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Tutorials and Examples

CRUNCH Direct Methods single crystal structure solution software by R. de Gelder and R.A.G. de Graaff

Installing and Running CRUNCH

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Tutorials page] [Crunch Page]

Download the various CRUNCH files (Crunchmake, Howto and crunch.tar.gz). CRUNCH - University of Nijmegen - R. de Gelder and R.A.G. de Graaff

This should give you the following files:


Type sh Crunchmake and when prompted give an appropriate amount of RAM depending on your system. It can be very bad to give Crunch more RAM than is physically available! In this case I have only given Crunch 48 Meg of RAM though it can be best to give Crunch 16 to 32 Meg less that the total amount of RAM on the system.
Automatic installation of Crunch and aditional utilities, version 1.1

Please provide the information requested as the installation proceeds

You are required to specify the maximum amount of memory you would
like to make available to the program.
Crunch needs a minimum of 16 Mb and will use a maximum of 512 Mb.
In general, more available memory will result in better performance
However, 128 Mb is usually adequate. Larger structures need more
Please give the amount of available ram now (in megabytes): 48

Crunch will then unpack the files and compile up the program.
Unpacking crunch.tar.gz now

Both autofour and deter will use a maximum of 48 million words

Standard optimization is -O3

Programs directory is: /web_disc/local/bin/crunch_1.1/programs
Sources  directory is: /web_disc/local/bin/crunch_1.1/source

Compile Utility Programs

Compile NORRED80
Compile Conhkl
Compile Contents
Compile Mat
Compile Crys
Compile Avrg
Compile Symt
Compile Pgrp
Compile Levy
Compile Eval
Compile Mkdetf
Compile Mkautf

Compile CRUNCH proper

Compile INIT
Compile THINKC
Compile DETER
f77 bkgen.f             -c -O3
f77 block.f             -c -O3
f77 blokop.f            -c -O3
f77 bloktel.f           -c -O3
f77 calce0.f            -c -O3
f77 cdin.f              -c -O3
f77 cell.f              -c -O3
f77 det1.f              -c -O3
f77 deter.f             -c -O3
f77 dump.f              -c -O3
f77 eentl2.f            -c -O3
f77 even.f              -c -O3
f77 exp1.f              -c -O3
f77 expa.f              -c -O3
f77 expa2.f             -c -O3
f77 fascom.f            -c -O3
f77 finhas.f            -c -O3
f77 getref.f            -c -O3
f77 hoofd.f             -c -O3
f77 infas.f             -c -O3
f77 inspec.f            -c -O3
f77 island.f            -c -O3
f77 jaap1.f             -c -O3
f77 leref.f             -c -O3
f77 lestr.f             -c -O3
f77 mains.f             -c -O3
f77 maintl.f            -c -O3
f77 matsor.f            -c -O3
f77 mattl2.f            -c -O3
f77 minma2.f            -c -O3
f77 mmtrx.f             -c -O3
f77 mxfill.f            -c -O3
f77 opdeta.f            -c -O3
f77 opdetb.f            -c -O3
f77 opdeti.f            -c -O3
f77 opinit.f            -c -O3
f77 opmatg.f            -c -O3
f77 opthas.f            -c -O3
f77 optima.f            -c -O3
f77 opwis.f             -c -O3
f77 pak.f               -c -O3
f77 plaats.f            -c -O3
f77 pricom.f            -c -O3
f77 prifas.f            -c -O3
f77 prihi.f             -c -O3
f77 prihkl.f            -c -O3
f77 prijpq.f            -c -O3
f77 prijzo.f            -c -O3
f77 prilo.f             -c -O3
f77 priref.f            -c -O3
f77 prmx2.f             -c -O3
f77 prstr.f             -c -O3
f77 pythag.f            -c -O3
f77 random.f            -c -O3
f77 reserv.f            -c -O3
f77 rest.f              -c -O3
f77 rijsort.f           -c -O3
f77 rotate.f            -c -O3
f77 rstrc.f             -c -O3
f77 safmat.f            -c -O3
f77 schar.f             -c -O3
f77 schuif.f            -c -O3
f77 singval.f           -c -O3
f77 sort.f              -c -O3
f77 stohas.f            -c -O3
f77 str1.f              -c -O3
f77 strace.f            -c -O3
f77 strsor.f            -c -O3
f77 strtfs.f            -c -O3
f77 svdrag.f            -c -O3
f77 swap.f              -c -O3
f77 swapal.f            -c -O3
f77 swapint.f           -c -O3
f77 swapsr.f            -c -O3
f77 sym.f               -c -O3
f77 teofas.f            -c -O3
f77 teofs.f             -c -O3
f77 tripel.f            -c -O3
f77 tsthas.f            -c -O3
f77 unpack.f            -c -O3
f77 unpk1.f             -c -O3
f77 val.f               -c -O3
f77 verba.f             -c -O3
f77 vulamx.f            -c -O3
f77 vuller.f            -c -O3
f77 wrfor.f             -c -O3
f77 wrfour.f            -c -O3
f77 zmla.f              -c -O3
f77 zmlc.f              -c -O3
f77 zpotr.for           -c -O3
             -o ../../programs/deter
ld32: INFO    136: In order to increase performance, the linker has decided to p
                 individual arrays within common block _BLNK__. Please see
                 -OPT:reorg_common in the fortran man pages for details.
Compile VEXFFT
Compile EXFFT80
Compile SEARCH80
f77 aantal.f            -c -O3
f77 afwkl.f             -c -O3
f77 algen.f             -c -O3
f77 atexp.f             -c -O3
f77 atomin.f            -c -O3
f77 autofour.f          -c -O3
f77 build.f             -c -O3
f77 cek.f               -c -O3
f77 centre.f            -c -O3
f77 centrm.f            -c -O3
f77 centro.f            -c -O3
f77 check.f             -c -O3
f77 cmplft.f            -c -O3
f77 coefft.f            -c -O3
f77 confft.f            -c -O3
f77 count.f             -c -O3
f77 daxpy.f             -c -O3
f77 ddot.f              -c -O3
f77 de2.f               -c -O3
f77 devine.f            -c -O3
f77 dffr.f              -c -O3
f77 diprp.f             -c -O3
f77 diverg.f            -c -O3
f77 dsifa.f             -c -O3
f77 dsisl.f             -c -O3
f77 dstnce.f            -c -O3
f77 dswap.f             -c -O3
f77 estmte.f            -c -O3
f77 eval.f              -c -O3
f77 even.f              -c -O3
f77 exfft.f             -c -O3
f77 fcalc.f             -c -O3
f77 fofofc.f            -c -O3
f77 fomfc.f             -c -O3
f77 frag.f              -c -O3
f77 gampr.f             -c -O3
f77 geom.f              -c -O3
f77 geom1.f             -c -O3
f77 geom2.f             -c -O3
f77 getatom.f           -c -O3
f77 getnum.f            -c -O3
f77 grid.f              -c -O3
f77 header.f            -c -O3
f77 heavy.f             -c -O3
f77 heavy2.f            -c -O3
f77 heavy3.f            -c -O3
f77 hermft.f            -c -O3
f77 idamax.f            -c -O3
f77 mains.f             -c -O3
f77 matinv.f            -c -O3
f77 mdftkd.f            -c -O3
f77 move.f              -c -O3
f77 mulref.f            -c -O3
f77 mult.f              -c -O3
f77 newatom.f           -c -O3
f77 orth.f              -c -O3
f77 output.f            -c -O3
f77 patt.f              -c -O3
f77 plaats.f            -c -O3
f77 pointr.f            -c -O3
f77 pp1.f               -c -O3
f77 prixyz.f            -c -O3
f77 prsnt.f             -c -O3
f77 prtst.f             -c -O3
f77 putbck.f            -c -O3
f77 putout.f            -c -O3
f77 r2cftk.f            -c -O3
f77 r3cftk.f            -c -O3
f77 r4cftk.f            -c -O3
f77 r5cftk.f            -c -O3
f77 random.f            -c -O3
f77 rdsect.f            -c -O3
f77 readhl.f            -c -O3
f77 readkl.f            -c -O3
f77 remove.f            -c -O3
f77 rfl2.f              -c -O3
f77 rflin.f             -c -O3
f77 rflin1.f            -c -O3
f77 rflsin.f            -c -O3
f77 rstrc.f             -c -O3
f77 savbes.f            -c -O3
f77 schar.f             -c -O3
f77 schft.f             -c -O3
f77 schft1.f            -c -O3
f77 seacon.f            -c -O3
f77 search.f            -c -O3
f77 select.f            -c -O3
f77 sim.f               -c -O3
f77 smlt.f              -c -O3
f77 solve.f             -c -O3
f77 sort.f              -c -O3
f77 sort1.f             -c -O3
f77 sort2.f             -c -O3
f77 sort3.f             -c -O3
f77 sort4.f             -c -O3
f77 sortf.f             -c -O3
f77 spesin.f            -c -O3
f77 srfp.f              -c -O3
f77 stab.f              -c -O3
f77 store.f             -c -O3
f77 strace.f            -c -O3
f77 symexp.f            -c -O3
f77 symext.f            -c -O3
f77 symtst.f            -c -O3
f77 unity.f             -c -O3
f77 upper.f             -c -O3
f77 val.f               -c -O3
f77 weed.f              -c -O3
f77 wlsn1.f             -c -O3
f77 wlsn2.f             -c -O3
f77 writey.f            -c -O3
f77  aantal.o             \
            afwkl.o              \
            algen.o              \
            atexp.o              \
            atomin.o             \
            autofour.o           \
            build.o              \
        cek.o                \
            centre.o             \
            centrm.o             \
            centro.o             \
            check.o              \
            cmplft.o             \
            coefft.o             \
            confft.o             \
            count.o              \
            daxpy.o              \
            ddot.o               \
            de2.o                \
            devine.o             \
            dffr.o               \
            diprp.o              \
            diverg.o             \
            dsifa.o              \
            dsisl.o              \
            dstnce.o             \
            dswap.o              \
            estmte.o             \
            eval.o               \
            even.o               \
            exfft.o              \
            fcalc.o              \
            fofofc.o             \
            fomfc.o              \
            frag.o               \
            gampr.o              \
            geom.o               \
            geom1.o              \
            geom2.o              \
            getatom.o            \
            getnum.o             \
            grid.o               \
            header.o             \
            heavy.o              \
            heavy2.o             \
            heavy3.o             \
            hermft.o             \
            idamax.o             \
            mains.o              \
            matinv.o             \
            mdftkd.o             \
            move.o               \
            mulref.o             \
            mult.o               \
            newatom.o            \
            orth.o               \
            output.o             \
            patt.o               \
            plaats.o             \
            pointr.o             \
            pp1.o                \
            prixyz.o             \
            prsnt.o              \
            prtst.o              \
            putbck.o             \
            putout.o             \
            r2cftk.o             \
            r3cftk.o             \
            r4cftk.o             \
            r5cftk.o             \
            random.o             \
            rdsect.o             \
            readhl.o             \
            readkl.o             \
            remove.o             \
            rfl2.o               \
            rflin.o              \
            rflin1.o             \
            rflsin.o             \
            rstrc.o              \
            savbes.o             \
            schar.o              \
            schft.o              \
            schft1.o             \
            seacon.o             \
            search.o             \
            select.o             \
            sim.o                \
            smlt.o               \
            solve.o              \
            sort.o               \
            sort1.o              \
            sort2.o              \
            sort3.o              \
            sort4.o              \
            sortf.o              \
            spesin.o             \
            srfp.o               \
            stab.o               \
            store.o              \
            strace.o             \
            symexp.o             \
            symext.o             \
            symtst.o             \
            unity.o              \
            upper.o              \
            val.o                \
            weed.o               \
            wlsn1.o              \
            wlsn2.o              \
            writey.o             \
              -o ../../programs/autofour
ld32: INFO    136: In order to increase performance, the linker has decided to p
                 individual arrays within common block _BLNK__. Please see
                 -OPT:reorg_common in the fortran man pages for details.

The installation is complete. The file crunch.tar.gz
may be removed
sv1 105#

(Remember: Crunch is trivial to use from within the Platon/System Suite based around Shelx style files (activated at the click of a single button). The complete System S install instructions are provided on the web.)

Enter the newly created crunch_1.0 subdirectory.

By default, CRUNCH runs in the background. You can change this behaviour and have run in the forground by editing the crunch script file and replacing p3=Background with p3=Foreground

Copying the crunch script to the /usr/local/bin directory will allow CRUNCH to be easily called.

Enter the newly created crunch_1.0/rn001 subdirectory.

You can clear up the unneeded files by typing ../crunch rn001 clear

xrdsv1 181% cd rn001
xrdsv1 182% ls
crunch.log    nohup.out     rn001.crysda  rn001.nrl     rn001.report
hits          output        rn001.crysin  rn001.par     rn001.spf
logfile       rn001.atoms   rn001.frefa   rn001.pdb
xrdsv1 183% ../crunch rn001 clear
xrdsv1 184% ls
rn001.crysin  rn001.frefa
xrdsv1 185%

The filename.crysin control file is quite simple to setup and the HKL data is in the filename.frefa file

CELL        10.64580   6.46230  13.52180  90.00000  95.21750  90.00000
CELLSD       0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
SPGR      P 21
FORMUL    C     21.00 H     28.00 O      3.00
Z                  2
WAVE      MO

To run CRUNCH on the test rn001 just type ../crunch rn001 try and select the Default option. (in the following case, Crunch has been setup to run in the forground)

Crunch interactive, always give return to choose defaults

The contents of the unit cell:
CELLCO C 42 H 56 O 6

The structure is an Equal_atom structure

[D]efault or [U]ser specified matrix construction?d
Mon Aug 16 22:23:26 BST 1999
Deter- Vexfft- Exfft- Search- Fragment- Autofour- end cycle  1  set  1
Structure SOLVED!
Final Search
Final Fragment

Check your structure
A full report can be found in /user2/lzc/crunch/crunch_1.0/rn001/rn001.report !

Refine /user2/lzc/crunch/crunch_1.0/rn001/rn001.spf now!

real    0m24.09s
user    0m6.78s
sys     0m2.49s
xrdsv1 188%

IF CRUNCH succeeds, you can then open up the PDB file in RASMOL or the SPF file in Ton Spek's Platon for checking.
  • rn001.pdb result file viewable in Roger Sayle's Rasmol
  • rn001.spf result file viewable in Ton Spek's Platon

  • Structure in RASMOL

  • Structure in Platon

Please note that Platon has a number of very powerful structure checking features including the ability to search for extra symmetry using ADDSYM and automatically create a Cambridge Structure Database QUEST query. (very useful for seeing if someone else has solved the structure and looking into related structures)

Platon - New Homepage - Ton Spek, Bijvoet Center - Utrecht University

Platon - Ton Spek

[Tutorials page] [Crunch Page]

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