_lg1.ps

Select <Interactive Display> cf the postscript file pf_lg2.ps

Select <Return to Main Menu>

Select <Find Orientation>

Select <Measure Spots on Image>

Select <Read Spots File>

input file name pf_lg 8 spots should be read & marked cf the postscript file pf_lg3.ps

Select <Measurement Complete>

input limit of h**2+k**2+l**2 of 10

input spot position error of 0.5

should give 1 soln (PhiX -178.6, PhiY -2.3, PhiZ 44.9)

Select <Show Solution>

Select <Solution 1>

predicted pattern should match image fairly well

Select <Return to Previous Menu>

Select <Select Solution>

Select <Solution 1>

Select <End Autoindexing>

Select <Process>

Select <Refine Orientation>

Select <Nodals Search and Refine>

Use default replies & refine default parameter list

should give rms of .080 for 60+ spots (from .321)

Select <Write .ge Files>

give file name of say pf_lgout

use default replies thereafter

Select <Return to Previous Menu>

Select <End Processing>

Select <Quit Program>

The output log file can be compared with the example log file pf_lg.log.

Test 2

Run the program using the command 'laue lauegen'

Log file: lys_lg.log

Select <Read Parameters File>

input file name lys_lg (VMS: lys_lg_vms )

Select <Laue Simulations>

Select <Colour Coded Display> cf the postscript file lys_lg1.ps

Select <Interactive Display> cf the postscript file lys_lg2.ps

Select <Return to Main Menu>

Select <Find Orientation>

Select <Measure Spots on Image>

Select <Read Spots File>

input file name lys_lg 5 spots should be read & marked cf the postscript file lys_lg3.ps

Select <Measurement Complete>

input limit of h**2+k**2+l**2 of 15

input spot position error of 0.75

should give 2 solns (PhiX -94.3, PhiY 15.2, PhiZ 76.4 for solution 1)

Select <Show Solution>

Select <Solution 1>

predicted pattern should match image fairly well

Select <Return to Previous Menu>

Select <Select Solution>

Select <Solution 1>

Select <End Autoindexing>

Select <Process>

Select <Refine Orientation>

Select <Nodals Search and Refine>

Use default replies & refine default parameter list

should give rms of .126 for 60+ spots (from .256)

Select <Write .ge Files>

give file name of say lys_lgout

use default replies thereafter

Select <Return to Previous Menu>

Select <End Processing>

Select <Quit Program>

The output log file can be compared with the example log file lys_lg.log.

NEWLAUE TESTS

Prerequisites

Test 1: pf_nl.gen, pf_nl.dmp

Test 2: lys_nl.gen, lys_nl.dmp

Test 1

Run the program using the command 'laue newlaue'

(Use default replies unless indicated)

Select the default option DATG; input file pf_nl.gen

Select option START

Select option PLOT 

Select option AUTO   no indices supplied
                     h**2+k**2+l**2 limit = 10
                     input file of spots - pf_nl.dmp
                     error in spot positions 0.5 mm
                     refine the single solution
                     reset with solution 1 and continue
Select option START

Select option PLOT

Select option STOP

The plots should give simulations as shown in the simulations supplied in the postscript files pf_nl1.ps and pf_nl2.ps respectively.

Test 2

Run the program using the command 'laue newlaue'

(Use default replies unless indicated)

Select the default option DATG; input file lys_nl.gen

Select option START

Select option PLOT 

Select option AUTO   no indices supplied
                     h**2+k**2+l**2 limit = 15
                     input file of spots - lys_nl.dmp
                     error in spots positions 0.75 mm
                     refine 2'nd solution PX=94, PY=-15, PZ=-103
                     reset with this solution and continue
Select option START

Select option PLOT

Select option STOP

The plots should give simulations as shown in the simulations supplied in the postscript files lys_nl1.ps and lys_nl2.ps respectively.

GENLAUE TESTS

Prerequisites

Test 1: pf_gl.gen, [pf1a.dat]

Test 2: lys_gl.gen, [lys.i2 (lys_swap.i2)]

Test 1

Run the program using the command 'laue genlaue'

(Use default replies unless otherwise indicated)

Root name of .gen file is pf_gl

Film data

Set delta to 0.45

Choose nodal spot selection index of 4

Select refinement option with no file of matched spots (defaults)

A film; film name ./pf1a.dat (VMS: lfilm:pf1a.dat )

Do not match spots on threshold plot

Spot diameter = 0.45

Box size = 0.45

Use all spots found (about 104)

Do not refine cell but refine all other parameters using the default LSR method (defaults)

rms deviation should be reduced from about 0.139 mm to about 0.068 mm.

Do not re-run refinement immediately

Write output files (Nodal index 12; Yes, happy with refinement; No, do not refine another film; root name for output files pf1 ; other replies are defaults)

The output log file can be compared with the example log file pf_gl.log.

Test 2

Run the program using the command 'laue genlaue'

(Use default replies unless otherwise indicated)

Root name of .gen file is lys_gl

Image-plate data

Set delta to 0.6

Choose nodal spot selection index of 5

Select refinement option with no file of matched spots (defaults)

Film file name ./lys.i2 (or ./lys_swap.i2 ) ( VMS: lfilm:lys.i2 )

Do not match spots on threshold plot

Spot diameter = 0.6

Box size = 0.6

Threshold above background for spot c_of_g = 100

Use all spots found (about 108)

Do not refine cell but refine all other parameters using the default LSR method (defaults)

rms deviation should be reduced from about 0.425 mm to about 0.125 mm.

Do not re-run refinement immediately

Write output files (Nodal index 12; Yes, happy with refinement; root name for output files lys ; other replies are defaults)

The output log file can be compared with the example log file lys_gl.log.

INTLAUE TESTS

Prerequisites

Test 1: pf_intl.ctl (VMS: pf_intl.ctlvax), pf_intl.gen, pf_intl.geasc, [pf1a.dat, pf1b.dat]

Test 2: lys_intl.ctl (VMS: lys_intl.ctlvax), lys_intl.gen, lys_intl.geasc, [lys.i2 (lys_swap.i2)]

Test 1

Create the required .ge1/.ge2 files from the ascii file pf_intl.geasc. This will be done automatically if pf_intl.geasc is copied using the 'lget' command; otherwise use 'laue exchge' (gives pf_intl.ge1, pf_intl.ge2)

Run the program using the command 'laue intlaue'

DATA file is pf_intl.ctl (VMS: pf_intl.ctlvax )

Run in background (or batch) mode.

The output log file can be compared with the example log file pf_intl.log.

Test 2

Create the required .ge1/.ge2 files from the ascii file lys_intl.geasc This will be done automatically if lys_intl.geasc is copied using the 'lget' command; otherwise use 'laue exchge' (gives lys_intl.ge1, lys_intl.ge2)

Run the program using the command 'laue intlaue'

DATA file is lys_intl.ctl (VMS: lys_intl.ctlvax )

Run in background (or batch) mode.

The output log file can be compared with the example log file lys_intl.log.

INTLDM TESTS

Prerequisites

Test 1: lys_ildm.ctl (VMS: lys_ildm.ctlvax) [lys.i2 (lys_swap.i2)]

Test 1

Run the program using the command 'laue intldm'

DATA file is lys_ildm.ctl (VMS: lys_ildm.ctlvax )

Run in background (or batch) mode.

The output log file can be compared with the example log file lys_ildm.log.

AFSCALE TESTS

Prerequisites

Test 1: pf_af.geasc, pf_af.vc

Test 1

Create the required .ge1/.ge2 files from the ascii file pf_af.geasc This will be done automatically if pf_af.geasc is copied using the 'lget' command; otherwise use 'laue exchge' (gives pf_af.ge1, pf_af.ge2)

Run the program using the command 'laue afscale'

(Use default replies unless otherwise indicated)

(At various stages (usually after a terminal bleep) press the carriage return key to continue)

Root name of .gen file is pf_af

Use Ix sigma limit of 20

Use Iy sigma limit of 20

Select option L

Load option 3

Victoreen file pf_af.vc

Select option P

Select option S

Select option F

Select option P

Select option S

Select option O

Name for output file: pf_af.afout

Select option E

The output log file can be compared with the example log file pf_af.log.

LSCALE TESTS

Prerequisites

Test 1: lys_lsc.ctl, lys_lsc1.geasc, lys_lsc2.geasc, lys_lsc3.geasc, lys_lsc.mtzasc

Test 1

Create the required .ge1/.ge2 files from the ascii files lys_lsc1.geasc, lys_lsc2.geasc and lys_lsc3.geasc (to give lys_lsc1.ge1, lys_lsc1.ge2, lys_lsc2.ge1, lys_lsc2.ge2, lys_lsc3.ge1, lys_lsc3.ge2). This will be done automatically if the .geasc files are copied using the 'lget' command; otherwise use 'laue exchge' to convert the .geasc files. Create the required .mtz file from the ascii file lys_lsc.mtzasc. This will be done automatically if lys_lsc.mtzasc is copied using the 'lget' command; otherwise use 'laue na4tomtz' (to give lys_lsc.mtz)

Run the program using the command 'laue lscale' 

DATA: lys_lsc.ctl
Run in interactive or background mode.

The output log file can be compared with the example log file lys_lsc.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file lys_lsc.mtzout. A log file of such a dump with the first 100 reflections is available for comparison as lys_lsc.mtzd

LAUENORM TESTS

Prerequisites

Test 1: pf_ln.ctl, pf1_ln.afout, pf2_ln.afout, pf3_ln.afout

Test 2: lys_ln.ctl, lys_ln.geasc

Test 1

Run the program using the command 'laue lauenorm' 
DATA: pf_ln.ctl
LAUEHKL1: pf1_ln.afout
LAUEHKL2: pf2_ln.afout
LAUEHKL3: pf3_ln.afout
LAUEHKL4:
HKLOUT: pf_ln.mtz
HKLMULT (optional):
MULTDIAG (optional):
Run in background (or batch) mode.

The output log file can be compared with the example log file pf_ln.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file e.g. pf_ln.mtz. A log file of such a dump with the first 100 reflections is available for comparison as pf_ln.mtzd.

Test 2

Create the required .ge1 file from the ascii file lys_ln.geasc This will be done automatically if lys_ln.geasc is copied using the 'lget' command; otherwise use 'laue exchge' (gives lys_ln.ge1, lys_ln.ge2)

Run the program using the command 'laue lauenorm' 

DATA: lys_ln.ctl
LAUEHKL1: lys_ln.ge1
LAUEHKL2:
HKLOUT: lys_ln.mtz
HKLMULT (optional): lys_ln_mult.mtz
MULTDIAG (optional):
Run in background (or batch) mode.

The output log file can be compared with the example log file lys_ln.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file e.g. lys_ln.mtz. A log file of such a dump with the first 100 reflections is available for comparison as lys_ln.mtzd. Similarly for the deconvoluted multiples file e.g. lys_ln_mult.mtz, there is an example dump file lys_ln_mult.mtzd for comparison.

LAUESCALE TESTS

Prerequisites

Test 1: pf_ls.ctl, pf_ls.afout, pf_ls.mtzasc

Test 2: lys_ls.ctl, lys_ls.geasc, lys_ls.mtzasc

Test 1

Create the required .mtz file from the ascii file pf_ls.mtzasc. This will be done automatically if pf_ls.mtzasc is copied using the 'lget' command; otherwise use 'laue na4tomtz' (gives pf_ls.mtz)

Run the program using the command 'laue lauescale' 

DATA: pf_ls.ctl
LAUEHKL: pf_ls.afout
HKLIN: pf_ls.mtz
HKLOUT1: pf_lsout.mtz
HKLOUT2 (optional):
SHELX (optional):
DIAGNOSTICS FILE NAME (optional):
Run in background (or batch) mode.

The output log file can be compared with the example log file pf_ls.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file e.g. pf_lsout.mtz. A log file of such a dump with the first 100 reflections is available for comparison as pf_lsout.mtzd.

Test 2

Create the required .mtz file from the ascii file lys_ls.mtzasc. This will be done automatically if lys_ls.mtzasc is copied using the 'lget' command; otherwise use 'laue na4tomtz' (gives lys_ls.mtz)

Create the required .ge1 file from the ascii file lys_ls.geasc. This will be done automatically if lys_ls.geasc is copied using the 'lget' command; otherwise use 'laue exchge' (gives lys_ls.ge1, lys_ls.ge2)

Run the program using the command 'laue lauescale' 

DATA: lys_ls.ctl
LAUEHKL: lys_ls.ge1
HKLIN: lys_ls.mtz
HKLOUT1: lys_lsout.mtz
HKLOUT2 (optional):
SHELX (optional):
DIAGNOSTICS FILE NAME (optional):
Run in background (or batch) mode.

The output log file can be compared with the example log file lys_ls.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file e.g. lys_lsout.mtz. A log file of such a dump with the first 100 reflections is available for comparison as lys_lsout.mtzd.

DIFFLAUE TESTS

Prerequisites

Test 1: zn_dl.ctl, zn_dl.mtzasc, zn1_dl.geasc, zn2_dl.geasc

Test 1

Create the required .mtz file from the ascii file zn_dl.mtzasc. This will be done automatically if zn_dl.mtzasc is copied using the 'lget' command; otherwise use 'laue na4tomtz' (gives zn_dl.mtz)

Create the required .ge1 files from the ascii files zn1_dl.geasc and zn2_dl.geasc. This will be done automatically if zn1_dl.geasc and zn2_dl.geasc are copied using the 'lget' command; otherwise use 'laue exchge' (gives zn1_dl.ge1, (zn1_dl.ge2), zn2_dl.ge1, (zn2_dl.ge2))

Run the program using the command 'laue difflaue' 

DATA: zn_dl.ctl
LAUEGE1: zn1_dl.ge1
LAUEGE2: zn2_dl.ge1
HKLIN: zn_dl.mtz
HKLOUT: zn_dlout.mtz
Run in background (or batch) mode.

The output log file can be compared with the example log file zn_dl.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file e.g. zn_dlout.mtz. A log file of such a dump with the first 100 reflections is available for comparison as zn_dlout.mtzd.

LAUEDIFF TESTS

Prerequisites

Test 1: zn_ld.ctl, zn_ld.mtzasc, zn1_ld.afout, zn2_ld.afout

Test 1

Create the required .mtz file from the ascii file zn_ld.mtzasc. This will be done automatically if zn_ld.mtzasc is copied using the 'lget' command; otherwise use 'laue na4tomtz' (gives zn_ld.mtz)

Run the program using the command 'laue lauediff' 

DATA: zn_ld.ctl
LAUEHKL1: zn1_ld.afout
LAUEHKL2: zn2_ld.afout
HKLIN: zn_ld.mtz
HKLOUT: zn_ldout.mtz
Run in background (or batch) mode.

The output log file can be compared with the example log file zn_ld.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file e.g. zn_ldout.mtz. A log file of such a dump with the first 100 reflections is available for comparison as zn_ldout.mtzd.

UNSCRAM TESTS

Prerequisites

Test 1: pf_unsc.geasc, pf_unsc.vc

Test 1

Create the required .ge1/.ge2 files from the ascii file pf_unsc.geasc. This will be done automatically if pf_unsc.geasc is copied using the 'lget' command; otherwise use 'laue exchge' (gives pf_unsc.ge1, pf_unsc.ge2)

Run the program using the command 'laue unscram'

(Use default replies unless otherwise indicated)

Root name of .ge1/.ge2 file is pf_unsc

Load option 3

Victoreen file pf_unsc.vc

Output 10~ spots to the log file

Name for output file: pf_unsc.afout

Class of spot to output: all

The output log file can be compared with the example log file pf_unsc.log. Also the output reflection data file e.g. pf_unsc.afout can be compared with the given output file pf_unsc.afout

DECONV TESTS

Prerequisites

Test 1: zn_dc.ctl1, zn_dc.ctl2, zn_dc.ctl3, zn_dc.ctl4, zn_dc.ctl5, zn1_dc.geasc, zn2_dc.geasc, zn1_dc.vc, zn2_dc.vc, zn_dc.mtzasc

Test 1

Create the required .ge1/.ge2 files from the ascii files zn1_dc.geasc and zn2_dc.geasc. This will be done automatically if they are copied using the 'lget' command; otherwise use 'laue exchge' (gives zn1_dc.ge1, zn1_dc.ge2, zn2_dc.ge1, zn2_dc.ge2). Also create the required .mtz file from the ascii file zn_dc.mtzasc. This will be done automatically if zn_dc.mtzasc is copied using the 'lget' command but otherwsie use 'laue na4tomtz' (gives zn_dc.mtz).

Run the program sequence using the command 'laue deconv' 

Control Data for FFT: zn_dc.ctl1
Control Data for DECONV_MMOD: zn_dc.ctl2
Control Data for SFALL: zn_dc.ctl3
Control Data for DECONV_DCON: zn_dc.ctl4
Control Data for LAUENORM: zn_dc.ctl5
Singles Reflection Data: zn_dc.mtz
Root Name of Laue Data1: zn1_dc
Victoreen Coefficients File: zn1_dc.vc
Root Name of Laue Data2: zn2_dc
Victoreen Coefficients File: zn2_dc.vc
Root Name of Laue Data3:
Output Data (singles + multiples): zn_dcout.mtz
Run in background (or batch) mode.

The output log file can be compared with the example log file zn_dc.log.

If required, the program mtzdump can be used to dump the contents of the created MTZ file e.g. zn_dcout.mtz. A log file of such a dump with the first 100 reflections is available for comparison as zn_dcout.mtzd.

LCHK TESTS

Prerequisites

Test 1: pf_lchk.dat

Test 1

Run the program using the command 'laue lchk'

(Use default replies unless otherwise indicated)

Select option DATG

Name of input file is pf_lchk.dat

Select option LOG

Output to log file: ON

Select option ROTATE

Choose number of steps as 4 and step size as 20.0

Analyse the overlaps...

Row number 1

Row number 0 (to terminate the option)

Select option RESOL

Select option STOP

The output log file lchk.log can be compared with the example log file pf_lchk.log.

INTANAL TESTS

Prerequisites

Test 1: pf_ia.ctl, pf_ia.geasc

Test 1

Create the required .ge1 file from the ascii file pf_ia.geasc. This will be done automatically if pf_ia.geasc is copied using the 'lget' command; otherwise use 'laue exchge' (gives pf_ia.ge1, pf_ia.ge2)

Run the program using the command 'laue intanal' 

DATA: pf_ia.ctl
LAUEHKL: pf_ia.ge1
Run in background (or batch) mode.

The output log file can be compared with the example log file pf_ia.log.

SPOTIN TESTS

Prerequisites

Test 1: pf_sp.gen, [pf1a.dat]

Test 1

Run the program using the command 'laue spotin'

The input file is pf_sp.gen

Film file name is ./pf1a.dat (VMS: lfilm:pf1a.dat )

Do not replot an image

When image has been displayed, position cursor to beam centre position and hit the space bar to enter the position. Then position the cursor on each of say 6 nodal spots (suggest using spots indicated in Laue simulation postscript file pf_sp.ps)

Enter 'e' followed by carriage return to complete spot input.

Write spots to file pf_sp.out

This spot dump file may be compared with the example file given as pf_sp.dmp. The exact spot positions may differ slightly from those in the reference file because the exact cursor positions may vary on different runs of the program.


John W. Campbell
CCLRC Daresbury Laboratory
Last update 21 Jan 1999