• acroread   -- read a .pdf file (on Ubuntu, use okular instead)
  
• alt-tab - toggle around different open windows
  
• apt-cache search x11-dev  - search for the libraries x11-dev (root needed)
• apt-get install libx11-dev - install the libraries libx11-dev (root needed)
  
• awk
  http://www.vectorsite.net/tsawk.html
  wc -l file | awk '{print "# Nr of data points: "$1}';
  awk '{s+=$1}END{print s}' file  - sums all entries in column #1
  awk '/best:/ {print $3,$3-$7}' file
  awk 'NF==0 {i=0;next} /BOND/ {i=1;next} /ANGLE/ {i=2;next}\
      /DIHED/ {i=3;next} /IMPRO/ {i=3;next}\
      i==1 {printf "%-6d\t6\t%9.4f\t10.0\t%s\n%-6d\t16\t%9.4f\t0.01\t%s\n",NR,$2,"%8.3f",NR,$3,"%10.5f"}\
      i==2 {printf "%-6d\t10\t%9.4f\t5.0\t%s\n%-6d\t22\t%9.4f\t1.0\t%s\n",NR,$2,"%8.3f",NR,$3,"%8.3f"}\
      i==3 {if($3!=0) printf "%-6d\t19\t%9.4f\t0.1\t%s\n",NR,$3,"%8.3f"}' frcmod.hemts
  

  Print every second line in a file (change 2 to 10 for every tenth line):
  awk ' NR % 2 ==0 {print; }' <filename>
  
  Calculate average energy:
  grep EPtot water_prod1.out | head -n -2 | awk '{if(NR>5000)sum+=$9}END{printf "%14.6f\n",sum/(NR-5000)}'

• (Open)Babel - a converter for molecular modeling data files
  For example:
  babel -icif file.cif -opdb file.pdb
  sudo apt-get install openbabel
  To get started type babel -H
  see more on  http://openbabel.sourceforge.net/
  
• batch queing system:
  qsub file
  qdel id
  qstat
  showq
  
• bc -l -- calculator
• bz2 format:
  bzip2 file
  bunzip2 file.bz2
  tar -jxvf file.tar.bz2
• cc - C-compilator (gcc finns, ej installerad)
• /CDROM
• cerius2 /teo/msi/molcas.log  - Tutorial for molcas GUI in cerius2
• chemtool:
  

  Jag hittade ett bra programm att rita kemiska struktur.
  Man kan läsa in pdb, rotera den och sedan exportera till Xfig för att jobba 
  vidare:
  
  http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
  
  Den ingår i Debian 'stable' package som jag har här hemma.

• chime  - available on the pc, not on sgi
• chmod -R +rX * - make all files readable and all directories executable
  
• convert - converts graphics files
  
• core files: dbx <abs_path_to_the_program>; where - to find out where the program crashed
• ctrl-alt-F1/F2 - switch to screen 1 or 2, turn off graphical interface
  ctrl-alt-F8/F7 turns on graphical interface again
  
• cut -f2,4-6 file - cut out columns 2, 4, 5, and 6 from file to stdout
  cut -c2,4-6 file - cuts out characters (f is fields)
  
• desktop: to change the desktopprogram:
  switchdesk KDE
  
  Multiple desktops: System Setting - Desktop Behaviour - Virtual Desktops
  
• dircolors - determine the colours of files in ls
• disk recovery - do not use Aurora - poor service and lying
  
• dos2unix - changes the line endings from windows to linux format
  
• du -sh
• dvd-burner (on skade = in Daniel's room), 4.7 GB:
  growisofs  -Z  /dev/dvd  -r  -J  -D   /directory/to/be/written
• dvips <dvi fil>; lp <ps fil> - outdvi -ps
• dvips -t landscape -t a4 <fil> - ks  ldpe
• dvips -f dvi_file >ps_file
• emacs and xemacs (editors)
• embla: cat /etc/motd
• enscript <flags> <text_file>  - writes the file on the printer after some formatting

enscript --help - gives the possible options
enscript -r -fCourier7 <text_file>  - writes a wide text file in landscape format
• eps: You can get coordinates from ghostview. 0 0 is the lower left corner.

To convert ps to eps, add

• eps2eps oldfile newfile - progarm to clean eps files
• extundelete - undelete files on ext3 or ext4 file systems (not so powerful)
  
• f77 - fortran compilator
• f90 -64 program.f90 The 64 bit option is used to handle large arrays.
• files:

/etc/lilo.conf    -   configuration
/proc/meminfo   - shows the physical memory size (alternative = top)
• find * -name <name> -print
• for ((i=0;i<=40;i++)) do
  ...
  done
  
  or
  for x in Hid Hip ; do
  ...
  done
  
• /free    on signe - free computers
• ftnchek
• /teo/thor/bin/forchk
• /teo/thor/bin/understand_f77
• /teo/thor/bin/flint
• /teo/thor/bin/xlint
• ftp transfer directories, etc:
  gftp (graphical)
  You normally need to use shh2 protocol
  
• garmquota
  
• gimp   - picture editing program (also xv and convert)

http://manual.gimp.org/
• grace The 2D data plotting/analysis program "Grace" has been installed. It is based on the (now discontinued) "xmgr" program, well known to many of you. It will run on Mandrake 9.2+ and RedHat machines, and is started with the command:
  xmgrace
  The ancient "xmgr" remains, of course, but be aware that while Grace reads xmgr files, the reverse will not work! For more information, see http://plasma-gate.weizmann.ac.il/Grace 
• grep med or: grep -E 'xxx|yyy' or egrep -e 'xxx|yyy'
  grep -A5 pattern file - gives the 5 next lines after pattern
  grep -B5 pattern file - gives the 5 lines before pattern
  more advanced grep:
  echo $i | tr -d '\n' ; grep -B 1 '$end' energy | head -1 | tr -d '\n'; echo '  ' |tr -d '\n' ; grep -c "convergence criteria satisfied after"  logd
  
• gr_osview -a visar alla processer
• groff -man <fil.man>  -- omvandlar man fil till ps fil
• gs - show ps fil; alt showps, ghostview
• ghostview - visa ps fil (best; here you can get coordinates for bounding box directly).

You can also view a pdf file.

• h-index: ISI - tab We of Science - search for an author - create citation report (on line just above first article on the very right)
• Hard drive
  mkfs /dev/... build a ext2 file system on the disk (reformat a disk; it must not be mounted)
  mkdir /backup6
  mount /dev/sdd3 /backup6
  chown ulf.teokem /backup6
  vi /etc/fstab
  /dev/sdd3 /backup6 ext2 defaults,rw 0 0
  mount /backup6
  mount -a
  
  hfsplus on Mac OK
  vfat or  ntfs on Windows
  ext2-4 on linux
  
  cfdisk /dev/sdd3  - partition a disk
  mke2fs - writes a file system (-j gives ext3 journaling)
  mkfs.ext4 -c -c /dev/...
  
• hdparm -tT /dev/sde1 -- measure the speed of the disk
  Typical result:
  /dev/sdc1:
   Timing cached reads:   33540 MB in  2.00 seconds = 16789.27 MB/sec
   Timing buffered disk reads: 380 MB in  3.01 seconds = 126.09 MB/sec
  
• hinv  - Visa memory etc for datorn
• homepage of the department, source /var/www/htdocs (but you do not have read permission there)
• html: To get Swedish letters right: set (directly after <head>)
  <meta http-equiv="CONTENT-TYPE" content="text/html; charset=UTF-8">
  
• if [ $a = "0.00" -o $a = "0.05" ]; then v=0 ; else v=1 ; fi
  
• ifconfig - gives lot of information, e.g. MAC number (ether on Mac) and ipaddress (getmac on windows)
  
• info - gives a whole book of information
• kde desktop
  If you get problems with it: move the directory ~/.kde to ~/.kde-backup and logout-login again
  
• keyboard settings in settings - input devices - keyboard - layout, click on +
• kill -9 pid    - kill job with pid
  kill -stop %1 - stop a job
  kill -cont %1 - continue to run a stopped job
  
• latex commands:
  latex file (using file.tex)
  bibtex file (using the files specified in file.tex)
  latex file
  xdvi file
  dvi2ps
  

bst files are found in:
signe:/usr/freeware/lib/texmf/bibtex/bst
garm:/usr/share/texmf/bibtex/bst/misc
• latex2html - convert latex to html text
• limit   - shows limitations on memory, stack, etc.
• limit stacksize 400000 kbytes  (or unlimited) -- set limit; systune can be needed sometimes

echo 2147483648 >/proc/sys/kernel/shmmax
The system-wide limits can be changed. Look into /etc/security/limits.conf
• lp  - print on normal printer
lp -dcolps : print on the colour printer
lp -dhp4500   - the colour printer at Bo J
lp -dps -c -o number-up=2  is appropriate to write out pdf articles in 71% reduction.
lp -dps -c -o number-up=2 -o sides=two-sided-short-edge
lp -dps -c -o sides=two-sided-long-edge
lp -dcolps -c -o sides=one-sided

• login: If you cannot login because the graphical interface does no show you name among the users do:
  ctr-alt-F1 (or F2)
  It closes down the graphics and allows you to log in with any user name and id.
  
• ls --colour   - ls with colour coding of files (cf. command dircolors)
ls -v  - gives a better sorting of files (especially on linux)
ls --ignore-'s --ignore=#*#' -- ignores backup files

• lunarc:
  Location of bio files on alarik: /lunarc/nobackup/projects/teobio
  projinfo -y
  qsub, qstat, qdel
  sbatch, squeue, scancel, scontrol
  
• lyx   - word processor for latex ;
manual: www.lyx.org

• mac-adress
  On PC:
  
• mailbox in netscape (see netscape)
• make -f <make-fil> <program>   - if the make-filen is not called make
• maple
• mathematica (no longer available)
• matlab
• Maximising windows - turn off in System Settings - Desktop ehaviour - Screen Edges
  
• mc (midnight commander) - quit the program with text string "exit"
  
• mkf2c to create the appropriate wrappers for C code
• mpg file on Mac: VLC (freeware): http://www.videolan.org/vlc/download-macosx.html
  
• /sw/molcas/default
• /sw/molcas/latest
• molden

/usr/local/bin/molden
/usr/local/bin/moldenogl
• molmol - graphic display of protein structures
• sudo mount /dev/sde1 /backup6
  the name (sde1) can be fround by dmesg:
  [101917.722471]  sde: sde1
  /backup6 must exist
  
• sudo mount -a    --- mount al files in /etc/fstab
  
• netscape automatically download *.pdf files

Edit: Preferences: Navigator: Application
Find the row: Portable Document Format
Insert /usr/local/bin/acroread %s
More suggestions, see below
File: Compact Folders  - to remove trash

• netscape mail:

chose POP3 i preferences and signe.teokem.lu.se as incoming as well as outgoin mail server (user ulf)

• netscape lock file location: /home/ulf/.mozilla/default/6yogqf9c.slt/lock
• netscape alternatives: firefox (browser) and thunderbird (mail)
  
• Nätverket på laptop startas om med:
  /etc/rc.d/init.d/network restart
• okular - new pdf viewer on Ubuntu Linux
  
• /opt/openoffice.org2.0/program/soffice (on gefion)
  
• PC you can get character #xxx by pressing alt and the number xxx
• pmount /dev/sde1 (try to mount without being root; dev name can be seen by dmesg)
• public key
  ssh-keygen
  creates ~/.ssh/id_dsa and id_rsa (the latter is the public key)
  This did not work on Linux 2013, only on Mac.
  
• Pymole - good program for pictures
  Instructions: http://www.pymolwiki.org/index.php/Publication_Quality_Images
  
  Command to get a high-resolution picture:
  png filnamn.png
  
  Alignment and RMS of two structures:
  fit (struct1 and resi 1-3), (struct2 and resi 1-3)
  
• concatenate pdf and ps files with ghostscript:
  gs -dNOPAUSE -sDEVICE=pdfwrite -sOUTPUTFILE=new.pdf -dBATCH XXXX.pdf XXXX.pdf <XXXX.ps XXXX.ps etc.>
  You may combine PDF and postscript files using GhostScript. The files to be combined are specified in the order required in the final PDF document. The name of the resulting file is specified by -sOUTPUTFILE=. Ghostscript requires that you supply the outputfile name.
  
• qdel -k <jobid>
• qprt - formats a text file for the printer This command does not work on SGI; use enscript instead

(print &l1O &a4L(8U(s0p16.67h8.5v0s0b3T ; cat $1 ; print '
' ) | qprt -B'nn' -P'pcl2' -w129 -v8 -l95 -b0 -t0 -i2 -
(cf. command /teo/ulf/Bin/lwulf)
• qsub <job>
• qstat
• qstat -a
• paste file1 file2 - paste the content of file2 line-wise after that of file1, separated by a tab (can be changed by -d " "); more files can be used
  
• pdfLaTeX - convert latex to pdf
• pdf
  pdfjoin filnamn1 filnamn2 filnamn3 --fitpaper false --paper a4paper --outfile allt.pdf
  Join several pdf files to one (and set A4 format)
  
• printer settings: /var/spool/lp/settings/ps.
  Ex:
  -FontSize 7 -P Option3 True -P Option4 10Meg -P PageSize A4 -P Duplex DuplexNoTumble
  New linux: Configuration - printing - XPP X Printing Panel
  22 chars/inch; 14 lines/inch; all margins 16 pt
  On linux: Configuration - printing - KUPS - select printer - instances - select default - settings
  Double sided: point at the printer icon on desktop and select properties.
  Printers: colps, hp4500.
  
• printf formats:
  %-6d  = fortran i6
  %9.4f = fortran f9.4
  %s    = string (fortran a)
  \t    = tab
  \n    = new line (fortran /)
  text  = written as it is (fortran 'text')
  
• ps: You show ps files with gs, showps, or ghostview
  
90 rotate  (rotates by 90 degrees; other measures also possible)
100 100 translate  (translates in x/y direction which you will need to fix it to the place}
Make sure to put it behind the bounding box (the stuff with the %)


• ps2eps -f -R + -g -s a4 input.ps output.eps
  Rotate ps and convert to esp. Good for plots from gnuplot.
  

• ps2epsi  - convert ps file to eps file + bit map
• ps2pdf   - convert ps to a pdf file
• Python
  python3 is better than python
  If you get module errors like
  ModuleNotFoundError: No module named 'scipy'
  then run (at least on Mac):
  pip3 install scipy
  
• r <part_of_command>  - gives the last command starting with the given characters
On linux (bash) ! has the same function
• renice -n 19 <pid>   : set nice -19 on a running job
• redirection of elog file:
  2> file or 2>&1
  
• scp file.source user@destination:file.destination    - secure copy
• Screencast-O-Matic - record teaching presentation from powerpoint
  
• scribus - good program to make posters
• sed 's/a/b/' file >newfile
  substitute a to b in file
  -i overwrites file instead of creating a new file
  's/a/b/g' replaces all occurrences on each line, not only the first one
  
  take every third line:
  sed -n "1~3 p" file
  
  take every second line, starting from the second:
  sed -n 2~2p file
  
  insert a line before a certain line
  sed '/$coord/i $esp_fit kollman/' file
  
  delete the first line of file
  sed -i -e "1d" file
  
  delete the last line of file
  sed -i -e "$d" file
  
  delete lines with word REMARK:
  sed '/REMARK/d' file
  
  
• setxkeymap SE   - ger svenskt keyboard
• sftp - secure ftp
  
• showps  - visar ps fil; alt gs
• showcase - presentations program (som PowerPoint)
• Source-Navigator " ... is a source code analysis tool. With it, you can edit your source code, display relationships between classes and functions and members, and display call trees. You can also build your projects, either with your own makefile, or by using Source-Navigator's build system to automatically generate a makefile."
  see more on  http://sourcenav.sourceforge.net/index.html
  To start this program, you only need to type  snavigator &
  or create an icon  with a link to  /opt/bin/snavigator   if you feel more a graphical-oriented person.
• ssh
  Normally it is best to use ssh -X to allow X-applications to work.
  The alternative is to use ThinLinc, see below (works with Mac).
  
  keeping connection via ssh:
  add to the $HOME/.ssh/config file
  host *
    ControlMaster auto
    ControlPath ~/.ssh/ssh_mux_%h_%p_%r
  Now you can open another terminal, and ssh and scp commands will not ask for the password.
  if you use mimer
  using something like: ssh -J teok-vve@mimer valera@idun
  will allow you to go immediately to your computer (especially nice with combination to
  the previous advice)
  VV 18/3-20
  
• sshfs ulf@milleotto.lunarc.lu.se:/disk/global/ulf Milleotto
  unmount with
  fusermount -u mountpoint
  
• spartan - only on tjaste
• spdbv  - SwissPDBViewer    http://www.expasy.ch/spdbv/mainpage.htm
• StarOffice: if disk is full; look at /var/tmp on oin
• sysinfo -vv   - ger serial number
• systune rlimit_stack_max 805306368; reboot - sets a new maximum limit for stack
• systune rlimit_rss_max 805306368; reboot - sets a new maximum limit for memory
• Problems with running out of memory and swapping can be solved by:
  perl -e '$a[100000]=0;'
  Increase the number of zeros until you get out of memory.
  This should empty the swap space.
  It did not solve problems when I tested it (e.g. changepdb Killed).
• talloc -l 1G file - allocates 1 GB of data in file
  
• tar - make an archive

tar -xv file - extract the archive
tar -cvf archive_name directories  - make an archive
• teo@signe,teoguest
• terminal: double click: Edit Profile "Shell", Mouse, Characters: @-./_~?&=%+#
  
• testdisk - undelete files on a fat file system. Very powerful
• time command - gives the time to run a command
  
• time machine: marienas ulf F (ML 14/3-18)
  
  1. Gå til System opsætning —> Time Machine —> Disable automatic backup
  2. Via en browser, log in på “marienas.teokem.lu.se”
  3. Find din backup fil (*.sparsebundle) og slet den. Det kan tage lidt tid!
  4. Gå til System opsætning —> Time Machine —> Enable automatic backup
• /home/roos/Bib/teokem.bib
• /usr/local/teTeX/bin/texi2html
• ThinLinc is a software to simplify remote ssh X-terminal export.
  It is free to download from  http://www.cendio.com/downloads/clients/.
  Then you can connect to any computer and use X applications.
  It works nicely with Macs, e.g. with rasmol.
  
• tiff:
  convert filnamn -colorspace CMYK -compress LZW nyttfilnamn.tif
  Convert pictures to figg with cmyk and LZW compression - the best format for publication.
  
• timeslave -H signe  - satter klocka efter signe (maste vara root)
• timex - ger timing for foljande kommando
• /dev/tape
• Toolbar: stack tasks: Task Manager Settings - General - Grouping and Sorting - Manally - By program name
  
• ulimit -s 102400    -- set the stack size to 100 MB, needed for statpt on Platon
  
• uname -R    -- gives the version of the operating system
• unix2dos - change line endings from unix to dos format
  
• unrar e x.rar -- extract an rar file
• vi
  Set the function of the tab button:
  :set tabstop=3 expandtab softtabstop=0 shiftwidth=3 smarttab'
  :set number (get line numbers)
  Replace a word:
  
• :s/foo/bar/ replace the first occurrence of the word foo on the current line with the word bar.
• :s/foo/bar/g replace all occurrences on the current line.
• :%s/foo/bar/g replace all occurrences in the current file.
• :%s/foo/bar/gc ask before each attempt to replace.
• vim - vi-like editor that can manipulate coloumns with cursor arrows after ctrl-v
• vi :.,$-1d -- means delete from cursor to the penultimate line
• www: The home page is now on mimer in /Shared/Ulf, see below
• X

startx  - starts the windows manager
ctrl-alt-backspace  - kills it

• xdrawchem - program to draw 2D molecules (struture formulae)
  XDrawChem "... is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. "
  see more on http://www.prism.gatech.edu/~gte067k/xdrawchem/
  >From the command line xdrawchem &
  Only with Mandrake-9.1 !!!
  Jfr chemtool
  
  
• xdvi - show a dvi file.
  
• xfig  - ritprogram; jfr chemtool
  
• xgrap; xgrapsc; screen dump; does not work
• xmaple
• xmgr  - plot program; see also grace
  
• xv - image editing software; c.f. gimp and convert
• xxdiff - diff program for graphical files (linux) (alt. fldiff, mgdiff)
  ldd xxdiff
  Other alternatives: Meld, Kompare
  
• winterm -name <namn> - ger nytt fonseter med namn
• yppasswd -  change your password
• MSWord -> html: http://www.wvWare.com/wvOnlineDemo.html
• MSWord -> pdf: make a ps file and convert it to pdf by ghostscript of ps2pdf
  
  
• $# Number of arguments
  $0 Shell script name
  $1 First argument
  $@ All arguments
  

Some Linux information

KUbuntu Linux - change setup

1. K-icon - Computer - System settings - Workspace appearance - Window decorations - Plastic
2. System settings - Workspace behavior - Screen edges - Uncheck Maximize windows by dragging them to the top of the screen
3. System settings - Window behavior - Window behavior - Titlebar actions - Titlebar double-click - Lower
   
   
   
4. Konsole - Settings - Configure current profile - Appearance - Black on light yellow
5. Konsole - Settings - Configure current profile - Advanced - Characters considered part of a word when double clicking - remove ":"
   

New Mac

On the M1 you can run x86 binary command line tools through Rosetta emulation. This is done automatically and in the background. To see if a file is arm or x86, use file <executable>

Copying files from local disk on Lunarc

Backup of /home

There exist a default .profile in /etc/profile.
/teo/etc/profile

ex. scp. if I want to copy a file from embla to my directory on my local temp1 disk
scp2 -1 username@embla:/usr/people/username/filename /temp1/username/

NOTE : Remember to take away all you alias and so on concerning location of ssh, ssh1, ssh2.
You just have to type ssh and automatically the correct ssh is used.

ROOT 30/5-01

Stage I. Preparing the presentation

Prepare your presentation in ps or pdf format, Login to pc.teokem.lu.se (uid scanner)

convert t.pdf -size 1024x768 a%02d.jpg or
convert t.ps -size 1024x768 a%02d.jpg

To rotate portrait-oriented slides to landscape type

convert a*.jpg -rotate "90<" %02d.jpg
rm a*.jpg

(landscape pictures will be intact)

Stage II. Moving the presentation to memory stick

The card reader is plugged into the machine 'lage', in the same room where the Windows machine is (non smoking room).
Mount the card reader

mount /mnt/reader  No longer needed.
mkdir /mnt/reader/Ulf
cp *.jpg /mnt/reader/Ulf
umount /mnt/reader

Stage III. Performing the presentation

Plug the memory stick into the projector. Press the Menu button, navigate to the Picture Viewer mode. Navigate into your directory on the memory stick, come to the first slide, 'enter', select 'Full Screen'. Use cursor keys 'left' and 'right' on the remote control for navigation.

Stage IV. After the presentation

#!/bin/sh
#======================================================================
#
# Shell script that does full/incremental backups /home/$USER
# revision 020318
#
#======================================================================
#
# Setup
#
SCP='no'
HOST='atle'
USER="patrik"
SDIR="/home/$USER"
TDIR="/backup"
RDIR="/biobig/patrik/laptop-backup"
TIME="$SDIR/.bup_time"
DATE=$(date "+%Y%m%d.%H%M%S")
if [ -r "$TIME" ]
then
   TARGET="$TDIR/backup.$DATE.inc.gz"
   MODE="inc"
else
   TARGET="$TDIR/backup.$DATE.full.gz"
   MODE="full"
fi
#
# Save some dot files
#
cd $SDIR
for file in `/bin/ls -F -d .[a-z]* .[A-Z]* | grep -v '/' | sed 's/\*//' | sed 's/@//'`
do
   cp $file "Save/x$file"
done
#
# Create list
#
LIST=""
cd $SDIR
for x in `/bin/ls -a`
do
   if [ "$x" = 'Install' ]
   then
     :
   elif [ "$x" = 'Cache' ]
   then
     : 
   else
      LIST="$LIST$x "
   fi
done
#
# Print information
#
echo "Source directory: $SDIR"
#echo "Target directory: $TDIR"
echo "Target file:      $TARGET"
echo "List:             $LIST"
#
# perform backup
#
if [ "$MODE" = 'full' ]
then
   cd $SDIR
   echo "Backup mode:      Full"
   echo "Wait ..."
   find $LIST -type f | tar -cz -X $SDIR/nobup -T - -f $TARGET
   touch $TIME
else
   cd $SDIR
   echo "Backup mode:      Incremental"
   echo "Wait ..."
   find $LIST -type f -newer $TIME | tar -cz -X $SDIR/nobup -T - -f $TARGET
   touch $TIME
fi
ls -l $TARGET
#
# Copy to server, if possible
#
if [ "$SCP" = 'yes' ] ; then
   scp $TARGET $LOGNAME@$HOST:$RDIR
   ssh $HOST -l $LOGNAME ls -l $RDIR
else
   if [ -w "$RDIR" ] ; then
      echo "Copying $TARGET to $RDIR ..."
      cp $TARGET $RDIR
   fi
fi
#
# Done
#
exit 0

.
..
Install
*.mp3
*.ogg
.Trash
Cache*
klblf0p0.default
.shosts
.thumbnails

Hej på er

Här följer en samling blandade tips och tricks jag samlat på mig under åren här.
Program som nämns nedan är:
ps2eps
convert (imagemagick)
pdfjoin
openoffice
pymol
scribus
eps2eps

Rotera ps och konvertera till eps
ps2eps -f -R + -g -s a4 input.ps output.eps
bra för att ta hand om eps från gnuplot

Konvertera bilder till tiff med cmyk och LZW kompression - bästa format för publicering
convert filnamn -colorspace CMYK -compress LZW nyttfilnamn.tif

Sammanfoga flera pdf-filer till en enda i bestämd ordning och gör till a4 samtidigt
pdfjoin filnamn1 filnamn2 filnamn3 --fitpaper false --paper a4paper --outfile allt.pdf

Hur man skapar numrerade formler i Openoffice Writer
skriv "fn" först på en rad, tryck sedan F3.

kommandon för högupplöst bild för tryck i pymol (konverteras sedan lämpligen med convert till tiff)
ray 3000x4000 (eller nåt sånt)
png filnamn.png

gör alignment och beräkna rmsd av två strukturer av samma molekyl i pymol
skriv följande kommande med de residue ids du vill aligna och 
struct1 och struct2 är namnen på de två strukturerna i pymol
fit (struct1 and resi 1-3), (struct2 and resi 1-3)

Göra posters grafiskt
använd programmet scribus

Rensa epsfiler till renare filer
eps2eps filnamn.eps nyttfilnamn.eps

Program för att hålla reda på projekt, anteckningar, tips m.m.
Zim (desktop wiki)

Subject: Multi-Machine