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 on all machines 45 Mbytes of memory. That means that the sum of the mega bytes RAM accessible to you plus the part of the swap file accessible to you must at least be 40 Mbytes.
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 you don't even need a swap file if you want to run WHAT IF three times in parallel.
The tape is written with the tar command. Just use tar to read it. The command:
tar -xv
tar -xvf /dev/mt/tps0d* (* is SCSI address of tape)
should do it. Ask a local computer user with 'tape-experience' or the local system people if you have trouble reading the tape. There is no need asking us about this, because we normally can not help with tape reading problems.
If your machine tells you that the tape is bad, try byte-swapping it (use 'man dd' and look for 'conv=swab'). Try for example something like:
dd if=/dev/tape bs=10k conv=swab | tar xvf -
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 about what 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 get messages that files named *.cpio* got 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 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 got 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 *.f and *.o.
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".
To run WHAT IF under Linux you need:
- About 43MB of memory+swap to be able to actually use the program. On an otherwise empty machine, 4MB of real memory is "sufficient" to run WHAT IF, 8MB is needed to work with the less memory intensive options of WHAT IF, but 16MB is definitely more comfortable. - Installed versions of numerous normal unix utilities, gnu zip, cpio and the libf2c and XFree86 packages. You also need f2c, and the gnu C compiler installed, such that you can recompile WHAT IF yourself. The f2c version MUST be newer than January 1994. If not, please get a newer version (e.g. by anonymous ftp from sunsite.unc.edu). The New GNU Fortran program can NOT be used to compile WHAT IF yet. We're waiting for new features in version 0.6!Recompiling takes approximately 75 minutes on a 486/33 with a reasonably fast hard disk. Recreating the database can add significant time (2 hours) at the end...
Follow the instructions above to install WHAT IF on your system
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.
- 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 in the "/whatif/support" subdirectory of our "swift.embl-heidelberg.de" ftp site. 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). Other files that one can edit to make WHAT IF behave differently are ICONFI.FIG and RCONFI.FIG. However, editing these files can lead to non-functioning 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 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
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 take that part of the '$DIR/whatif` line without much problems for WHAT IF.
The last three 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. If you get out with control-C WHAT IF punishes you by leaving these files in your project directory.
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.
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 artefacts.
The last line is important for SG 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 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/The 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 or 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.
-1 : 1) Initial atom colours.
1 : 2) Colour of help text in pop up help boxes.
7 : 3) Colour of top/identifier bar.
1 : 4) Colour of top/identifier text.
5 : 5) Colour of toptxt (right top of screen messages).
40 : 6) Shift (in pixels) of default X coords of text window.
10 : 7) Shift (in pixels) of default Y coords of text window.
1 : 8) Colour of bottom of screen button text
1 : 9) ZFUNCT parameter (operating system dependent)
30 : 10) Degrees error in phi and psi allowed in DG* options
0 : 11) Cycles of optimization in modeling by homology
1 : 12) Internal debugging level (0 is production mode)
0 : 13) Reserved
1 : 14) First amino acid in topology file
23 : 15) Last amino acid in topology file
24 : 16) First nucleotide in topology file
27 : 17) Last nucleotide in topology file
1 : 18) Colour of the text in the status box
290 : 19) WHAT IF colour of N-C=O part of peptide plane
310 : 20) WHAT IF colour of H-N-C part of peptide plane
0 : 21) 21-24: X-low, H-high, Y-low, Y-high of the graphics port
1279 : 22) in pixels. Unless you know what you are doing, you should
0 : 23) keep these four values at 0 (zero). On the IBM-PC they need
1023 : 24) to be set. See the installation notes. (org. 0,1279,0,1023)
0 : 25) 25-28: As 21-24, but now for the inner window, the one
1105 : 26) in which the coordinates are written. If no menu updates
65 : 27) are needed, then redrawing the inner window alone is enough,
1000 : 28) unless there is an active pull-down menu.
0 : 29) if not zero use the attached groups
13 : 30) Maximal length of groups to be used in DGLOOP options
230 : 31) A The configuration values 31-50 are reserved
180 : 32) C for the COLSPC colours of the first 20
120 : 33) D residues in the TOPOLOGY file.
120 : 34) E
240 : 35) F
230 : 36) G
30 : 37) H
240 : 38) I
30 : 39) K
250 : 40) L
180 : 41) M
70 : 42) N
230 : 43) P
70 : 44) Q
30 : 45) R
300 : 46) S
300 : 47) T
240 : 48) V
240 : 49) W
300 : 50) Y
1 : 51) colour index of pick labels (15=white)
: 52)
The only two parameters that are critical are 12 and 29. Parameter 12
should be 0, unless you are looking for a bug somewhere in which case
putting it at 1 will tell WHAT IF to debug itself (by crashing instead
of recovering). Parameter 29 should normally be 0, but if you want to
run WHAT IF with "attached groups", this flag should be 1.
0.5 : 1 Weight on backbone fit in homology building
1.0 : 2 Weight on rotamer density in homology building
1.0 : 3 Weight on quality control in homology building
4.0 : 4 Weight on bumps in homology building
0.2 : 5 Weight on phi-psi misfit in homology modeling
4.3 : 6 H-bond MC cutoff
: 7 Reserved
: 8 Reserved
20.0 : 9 Initial slab value
: 10 Reserved
: 11 Reserved
2.0 : 12 Weight on hydrogen bonds in homology building
As you really should not use these, I will not explain what they do.
DIR (this is /usr/people/vriend in my case) 3ssp.f gradb.o rjread.o 3ssp.o graext.f robmenu.f ANATRA.INC graext.o robmenu.o BIGINC.INC grafic.f scan3d.f BOX.INC grafic.o scan3d.o CHESS.INC gratls.f scan3e.f CLUFAM.INC gratls.o scan3e.o CMPINC.INC gratwo.f scan3s.f CNTINC.INC gratwo.o scan3s.o COMINC.INC grids.f scnsdb.f CONFAC.INC grids.o scnsdb.o DATBAS.INC group.f search.f DGLOOP.INC group.o search.o DGMUT.INC hbond2.f secstr.f DO_WHATIF.COM hbond2.o secstr.o EAAINC.INC hbonds.f select.f ELMDAT.INC hbonds.o select.o ELMINC.INC hssp.f server.f EPSINC.INC hssp.o server.o EQUFLD.INC hydro.f setvdw.f ESPACE.INC hydro.o setvdw.o ETMINC.INC i.i spcchk.sh FDEVIC.INC ini.f spcial.f FGLINC.INC ini.o spcial.o FRACTI.INC iridem.f spcian.f HB2INC.INC iridem.o spcian.o HBONDS.INC iridial.f spctls.f HGRINC.INC iridial.o spctls.o HSPINC.INC irigra.f strand.f HSTINC.INC irigra.o strand.o INDCES.INC iriini.f support.c IRIGRA.INC iriini.o support.o JUNIOR.INC irinew.f suppos.f LABELS.INC irinew.o suppos.o MAPINC.INC iriobj.f supps2.f MCXINC.INC iriobj.o supps2.o MDFINC.INC iripick.f sym.f MOLITM.INC iripick.o sym.o MR irisup.f symcon.f MR.c irisup.o symcon.o MUTDAT.INC items.f symrea.f Makefile items.o symrea.o NEURON.INC junior.f symrep.f NQAINC.INC junior.o symrep.o OLDTXT.INC label.f symtls.f OPTION.INC label.o symtls.o PDBINC.INC makdb.f system.o PIRINC.INC makdb.o tables.f QUALTY.INC map.f tables.o REFINC.INC map.o teach.f RESULT.INC mapcon.f teach.o SEARCH.INC mapcon.o tlsarr.f SELECT.INC mapfls.f tlsarr.o SPCIAL.INC mapfls.o tlsbyt.f STKVLD.INC mapp.f tlsbyt.o SUPPOS.INC mapp.o tlsfil.f SYMANA.INC masmap.f tlsfil.o SYMDAT.INC masmap.o tlsio.f SYMINC.INC mcxalg.f tlsio.o TABLES.INC mcxalg.o tlslog.f VECTOR.INC mdf.f tlslog.o WALIGN.INC mdf.o tlsmio.f WHATIF.FIG menus.f tlsmio.o aamain.f menus.o tlsmvc.f aamain.o mol.f tlsmvc.o access.f mol.o tlsn77.f access.o mol1.f tlsn77.o anatra.f mol1.o tlsort.f anatra.o mol2.f tlsort.o build.f mol2.o tlssts.f build.o mol3.f tlssts.o cdbfil.f mol3.o tlssup.f cdbfil.o mol4.f tlssup.o cell.f mol4.o tlstxt.f cell.o mol5.f tlstxt.o chess.f mol5.o tools.f chess.o mol6.f tools.o chesstls.f mol6.o tragra.f chesstls.o neibrs.f tragra.o chiang.f neibrs.o usegro.f chiang.o neural.f usegro.o chr.f neural.o vaxmap.f chr.o neutls.f vaxmap.o clufam.f neutls.o walcor.f clufam.o newqua.f walcor.o colour.f newqua.o walgra.f colour.o nmr.f walgra.o contac.f nmr.o walhid.f contac.o notes.f walhid.o david.txt notes.o walign.f debump.f oldqua.f walign.o debump.o oldqua.o walprf.f depends ostools.f walprf.o dgloop.f ostools.o walsdb.f dgloop.o params.f walsdb.o dgmut.f params.o walseq.f dgmut.o pcdummy.f walseq.o diana.f pdbcheck.f walsrt.f diana.o pdbcheck.o walsrt.o difout.f pdbout.f waltls.f difout.o pdbout.o waltls.o doself.f pirpsq.f water.f doself.o pirpsq.o water.o drug.f plotit.f whatif drug.o plotit.o wifgen.f eaa.f porno.f wifgen.o eaa.o porno.o wifsp2.f elemnt.f process.o wifsp2.o elemnt.o prompt.f wifsp3.f espace.f prompt.o wifsp3.o espace.o pstnew.f wifsup.f essdyn.f pstnew.o wifsup.o essdyn.o pstplt.f wiftxt.f extra.f pstplt.o wiftxt.o extra.o quaprp.f wregro.f f77_cpp readonly.f wregro.o f77_f2c readonly.o x.x f77_oldf2c refine.f xray.f files.val refine.o xray.o flex_control.o result.val y.y gradb.f rjread.f DIR/ascdata: ALLACC.ACC ALLHYD.HYD CHI001.CHI CHI005.CHI NQAPTR.TXT ALLCYS.CYS ALLOME.GAS CHI002.CHI HBONDS.HBO NQASTR.DAT ALLDSP.DSP ALLPHI.PHI CHI003.CHI MUTDB.IND TOTALS.SEQ ALLHST.HST ALLPSI.PSI CHI004.CHI NQANOR.DAT DIR/bindata: ALCONT.ACT ALDRUG.XYZ ALLNUM.NAM NQABOX.DAT ALCONT.WHT ALHASH.CON CACA.NEW PROFIL.SEQ ALCOOR.XYZ ALLNEA.DIS CONSER.HSP DIR/ccode: Check.h DevEmul.c GraphFunc.c Port.h CmdStore.c DevEmul.h GraphFunc.h Win2d.c CmdStore.h DevError.c Graphics.c Win2d.h DFunc.h DevError.h Graphics.h X11Graph.c Dev2d.c DevMatrix.c Makefile X11Graph.h Dev2d.h DevMatrix.h Matrix.c emul.h Dev3d.c DevNoop.c Matrix.h sys.h Dev3d.h DevNoop.h Matrix1.c xdummy.c Dev3df.c DevObject.c Matrix1.h xemul.c Dev3df.h DevObject.h MiscEmul.c xemul.h DevAscii.c DevPort.c MiscEmul.h xport.c DevAscii.h DevPort.h Param.c xport.h DevColl.c Device.c Param.h DevColl.h Device.h Port.c DIR/conf: ChangeLog STAGE2.SH maketape DOUBLE.SH STAGE3.SH maketapemips2 DO_INSTALL.SH distrib mkfilelist DO_INSTALL.ULTRIX kwik 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: ARBPOS.POS EVACHI.CHI PICKITEM.HLP TRAILER.TEX BLOSUM.MAT FILE.PDB QUALITY.LUP TRAILER.TXT BONDS.13 HBOFIELD.DAT RCONFI.FIG TRAIN.NEU CCONFI.FIG HEADER.TEX REFINE.DAT VALUE.CHI CHARGES.PRT HEADER.TXT SCRIPT.BLD XBFACT.DAT CHEBY.DAT ICONFI.FIG SEQCOL.FIL chappg.sty COMMANDS.NEW MESSAGES.TXT SGRDAT.DAT epsfig.sty COMMANDS.PCT MOUSE.FIG SPCSYM.DAT glossary.txt DAYHOF.MAT MOUSE_DEF.FIG TEST.NEU new.seq DNA.BRK MOUSE_TWO.FIG TODO.CHK old.seq DOCHEAD.TEX MY_MENU.DAT TOPOLOGY.FIL supertab.sty DUMMY.HED NQUAL.DAT TOPOLOGY.H ENGHU1.DAT PARAMS.FIG TOPOLOGY.NEW EVAACC.ACC PDBFIND.TXT TOPOLOGY.ROB DIR/demo: FILE.PDB RHINO.PDB 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 flexx static_data bin moletopi whatif bsp sca zerlege DIR/getline: Makefile getline.h wifconn.c getline.c getline.o wifconn.o 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 DUMMY.INF LABEL.INF SEARCH.INF ACCESS.INF ESSDYN.INF MAP.INF SELECT.INF ANATRA.INF EXTRA.INF MAPEDT.INF SEQ3D.INF BUILD.INF FAMCLU.INF MASMAP.INF SETVDW.INF CHECK.INF GENERAL.INF NEURAL.INF SOUP.INF CHIANG.INF GRAEXT.INF NMR.INF SUPPOS.INF CHKMDF.INF GRAFIC.INF NOTES.INF SYMTRY.INF COLOUR.INF GRATWO.INF PIRPSQ.INF TABLES.INF CONOLY.INF GRID.INF PLOTIT.INF TEACH.INF CONTAC.INF GROMOS.INF PORNO.INF WALIGN.INF DGLOOP.INF HBONDS.INF QUALTY.INF WATER.INF DOSELF.INF HSSP.INF REFINE.INF XRAY.INF DRUG.INF ITEMS.INF SCAN3D.INF DIR/pluton: (only if you buy this) bdftops gs gsdj gslp pluton font2c gsbj gslj gsnd DIR/poth2o: FKALAVS.DAT FKGLNVS.DAT FKLEUVS.DAT FKSERVS.DAT FKARGVS.DAT FKGLUVS.DAT FKLYSVS.DAT FKTHRVS.DAT FKASNVS.DAT FKGLYVS.DAT FKMETVS.DAT FKTRPVS.DAT FKASPVS.DAT FKHISVS.DAT FKPHEVS.DAT FKTYRVS.DAT FKCYSVS.DAT FKILEVS.DAT FKPROVS.DAT FKVALVS.DAT DIR/predata: ALCOOR.FMT.Z NQABOX.FMT WHATIF.FIG ALLNUM.FMT.Z PROFIL.FMT.Z helix CONSER.FMT.Z STARTUP.FIL 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/tcl: Makefile tclwhatif.c tclwhatif.o DIR/teach: 1ABE.BRK.Z SHOSPC.SCR.Z TEACH.AA0306.Z 1AT1.BRK.Z SUPPOS1.BRK.Z TEACH.AA0307.Z 1CDL.BRK.Z SUPPOS2.BRK.Z TEACH.AA0308.Z 1ENT.BRK.Z SUPPOS3.BRK.Z TEACH.AA0309.Z 1ERA.BRK.Z SUPPOS4.BRK.Z TEACH.AA0310.Z 1INV.BRK.Z SUPPOS5.BRK.Z TEACH.AA0401.Z 1PNC.BRK.Z SUPPOS6.BRK.Z TEACH.AA0402.Z 1PPK.BRK.Z SUPPOS7.BRK.Z TEACH.BB0000.Z 2APR.BRK.Z TEACH.AA0001.Z TEACH.BB0101.Z 2MHR.BRK.Z TEACH.AA0002.Z TEACH.BB0102.Z 2RSP.BRK.Z TEACH.AA0003.Z TEACH.BB0103.Z 4FXN.BRK.Z TEACH.AA0004.Z TEACH.BB0104.Z 9HVP.BRK.Z TEACH.AA0005.Z TEACH.BB0105.Z ALPHA.BRK.Z TEACH.AA0006.Z TEACH.BB0106.Z BETA1.BRK.Z TEACH.AA0007.Z TEACH.BB0107.Z BETA2.BRK.Z TEACH.AA0008.Z TEACH.BB0108.Z BRD.BRK.Z TEACH.AA0009.Z TEACH.BB0200.Z COLATM.SCR.Z TEACH.AA0010.Z TEACH.BB0201.Z COLHST.SCR.Z TEACH.AA0101.Z TEACH.BB0202.Z CORRECT.SCR.Z TEACH.AA0102.Z TEACH.BB0203.Z GRAACC.SCR.Z TEACH.AA0201.Z TEACH.BB0204.Z HIVP.BRK.Z TEACH.AA0202.Z TEACH.BB0205.Z HIVPA.BRK.Z TEACH.AA0203.Z TEACH.BB0206.Z HIVPA.SEQ TEACH.AA0204.Z TEACH.BB0207.Z HIVPB.BRK.Z TEACH.AA0205.Z TEACH.BB0301.Z HIVPB.SEQ TEACH.AA0206.Z TEACH.BB0302.Z HLA.BRK.Z TEACH.AA0207.Z TEACH.BB0303.Z HYPOTHASE.BRK.Z TEACH.AA0301.Z TIM.BRK.Z INDEX.Z TEACH.AA0302.Z TIMA.BRK.Z SHHB.BRK.Z TEACH.AA0303.Z chap88.rno.Z SHOALL.SCR.Z TEACH.AA0304.Z manual.ps.Z SHOHBO.SCR.Z TEACH.AA0305.Z tex.88 DIR/tutorial: 1CRN.PDB FOR041.DAT TAPEOUT.DAT 1crn.made FOR042.DAT TEACH.1 2CRN.PDB FOR043.DAT TEACH.2 3hla.brk FOR044.DAT TEACH.3 A.WPL FOR045.DAT TEACH.4 B.WPL FOR046.DAT TEACH.5 BRD.BRK FOR047.DAT TEACH.6 C.WPL FOR048.DAT TEACH.7 COLATM FOR049.DAT TEST.NEU COLHST FOR050.DAT TRAIN.NEU D.WPL GRAACC W.WPL E.WPL HLA.PDB WHATIF.FIG F.WPL HYPOTHASE.BRK WHATIF.FIG.Z FOR021.DAT Q.WPL WREH2OGRO10.DAT FOR022.DAT R.WPL WREPREGRO10.DAT FOR023.DAT SCRIPT.BLD align.mls FOR024.DAT SCRIPT.BUILD bad.model FOR025.DAT SCRIPT.HOM errors.pdb FOR026.DAT SHHB.PDB new.seq FOR027.DAT SHOALL old.seq FOR028.DAT SHOHBO pdbout.tex FOR029.DAT SHOSPC pdbout.txt FOR030.DAT START.WHATIF wrong.hbo FOR040.DAT TAPEIN.DAT x.x DIR/usegro: (this part of GROMOS everybody gets) 1HB.SCP PUT-MD.EXE davadrug.old 1HB.SCR PUTBOX.EXE davadrug.older 1PP.SCP PUTGCH.EXE davadrug.x 1PP.SCR PUTGM2.EXE eigen1.f ACC.SCP PUTGMT.EXE eigen1.o ACC.SCR PUTGWH.EXE formatdoc.html ANG.SCP PUTION.EXE formatdoc.txt ANG.SCR TRAGEO.EXE formatdoc_ToC.html DAVADRUG.EXE TRS.SCP get-em.f DAVADRUG.TOP TRS.SCR get-md.f DIH.SCP WEDEI2.EXE getbox.f DIH.SCR WEDEIG.EXE getgch.f DIS.SCP WEDMAS.DAT getgmt.f DIS.SCR WEDPRJ.EXE getgwh.f FLC.SCP WEDPRTCCF.COM getion.f FLC.SCR WEDPRTCCF.PAR promti.f GET-EM.EXE WEDPRTCFL.COM put-em.f GET-MD.EXE WEDPRTCFL.PAR put-md.f GETBOX.EXE WEDPRTCMP.COM putbox.f GETGCH.EXE WEDPRTCMP.PAR putgch.f GETGM2.EXE WEDPRTPRJ.COM putgmt.f GETGMT.EXE WEDPRTPRJ.PAR putgwh.f GETGWH.EXE WEDPRTRMS.COM pution.f GETION.EXE WEDPRTRMS.PAR trageo.f GYR.SCP WEDPRTVAL.COM wedei2.f GYR.SCR WEDPRTVAL.PAR wedei2.o HBO.SCP WEDTRA.EXE wedeig.f HBO.SCR a.out wedeig.o HST.SCP bsup.f wedprj.f HST.SCR bsup.o wedprj.o IFP37C4.DAT davadrug wedtra.f Makefile davadrug.cop wedtra.o PUT-EM.EXE davadrug.f x.x DIR/wregro: (only if you buy this) IFP26C1.DAT RT26C.DAT IFP37C2.DAT RT37C.DAT IFP37C4.DAT RT37CNEW.DAT IFP37C4NEW2.DAT RT37D.DAT IFP37D2.DAT RT37D.DAT_ORIGINAL IFP37D4.DAT RT37DNEW.DAT IFP37D4.DAT_ORIGINAL SPC216.DAT IFP37D4NEW2.DAT SSS.RESLIB IFP37D4_NH.DAT STRESC.DAT Makefile atoms.pfw PROBOXL.EXE proboxl.f PROEMAL.EXE proemal.f PROEML.EXE proeml.f PROGCHL.EXE progchl.f PROGMTL.EXE progmtl.f PROGWHL.EXE progwhl.f PROIONL.EXE proionl.f PROMDL.EXE promdl.f PROMDL.EXE_1P prommtl.f PROMDL.EXE_MP prormtl.f PROMMTL.EXE prosdl.f PRORMTL.EXE proseml.f PROSDL.EXE prossdl.f DIR/writeup: FAQ chap33.rno chap91.rno READ.ME chap34.rno chap95.rno SUBS.LIST chap35.rno chap96.rno TRANSL.FIL chap36.rno chap97.rno WHATIF.FIG chap37.rno chap98.rno chap01.rno chap40.rno chap99.rno chap02.rno chap41.rno fort.4 chap03.rno chap42.rno html chap04.rno chap43.rno iscomplete.list chap05.rno chap44.rno iscomplete.script chap06.rno chap45.rno leftover.rno chap07.rno chap46.rno list1 chap08.rno chap51.rno list2 chap09.rno chap52.rno list3 chap10.rno chap53.rno manual.aux chap11.rno chap54.rno manual.dvi chap12.rno chap55.rno manual.idx chap13.rno chap56.rno manual.ilg chap14.rno chap57.rno manual.ind chap15.rno chap58.rno manual.log chap16.rno chap71.rno manual.ps chap17.rno chap72.rno manual.tex chap18.rno chap73.rno manual.toc chap19.rno chap74.rno replace.all chap20.rno chap75.rno tex.1_7 chap21.rno chap78.rno tex.3 chap22.rno chap80.rno tex.35 chap23.rno chap81.rno tex.48 chap24.rno chap82.rno tex.8 chap25.rno chap83.rno tex.98 chap26.rno chap84.rno tex.list chap30.rno chap85.rno tex.one chap31.rno chap88.rno trageo.rno chap32.rno chap90.rno whatif.pricesThe directories labelled with an * are not redistributed by us.
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.
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 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 installation problems, if the FAQ does not help contact:
Hooft@EMBL-Heidelberg.DE
In case of execution problems or bugs, contact:
Vriend@EMBL-Heidelberg.DE
If you tell them that you saw this line in the writeup they respond faster!
Good luck Rob Hooft, Gert Vriend.