In case you want to use WHAT IF without databases, make sure 60 Mbytes of disk space are available. 30 Mbytes will in this case be returned after the installation, and the experienced user can remove another 5 Mbytes or so.
WHAT IF requires 45 Mbytes of "virtual" memory on all machines. That means that the sum of the MegaBytes RAM accessible to you plus the part of the swap file accessible to you must at least be 45 Mbytes. (Although a much larger swap file is highly recommended, because that allows you to keep a WWW browser open, read your Email, etc., while at the same time running WHAT IF).
If you can run any of the commercial molecular modelling programs on your machine (e.g. Insight, Quanta or Sybyl) then you do not have to worry about any other system resources than disk space. A machine that can run any of those commercial programs can run WHAT IF for sure.
For example, on a PC with 8 Mbytes of memory you should install a swap file of at least 37 Mbytes (a bit more will not hurt of course). On a big SG workstation with 128 Mbytes memory in theory you don't even need a swap file if you want to run WHAT IF three times in parallel.
0) If this is the first time you use WHAT IF, go to point 2. 1) Make a GOOD backup of your present version. If your version has a file .../dbdata/MUTDB.IND, please remove EVERYTHING that is in the old version, because a number of files were moved since! Anyway, starting from an empty directory has other advantages, so you might want to consider throwing everything old away in any case. 2) Login as "whatif" (if needed create the account). Get the script "DO_INSTALL.SH" and put it in the "whatif" home directory (that is the directory where the file "DO_WHATIF.COM" and "whatif" are located [or otherwise will be after the installation]). 3) Check the disk space available. A full installation of WHAT IF including the standard databases will take about 150MB of disk space. During the installation you will need about 300MB of disk space. If you do not have this space, you MUST install WITHOUT the database: in that case 100MB is more than enough. You will be asked for this during point (4). See the manual to learn about the things you will be missing..... 4) Execute the script "DO_INSTALL.SH" by typing "sh DO_INSTALL.SH" from the "whatif" home directory. You will be prompted for a password. This password you can only get from me. It is forbidden to make this password available to others. This password stays valid for 7 days after you got it. 5) You will now see messages that files named *.cpio* are ftp-ed. If this takes more than 5 minutes per file, you better try again in the weekend, or at a time outside your and our (Central European) working hours. 6) Sometimes the automatic FTP really does not work on a machine (It hangs for hours after getting a number of files). If this is the case, you need to FTP the files manually. For this, type "ftp swift.embl-heidelberg.de", if it prompts you for a username, use "ftp", and if it asks you for a password, type your E-mail address. type "binary", and "prompt" and "cd private/<password>" where you substitute the password you got via E-mail for <password>. Now get the necessary packages using "mget": you will always need "general*", "source*" and "doc*", if you want the database as well, you need "ascdata*" and "predata*" too. With these files in the current directory, restart the "DO_INSTALL.SH" script and answer the questions. 7) After some time (2 minutes - 6 hours, depending on your hardware, and on how much of the database must be installed) you will have WHAT IF ready to go. Log off, log in as another user and type: .../whatif/DO_WHATIF.COM where .../whatif/ is the complete path to the location where WHAT IF was installed. In case something went wrong, you can read the installation notes and redo (parts of) the installation by hand. 8) If you need the space, the installation has gone smoothly and you have verified that WHAT IF runs correctly, the directory "predata" and all files in it can be removed, as well as all files *.o. If you are really short on space, you can remove *.f as well, but if you do that we cannot give you any help if you encounter specific problems later.
1) Create a user called 'whatif', and log in as 'whatif'. Make
sure you're working in an "empty" directry before you continue.
2) Put the tape in the tape unit.
3) Read the tape with the tar command.
You either type:
tar xv
or, on SGI systems with more than 1 tape drive:
tar xvf /dev/mt/tps0d* (where * is 1-7)
With newer versions of the IRIX operating systems and with other
computers you may need to "byte-swap" the archive. You can recognize
this situation by the fact that "tar" will tell you that "this is
not a tar archive". Please look for help in the manual pages for
"dd" (the "conv=swab" option), or on a SGI machine use the
/dev/mt/tps0d*ns device instead.
If you are prompted for a second tape, just give control-C and neglect
the request for a second tape. This is a bug in tar on some systems.
WHAT IF fits on one tape easily, there is NO second tape.
4) Check the disk space available. A full installation of WHAT IF
including the standard databases will take about 150MB of disk
space. During the installation you will need about 300MB of free disk
space. If you do not have this space, you must delete the database
files that are stored in the files "ascdata*" and "predata*"
before you proceed with the next point. In that case, however,
100MB is more than enough. See the manual about what you will be
missing.....
5) Type:
sh conf/DO_INSTALL.SH
This starts a rather elaborate script which will prompt you for the
information it can not easily obtain otherwise.
6) After some time (2 minutes - 6 hours, depending on your hardware
and what parts of the database need to be installed) you will have
WHAT IF ready to go. Log off, log in as another user and type:
".../whatif/DO_WHATIF.COM" where .../whatif/ is the complete path to
the location where WHAT IF got installed. In case something went
wrong, you can read the installation notes and redo (parts of) the
installation by hand.
PS: If at any time you need to restart the installation script,
answer "No" to the question "do we need to get the new version
via FTP".
You can install WHAT IF from the CD on most computers I have seen the last two years.
Make a completely EMPTY directory and cd to it.
Make sure the CD ROM is mounted and type sh /cdrom/CDINSTALL.SH
Answer the questions to the best of your intellectual limitations.
Be aware that the script will not install the WHAT IF database if there is less than 300MBytes of free diskspace. You can save some time by making sure that there is 300 Mbytes free diskspace if you install the entire package from the CD.
1) Put floppy 1 in the drive 2) Give the installation command as indicated on the sticky label on the floppy disk. 3) Do what the installation procedure tells you to do. Use defaults in all cases where you don't know what to do.
1) Backup your old version. 2) Remove the old version. 3) Create a WHAT IF root directory (e.g. c:\whatif ). If at all possible, call it exactly c:\whatif because that saves you some editing later. 4) In this WHAT IF root directory, insert the LAST floppy you received into your floppy drive (A: or B:) and type "A:PKUNZIP -d A:WHATIF" The "pkunzip" program will ask you to change floppies. 5) Go to the RUN directory 6) In the RUN directory you find several files called WHATIF.*** where *** is for example: BAT, FIG, or VMC One by one get these files in the editor and make sure that the directories in all the files in this directory are in agreement with the location where you stored WHAT IF. The easiest is if you installed WHAT IF in c:\whatif because in that case not a single directory path has to be changed. See the notes on WHATIF.FIG and DO_WHATIF.COM if the required changes seem non-trivial (they realy are trivial). 7) Learn how WHAT IF works. 8) Now comes the difficult part. In WHATIF.BAT you find the command SET WIFMODE=28. This number 28 is a magical number that has to be set in agreement with your graphics card. Good numbers to try are around 16 and around 26. The more you paid for the graphics card, the higher the number you can try, and the better the graphics will look. It might be that this process takes more than an hour of stupid trial and error, but it is worth it, because optimising this number means that you get the best possible graphics. Sorry for the extra work this causes. 9) At a later stage, look at the aspect ratio of the screen. It the molecules are too flat or to high, go to the dbdata directory and modify parameter 386 in the file PARAMS.FIG. This parameter is 100* the aspect ratio. That means that on a perfectly square tuned screen you need this parameter to be 100. Making it bigger makes the molecules flatter, making it smaller makes the molecules higher. Try with steps of 10%.
- SCATTER: a program to create scatter diagrams - TRANSFIG: a program to make postscript plotsYou might also want to have the following associated program:
- XFIG: facility for interactive creation of graphics for X-windowsThe packages needed to get these (free) programs running on your system can be found on our ftp site:
ftp://swift.embl-heidelberg.de/whatif/support/When you install them, make sure that the programs are in your PATH, such that WHAT IF can find them.
WHAT IF executes from a directory called the WHAT IF home directory. For now we will call this directory DIR. In practice it will often be something like /usr/people/whatif or /progs/whatif or something like that.
In this directory you need the files DO_WHATIF.COM (or whatif.bat and whatif.vmc under PCDOS) and WHATIF.FIG. These files are described below. You need several sub-directories in the DIR directory. The sub-directory DIR/dbdata is obligatory. In this DIR/dbdata directory you will find several files. The only one that a non-experienced WHAT IF manager should ever touch is CCONFI.FIG (although altering this file is not recommended). Another file that one can edit to make WHAT IF behave differently is PARAMS.FIG. However, editing this file can lead to non-functioning of (parts of) WHAT IF if done unintelligently.
To execute WHAT IF you have to run DO_WHATIF.COM this is best done via an alias in your .cshrc that looks like
alias whatif DIR/DO_WHATIF.COM
DO_WHATIF.COM will copy DIR/WHATIF.FIG to the local directory where you want to run WHAT IF. This file WHATIF.FIG tells WHAT IF what kind of computer it is running on, what sorts of graphics hardware are available, and where certain files are located.
#!/bin/sh
DIR=/usr2/people/vriend
umask 001
stty intr '^C'
[ -f WHATIF.FIG -a ! $DIR = `pwd` ] && /bin/rm WHATIF.FIG
[ ! $DIR = `pwd` ] || {
echo Please do not run WHAT IF in the whatif directory 1>&2
exit 1
}
/bin/cp $DIR/WHATIF.FIG WHATIF.FIG || {
echo Cannot copy WHATIF.FIG to current directory, sorry. 1>&2
exit 1
}
$DIR/whatif ${1+$@}
/bin/rm -f FOR0[2345][0-9].DAT TAPEIN.DAT TAPEOUT.DAT
/bin/rm -f AUTPLT.PLT CONNEC.DAT HATOMS.DAT PICK.IDX PLANES.DAT
/bin/rm -f RT37D.DAT TEXSTORE.DAT TEXTABLE.DAT ESP*.ESP
/bin/rm -f $DIR/dbdata/TIME.STAMP
/bin/rm -f WHATIF.FIG
The installation script (DO_INSTALL.SH) knows how to make this file on
the following platforms: SG (all types and hardware mixes), HP, IBM
RS6000 and similar machines running AIX, IBM PC (and clones) under
LINUX, DEC Ultrix stations, DEC alpha running OSF, SUN running SunOS
4.x or Slowlaris.
In summary: `DIR` is the same as DIR earlier in this chapter. The `umask` commands is needed to make my machine understand that WHAT IF is allowed to operate on its own files. The `stty` command allows me to break the program using control-C. The script than checks that you are not doing stupid things like running WHAT IF in its own directory, which could be fatal to the program... The `/bin/cp` command copies WHATIF.FIG to the local directory skipping any aliasses that might have been set on the cp command.
The '$DIR/whatif ${1+$@}` command finally starts the executable (which is called whatif, and sits in the directory DIR). In case of error messages with the magic `${1+$@}` in it, you can remove the `${1+$@}` from the '$DIR/whatif` line without much problems for WHAT IF.
The last five lines make sure that some of the most useless big files that WHAT IF normally generates are deleted after you stop the program in a friendly manner.
logdevnam=PS300A/phydevtyp=ETHERNET . 0 2 /usr2/people/vriend/dbdata/ YES DATABASE /usr2/people/vriend/qualty/ IN%VRIEND@EMBL-Heidelberg.DE IRIS IRIF FFTFFFFFFFFFFFTFFFFFOn other machines differences can be needed. The installation script (DO_INSTALL.SH) knows how to make this file on the following platforms: SG (all types and hardware mixes), HP, IBM RS6000 and similar machines running AIX, IBM PC (and clones) under LINUX, DEC Ultrix stations, DEC alpha running OSF, SUN running SunOS 4.x or Slowlaris.
The first three lines are an historical artefact from the days of the Evans and Sutherland PS300 machines. It seems likely that these three lines will one day be removed from WHATIF.FIG....
The fourth line should point at the DIR/dbdata directory (which is the dbdata subdirectory of the directory called DIR).
The fifth line should read `YES DATABASE` or `NO DATABASE` in agreement with you installing WHAT IF with or without database...
The sixth line is the location of the (rather large) quality control boxes. If you are not interested in predicting mutants, modelling by homology and structure verification, you don't need the quality control boxes at all. If you want to use them, then this line should hold the name of their directory, which normally should be DIR/qualty. However, you can put them at any other location, as long as you maintain the sub-directory structure in the `qualty` directory the same as it was upon installation.
The next two lines are historical artifacts. And are likely to be romoved from WHATIF.FIG one day soon.
The last line is important for SGI users only. This line holds the FLAGS that determine how WHAT IF looks at its hardware. The following can be done with these flags:
1) Should normally be FALSE
2) Should normally be FALSE, except for machines with DIALS
But we don't have dials, so we can't see when this starts failing....
3) Should always be TRUE
4) Switches on graphical debug output if set to TRUE
5) Switches WHAT IF into HELP mode if set to TRUE
6) Activates the personal menu if set to TRUE
7) Is needed on a few VERY old SG types only.
8) Experimental. Set to TRUE only if you are under 30 years old
9) Keep at FALSE
10) If set to TRUE WHAT IF can only run the DEMO option
11) Better keep at FALSE
12) Activates full screen stereo upon startup if TRUE (keep FALSE)
13) Keep at FALSE
14) Use full screen stereo if TRUE. Side by side if FALSE.
15) Can be set to TRUE for most 24 bit-plane SGI machines.
16) Set to TRUE on Indigo 1 with 1024x768 pixel screens.
17) Set to TRUE in case you have 'funny' lines in graphics mode.
18) Keep at FALSE.
19) Set to TRUE if you want cross-eye side-by-side stereo
20) and higher, better keep at FALSE.
Several combinations of FLAGS are not allowed. E.g., 16 can not
be combined with 14 or 15. 17 can not be combined with 14 or
15. 16 better is not combined with 8. 7 can not be combined
with 16, but works best if combined with 17.
For X11 versions of WHAT IF, all flags are FALSE except for the third one, which MUST be TRUE.
After you ran the script, you will need to execute make in a few directories. It will tell you exactly how when it finishes.
I repeat: this is an EXPERIMENTAL script in DIR/conf. Use at your own risk... Backup frequently...
/data/pdb/ %!PS-Adobe-2.0 lpr -Pfiery /data/hssp/ zip -f lpr -h -Pps17a /bin/wsh SHELL /usr/bin/xmgr Mosaic http://www.sander.embl-heidelberg.de/whatif/ ghostviewThe first line is the address of the PDB directory on your machine or cluster. Often this is a CD-player. If you do not have a centralised PDB directory, don't worry. If this line stays empty, WHAT IF will work just as well, but you will always have to type the entire path as part of the filename if a PDB file is not in the local directory.
The second line is the header line that your postscript plotter or laser writer expects in postscript files.
Line three is the local command needed to send a colour postscript file to the laser writer. If you allow your six year old son to play with WHAT IF, it might be cheaper to make this command point to a black and white printer....
Line four is the location of the hssp files on your machine or cluster. Most people will not need/have this. So don't worry if this line stays empty, or holds garbage.
Line five is the command to invoke the editor in a sub-process. The default is `vi`. If you use any other editor, make sure that you add the necessary flags to hold the calling program (i.e. WHAT IF) till the edit session is terminated. So do NOT use a self-backgrounding editor!!!
Line six is the command needed to submit a black and white postscript file to a laser writer or plotter.
Line 7 is the command needed to start a shell on your machine.
Line 8 is the command you want to use to start a shell. I express my deep admiration for the user frienlyness of UNIX by calling this command VMS....
GROMOS users can preview some of the output from the trajectory analysis module using the program `xmgr'. If you have this program installed, then line 9 should be the command needed to run it. Otherwise line 9 should stay empty.
Line 10 is the command to get to the HTML version of the WHAT IF writeup. You can get the HTML writeup from the anonymous FTP at our site if you want to make a local copy. Dont touch this line unless you have installed and tested your local copy of the writeup.
Line 11 is the program to be used for previewing PostScript files.
DIR (this is /usr/people/vriend in my case) 3ssp.f anaold.o hydro.f pdbcheck.f teach.f 3ssp.o anatra.f hydro.o pdbcheck.o teach.o ANATRA.INC anatra.o ini.f pdbout.f testsuite BACKUP.INC build.f ini.o pdbout.o tlsarr.f BIGINC.INC build.o iridem.f pirpsq.f tlsarr.o BOX.INC ccode iridem.o pirpsq.o tlsbyt.f CHARGE.INC cdbfil.f iridial.f planar.f tlsbyt.o CHESS.INC cdbfil.o iridial.o planar.o tlsfil.f CLUFAM.INC cell.f irigra.f plotit.f tlsfil.o CMPINC.INC cell.o irigra.o plotit.o tlsio.f CNTINC.INC chess.f iriini.f porno.f tlsio.o COMINC.INC chess.o iriini.o porno.o tlslog.f CONFAC.INC chesstls.f irinew.f povray.f tlslog.o CRDINC.INC chesstls.o irinew.o povray.o tlsmio.f CVS chiang.f iriobj.f prompt.f tlsmio.o D2DINC.INC chiang.o iriobj.o prompt.o tlsmvc.f DATBAS.INC chr.f iripick.f proton.f tlsmvc.o DGLOOP.INC chr.o iripick.o proton.o tlsn77.f DGMUT.INC clufam.f irisup.f pstnew.f tlsn77.o DIGITA.INC clufam.o irisup.o pstnew.o tlsort.f EAAINC.INC colour.f items.f pstplt.f tlsort.o ELECTR.INC colour.o items.o pstplt.o tlssts.f ELMINC.INC contac.f junior.f pucker.f tlssts.o EPSINC.INC contac.o junior.o pucker.o tlssup.f EQUFLD.INC dbdata klonk.f readonly.f tlssup.o ESPACE.INC debump.f klonk.o readonly.o tlstxt.f ETMINC.INC debump.o label.f refine.f tlstxt.o FDEVIC.INC depends label.o refine.o tools.f FGLINC.INC dgloop.f makdb.f result.val tools.o FRACTI.INC dgloop.o makdb.o rjread.f tragen.f GENINC.INC dgmut.f makpln.f rjread.o tragen.o GETMOL.INC dgmut.o makpln.o robmenu.f tramov.f GRPINC.INC diana.f map.f robmenu.o tramov.o HB2INC.INC diana.o map.o scan3d.f usegro HBONDS.INC difout.f mapcon.f scan3d.o usegro.f HGRINC.INC difout.o mapcon.o scan3e.f usegro.o HSPINC.INC digit.f mapp.f scan3e.o version.f HSTINC.INC digit.o mapp.o scan3s.f version.o INDCES.INC doself.f masmap.f scan3s.o walcor.f IRIGRA.INC doself.o masmap.o scnsdb.f walcor.o JUNIOR.INC drawat.f masmp2.f scnsdb.o walgra.f LABELS.INC drawat.o masmp2.o scripts walgra.o LANGUA.INC drug.f mcxalg.f search.f walhid.f MAPINC.INC drug.o mcxalg.o search.o walhid.o MCXINC.INC eaa.f mdf.f secstr.f walign.f MDFINC.INC eaa.o mdf.o secstr.o walign.o MOLITM.INC electr.f menus.f select.f walprf.f MR.c electr.o menus.o select.o walprf.o Makefile elemnt.f mkversion server.f walsdb.old NEURON.INC elemnt.o mol.f server.o walseq.f NQAINC.INC espace.f mol.o setvdw.f walseq.o OLDTXT.INC espace.o mol1.f setvdw.o walser.f OPTION.INC essdyn.f mol1.o shadbg.f walser.o OTHINC.INC essdyn.o mol2.f shadbg.o walsrt.f PDBINC.INC extra.f mol2.o shake.f walsrt.o PIRINC.INC extra.o mol3.f shake.o waltls.f QUALTY.INC genmen.f mol3.o spcial.f waltls.o REFINC.INC genmen.o mol4.f spcial.o water.f RESULT.INC getiets.f mol4.o spcian.f water.o SCTINC.INC getiets.o mol5.f spcian.o wdgeom.f SEARCH.INC getline mol5.o spctls.f whatif SELECT.INC gradb.f mol6.f spctls.o wifgen.f SPCIAL.INC gradb.o mol6.o strand.f wifgen.o STKVLD.INC graext.f neibrs.f strand.o wifsp2.f SUPPOS.INC graext.o neibrs.o support.c wifsp2.o SYMANA.INC grafic.f neural.f support.o wifsp3.f SYMDAT.INC grafic.o neural.o suppos.f wifsp3.o SYMINC.INC gratls.f neutls.f suppos.o wifsp4.f TABLES.INC gratls.o neutls.o supps2.f wifsp4.o TEACH.INC gratwo.f newqua.f supps2.o wifsup.f TODO gratwo.o newqua.o sym.f wifsup.o TRANSL.INC grids.f nmr.f sym.o wiftxt.f VECTOR.INC grids.o nmr.o symcon.f wiftxt.o WALIGN.INC gromac.f notes.f symcon.o wregro.f WALSER.INC gromac.o notes.o symrea.f wregro.o WDGEOM.INC group.f oldqua.f symrea.o writeup aamain.f group.o oldqua.o symrep.f xray.f aamain.o hbond2.f ostools.f symrep.o xray.o access.f hbond2.o ostools.o symtls.f xtc access.o hbonds.f other.f symtls.o ahead.f hbonds.o other.o tables.f ahead.o hssp.f params.f tables.o anaold.f hssp.o params.o tcl DIR/ascdata: ALLACC.ACC ALLHYD.HYD BBCDAT.DAT CHI004.CHI MUTDB.IND ALLCYS.CYS ALLOME.GAS CHI001.CHI CHI005.CHI SYMMAT.MAT ALLDSP.DSP ALLPHI.PHI CHI002.CHI HBONDS.HBO TOTALS.SEQ ALLHST.HST ALLPSI.PSI CHI003.CHI IMPROPER.DAT DIR/bindata: ALCONT.ACT ALCOOR.XYZ ALLNEA.DIS CACA.NEW PROFIL.SEQ ALCONT.WHT ALHASH.CON ALLNUM.NAM CONSER.HSP DIR/ccode: CVS DevAscii.h DevObject.h Matrix1.c X11Graph.h Check.h DevColl.c DevPort.c Matrix1.h emul.h CmdStore.c DevColl.h DevPort.h MiscEmul.c sys.h CmdStore.h DevEmul.c Device.c MiscEmul.h whatif.xbm DFunc.h DevEmul.h Device.h Param.c xdummy.c Dev2d.c DevError.c GraphFunc.c Param.h xemul.c Dev2d.h DevError.h GraphFunc.h Port.c xemul.h Dev3d.c DevMatrix.c Graphics.c Port.h xport.c Dev3d.h DevMatrix.h Graphics.h Trans xport.h Dev3df.c DevNoop.c Makefile Win2d.c Dev3df.h DevNoop.h Matrix.c Win2d.h DevAscii.c DevObject.c Matrix.h X11Graph.c DIR/connolly: (only if you buy this) PQMS.EXE pqmsh.c.Z srfb.c.Z trba.c.Z TRB.EXE pqmsi.c.Z srfc.c.Z trbb.c.Z convert pqmsm.c.Z srff.c.Z trbf.c.Z convert.f pqmsn.c.Z srfh.c.Z trbh.c.Z makefile pqmso.c.Z srfi.c.Z trbi.c.Z makefilesave pqmsr.c.Z srfl.c.Z trbm.c.Z msp.h.Z pqmss.c.Z srfm.c.Z trbn.c.Z mspmath.c.Z pqmsu.c.Z srfn.c.Z trbo.c.Z mspmem.c.Z pqmsv.c.Z srfo.c.Z trbp.c.Z pqms res_acc srfr.c.Z trbs.c.Z pqms.h.Z res_acc.f srft.c.Z trbu.c.Z pqmsa.c.Z srf srfu.c.Z trbv.c.Z pqmsc.c.Z srf.h.Z trb trby.c.Z pqmsg.c.Z srfa.c.Z trb.h.Z DIR/dbdata: 7TM.FILES GRO.H QUALITY.LUP TOPOLOGY.FIL ARBPOS.POS HBOFIELD.DAT RAMA.LIN TRAILER.TEX BASE.PRS HEADER.TEX RCONFI.FIG TRAILER.TXT BLOSUM.MAT HEADER.TXT SCATTER.DAT TRAIN.NEU CCONFI.FIG ICONFI.FIG SCATTER.SCC XBFACT.DAT CHEBY.DAT INOUTF.DAT SCRIPT.TST XCALIB.DAT COMMANDS.NEW MESSAGES.TXT SEQCOL.FIL chappg.sty COMMANDS.PCT MOUSE.FIG SGRDAT.DAT getpdbfile DAYHOF.MAT MOUSE_DEF.FIG SHALIM.LIM glossary.txt DNA.BRK MOUSE_TWO.FIG SHORT.PRS header.pov DOCHEAD.TEX MY_MENU.DAT SPCSYM.DAT new.seq DUMMY.HED PAIRS.TXT TEST.NEU old.seq EVAACC.ACC PARAMS.FIG TEXSTORE.DAT supertab.sty EVACHI.CHI PDBFIND.TXT TEXTABLE.DAT DIR/demo: FILE.PDB RHINO.PDB digit DIR/dgeom: (only if you buy this) CONECT.CARDS dgeom example.cnt DIR/dssp: (only if you buy this) DSP.X README dssp.c dssp.p2c p2c.h DSSP.EXE dssp dssp.ins dssp.shar p2clib.c DSSP.OK dssp..c dssp.man dssp.undec p2crc Makefile dssp.astra dssp.p p2c.awk DIR/flexx: (only if you buy this) CONFIG.DAT bsp moletopi static_data zerlege bin flexx sca whatif DIR/getline: CHANGES Makefile getline.3 getline.h testgl.c wifconn.o CVS README getline.c getline.o wifconn.c DIR/grid: (only if you buy this) GRID.EXE GRIN.EXE PROBES.PRO quick.start.Z GRID.PAS GRUB.DAT begin.here.Z user.txt.Z DIR/helpfil: 3SSP.INF DIGIT.INF GRATWO.INF NEURAL.INF SEQ3D.INF ACCESS.INF DOSELF.INF GRID.INF NMR.INF SETVDW.INF ANATRA.INF DRUG.INF GROMOS.INF NOTES.INF SOUP.INF BUILD.INF DSSP.INF HBONDS.INF PIRPSQ.INF SUPPOS.INF CHECK.INF ELECTR.INF HSSP.INF PLOTIT.INF SYMTRY.INF CHIANG.INF ESSDYN.INF HYDRO.INF PORNO.INF TABLES.INF CHKMDF.INF EXTRA.INF ITMADM.INF QUALTY.INF TEACH.INF COLOUR.INF FAMCLU.INF LABEL.INF REFINE.INF WALIGN.INF CONOLY.INF GENERA.INF MAP.INF SCAN3D.INF WATER.INF CONTAC.INF GRAEXT.INF MAPEDT.INF SEARCH.INF XRAY.INF DGLOOP.INF GRAFIC.INF MASMAP.INF SELECT.INF DIR/nqual NQABOX.DAT NQAPTR.TXT NQUAL.DAT NQANOR.WAT NQASTR.WAT NQUAV.DAT DIR/pluton: (only if you buy this) bdftops gs gsdj gslp pluton font2c gsbj gslj gsnd DIR/poth2o: FKALAVS.DAT FKCYSVS.DAT FKHISVS.DAT FKMETVS.DAT FKTHRVS.DAT FKARGVS.DAT FKGLNVS.DAT FKILEVS.DAT FKPHEVS.DAT FKTRPVS.DAT FKASNVS.DAT FKGLUVS.DAT FKLEUVS.DAT FKPROVS.DAT FKTYRVS.DAT FKASPVS.DAT FKGLYVS.DAT FKLYSVS.DAT FKSERVS.DAT FKVALVS.DAT DIR/predata: ALCOOR.FMT.Z CONSER.FMT.Z STARTUP.FIL helix ALLNUM.FMT.Z PROFIL.FMT.Z WHATIF.FIG rest DIR/qualty: helix rest DIR/ribbons: (only if you buy this) analysis data fithx misc ps src bin doc install ms showcase utils DIR/sobolev: (only if you buy this) LIGIN.EXE DIR/teach: 1ABE.BRK.Z AA0201.Z BB0104.Z HIVPA.SEQ 1AT1.BRK.Z AA0202.Z BB0105.Z HIVPB.BRK.Z 1CDL.BRK.Z AA0203.Z BB0106.Z HIVPB.SEQ 1ENT.BRK.Z AA0204.Z BB0107.Z HLA.BRK.Z 1ERA.BRK.Z AA0205.Z BB0108.Z HLAMAP.WMP.Z 1INV.BRK.Z AA0206.Z BB0200.Z HYPOTHASE.BRK.Z 1PNC.BRK.Z AA0207.Z BB0201.Z INDEX.Z 1PPK.BRK.Z AA0301.Z BB0202.Z SHHB.BRK.Z 2APR.BRK.Z AA0302.Z BB0203.Z SHOALL.SCR.Z 2MHR.BRK.Z AA0303.Z BB0204.Z SHOHBO.SCR.Z 2RSP.BRK.Z AA0304.Z BB0205.Z SHOHST.SCR 4FXN.BRK.Z AA0305.Z BB0206.Z SHOSPC.SCR.Z 9HVP.BRK.Z AA0306.Z BB0207.Z SUPPOS1.BRK.Z AA0001.Z AA0307.Z BB0301.Z SUPPOS2.BRK.Z AA0002.Z AA0308.Z BB0302.Z SUPPOS3.BRK.Z AA0003.Z AA0309.Z BB0303.Z SUPPOS4.BRK.Z AA0004.Z AA0310.Z BETA1.BRK.Z SUPPOS5.BRK.Z AA0005.Z AA0401.Z BETA2.BRK.Z SUPPOS6.BRK.Z AA0006.Z AA0402.Z BRD.BRK.Z SUPPOS7.BRK.Z AA0007.Z AA20.BRK.Z COLATM.SCR.Z TEACH.OK.Z AA0008.Z ALPHA.BRK.Z COLHST.SCR.Z TIM.BRK.Z AA0009.Z BB0000.Z CORRECT.SCR.Z TIMA.BRK.Z AA0010.Z BB0101.Z GRAACC.SCR.Z AA0101.Z BB0102.Z HIVP.BRK.Z AA0102.Z BB0103.Z HIVPA.BRK.Z DIR/tutorial: 1CRN.PDB.Z PUDDING.PDB.Z STARTUP.FIL.Z TEST.NEU.Z 1crn.made.Z SCRIPT.BLD.Z TABLES.BIG.Z TRAIN.NEU.Z 2CRN.PDB.Z SCRIPT.BUILD.Z TABLES.TAB.Z WHATIF.FIG.Z 3hla.brk.Z SCRIPT.HOM.Z TEACH.1.Z align.mls.Z BRD.BRK.Z SELECT.BIG.Z TEACH.2.Z bad.model.Z COLATM.Z SHHB.PDB.Z TEACH.3.Z errors.pdb.Z COLHST.Z SHOALL.Z TEACH.4.Z new.seq.Z GRAACC.Z SHOHBO.Z TEACH.5.Z old.seq.Z HLA.PDB.Z SHOSPC.Z TEACH.6.Z HYPOTHASE.BRK.Z START.WHATIF TEACH.7.Z DIR/usegro: (this part of GROMOS everybody gets) 1HB.SCP DST.SCP PUT-MD.EXE get-md.f 1HB.SCR DST.SCR PUTBOX.EXE getbox.f 1PP.SCP FLC.SCP PUTGCH.EXE getgch.f 1PP.SCR FLC.SCR PUTGM2.EXE getgmt.f ACC.SCP GET-EM.EXE PUTGMT.EXE getgwh.f ACC.SCR GET-MD.EXE PUTGWH.EXE getion.f ANG.SCP GETBOX.EXE PUTION.EXE params.f ANG.SCR GETGCH.EXE RMS.SCP put-em.f CCF.SCP GETGM2.EXE RMS.SCR put-md.f CCF.SCR GETGMT.EXE TRAGEO.EXE putbox.f CFL.SCP GETGWH.EXE TRS.SCP putgch.f CFL.SCR GETION.EXE TRS.SCR putgmt.f CMP.SCP GYR.SCP VAL.SCP putgwh.f CMP.SCR GYR.SCR VAL.SCR pution.f COR.SCP HBO.SCP WEDEI2.EXE trageo.f COR.SCR HBO.SCR WEDEIG.EXE wedei2.f CUM.SCP HST.SCP WEDMAS.DAT wedei2.o CUM.SCR HST.SCR WEDPRJ.EXE wedeig.f CVS Makefile WEDTRA.EXE wedeig.o DAVADRUG.EXE Makefile.alpha bsup.f wedprj.f DAVADRUG.TOP Makefile.shit bsup.o wedprj.o DIH.SCP Makefile.swift davadrug.f wedtra.f DIH.SCR PRJ.SCP eigen1.f wedtra.o DIS.SCP PRJ.SCR eigen1.o DIR/wregro: (only if you buy this) IFP37C4.DAT PROCMTL.EXE PROMDL.EXE SPC216.DAT IFP37C4.DAT_BB PROEML.EXE PROMMTL.EXE main IFP37D4.DAT PROGCHL.EXE RT37C.DAT sub IFP37D4.DAT_BB PROGMTL.EXE RT37C.DAT_BB Makefile PROGWHL.EXE RT37D.DAT PROBOXL.EXE PROIONL.EXE RT37D.DAT_BB DIR/writeup: CVS chap18.rno chap36.rno chap60.rno chap94.rno chap01.rno chap19.rno chap37.rno chap71.rno chap95.rno chap02.rno chap20.rno chap38.rno chap72.rno chap96.rno chap03.rno chap21.rno chap40.rno chap73.rno chap97.rno chap04.rno chap22.rno chap41.rno chap74.rno chap98.rno chap05.rno chap23.rno chap42.rno chap75.rno chap99.rno chap06.rno chap24.rno chap43.rno chap78.rno manual.aux chap07.rno chap25.rno chap44.rno chap79.rno manual.dvi chap08.rno chap26.rno chap45.rno chap80.rno manual.idx chap09.rno chap27.rno chap46.rno chap81.rno manual.ilg chap10.rno chap28.rno chap51.rno chap82.rno manual.ind chap11.rno chap29.rno chap52.rno chap83.rno manual.log chap12.rno chap30.rno chap53.rno chap84.rno manual.ps chap13.rno chap31.rno chap54.rno chap85.rno manual.tex chap14.rno chap32.rno chap55.rno chap88.rno manual.toc chap15.rno chap33.rno chap56.rno chap90.rno manual2.ps chap16.rno chap34.rno chap57.rno chap91.rno tex.digit chap17.rno chap35.rno chap58.rno chap92.rno tex.listThe directories labelled with "(only if you buy this)" normally are not redistributed by us. See the WWW pages about what we redistribute and what not.
If you want to reduce disk space ocupied by WHAT IF, do the following first:
1) Check that WHAT IF works.
2) Make a good backup.
After that, you can throw away ALL *.o, *.f, *.INC, *.c, *.h files in all directories. You can throw away the entire predata directory.
Make sure that there are no files called ALCONT.* in any directory. These are VERY big, used by only two options, and can easily be reconstructed (with the PRP011 option in the SEQ3D menu).
Many people do not need the `quality control boxes` very often. These are stored in subdirectories of the DIR/qualty directory. You can compress all these files. (They are used in verification and modelling).
You can remove the tutorial and the teach directories, that wont cripple WHAT IF, but these directories have their advantages, especially if you are a WHAT IF novice.
If that does not help, you can throw away some of the less frequently used database files: ALLNEA.DIS, CONSER.HSP and PROFIL.SEQ.
If that still does not help, you will have to work without databases. Throw away the directories DIR/ascdata, DIR/bindata, DIR/qualty, DIR/nqual and DIR/predata. You could additionally decide to delete CHEBY.DAT and PDBFIND.TXT from DIR/dbdata. CHEBY.DAT is only used to draw smooth ribbons. The PDBFIND.TXT file is also accessible over the World Wide Web using SRS.
In case of problems, if the FAQ does not help contact:
Vriend@EMBL-Heidelberg.DE
If you tell me that you saw this line in the writeup I normally respond faster!
Good luck Rob Hooft, Gert Vriend.