Nice electron density maps with pymol.

a new high tech cell phone
i guess the plug goes in your ear

batch processing on Lisa

It uses Torque as the scheduling framework and Maui as the scheduler.

working with sara>_

Grid Information

Rocks Clusters

cfengine - Configuration engine

OpenPBS - The old and "reliable" PBS.

Torque - A newer queueing system

Grid Howto for the LHC (Large Hadron Collider) at CERN in Switzerland.

What an intriguing concept, dining in the dark.

steven ness in bizzaro world.

Whoops! Your tongue is now a magnet. Whatever will you use for silverware?

software organizes email by task. Yes, but is there an emacs mode for it?

lonely voyager

A neat new software oscilloscope

A very nice GIF animation showing the viewing conditions in the US for the upcoming April 8, 2005 eclipse over the Pacific. Nice use of animation to show the concept.

etruscan sunrise

The Unix Philosophy explained. Now, if we could only get more scientist programmers to read this. Simple and powerful techniques, and if you apply them rigorously, you will occasionally save yourself (or some other poor sod who has to read your code) months of work.

Where I will be this afternoon

This is neat, a new card/chip to offload physics computations. Would be neat for games, but might be excellent for molecular dynamics and simulations. I should check it out. A couple links about it, first: A short press release from Yahoo. Also, a interview with the developers.

spring is coming!

ned khan is an installation artist who installs like kinda sciency art installations.

hmm

To remove all HTML/XML tags from a document in Xemacs

M-x query-replace-regexp

and replace:

<[a-zA-Z0-9"/= ]*>

with:

[RET]

hitchhiker's walthrough. again.

Ono! - Actually, it's OK, it's just the name of the executable.

If your Tcl program can't find a library, try the following:

1) Make sure the .so library you are trying to load is in your LD_LIBRARY_PATH environment variable

2) Check to see if the Tcl code is in $TCLLIBPATH

Emacs nXML mode - a new mode for editting XML in Emacs. Too bad it's not available for XEmacs.

sness at flickr. The first picture is a painting that my Mom did of water lilies. beautiful.

very appropriate : hand powered iPod Shuffle.

Wow. I got an iPod Shuffle last weekend, and I love it. I absolutely love it. so light, so small, perfect for someone like me who likes having lots of music, and music when travelling by bike and foot.

It has a great interface, with two circles, the inner one is pause/play and the outer one has volume in the vertical direction and forward reverse with the other. on the back is a slider with off/play/shuffle positions, although it's tricky to get it into "play", it just wants to "shuffle". the other is a battery indicator button and light.

however, what the iPod shuffle needs is one more little button, a button you can press to increase the ranking of the song. or, a rocker, to increase and decrease it. have it just in 5 steps, to make it simple, and if you could have some cute way of indicating the selection on the main LED that would be great. the main LEDs are underutilized anyways, but we are dealing with humans here. i would love to have the name of the song spelled out it morse code, for instance. ok, i was joking there.

Having this iPod Shuffle has made me realize that I don't really need a display, the intro of the song can function as the display. interesting. works well with 512MB, but 1GB might be more of a stretch. still, at work I have 15GB that I shuffle through randomly, so it's possible.

It's a little tricky to define a menu on the fly in CCP4 Tcl. The trouble is mainly with where to put the quotation marks. I adapted this from dhm_tool.tcl in CCP4i:

                                                                          
    puts "test=($test)"
                                                                                                                                                               
    for { set i 0 } { $i <= $test } { incr i } {
         lappend menulist "$i"
         lappend fileselect(ALIASLIST) $i
    }
                                                                                                                                                               
    incr test
                                                                                                                                                               
    DefineMenu _input_columns $menulist $fileselect(ALIASLIST)

For truly dynamic menus, try varmenus.

From here:

Some particularly useful CVS commands are:
cvs -nq update lists the files that may need updating but do not update them.
cvs update updates your snapshot to the most current version in the repository.
cvs -n diff -rHEAD shows the differences between your snapshot and the most current version in the repository.

Working with binary files in CVS.

Upshot:

Add files with

cvs add -kb file

If you accidentally added a file as text and want to switch it to binary:

cvs admin -kb file

How to do a variable menu in CCP4i Tcl:

First, add a typedef for the new varmenu we are about to create:

   set typedef(_input_columns) { varmenu INPUT_COLUMNS_LIST INPUT_COLUMNS_ALIAS 8 }

Then, add code to the place where you want to change the varmenu (for example, a subroutine like "add_an_input_column".

   UpdateVariableMenu $arrayname initialise [llength $array(INPUT_COLUMNS_LIST,0)]           INPUT_COLUMNS_LIST $columns           INPUT_COLUMNS_ALIAS $columns

Then add code for INPUT_COLUMNS to your .def file:

INPUT_COLUMNS,0                _input_columns      ""
INPUT_COLUMNS_LIST,0           _list_of_text       {"test1" "test2" }
INPUT_COLUMNS_ALIAS,0          _list_of_text       {"TESTT1" "TESTT2" }

Finally, create the widget as you would do so normally:

                                                                     
    CreateLine line         label "Input columns"         widget INPUT_COLUMNS 

Although it is hard to find out how to completely turn off syntax highlighting in vim, it is quite simple. To turn off highlighting in vim, create a .vimrc file and put "syntax off" inside it.

csness-fwnc0200 29 [~] % cat .vimrc
syntax off

Tcl Wiki has some good links to resources to learn Tcl and Tk. I found lots of good resources for Tcl, but Tk seems harder to find good program samples. Maybe these links will help.

umm, hello? why wasn't I told of plotutils before? it looks awesome, if seldom updated

-rw-r--r--    1 0        0         1986497 Sep 25  1997 plotutils-1.3.tar.gz
-rw-r--r--    1 0        0         2161722 Jan 29  1998 plotutils-2.0.tar.gz
-rw-r--r--    1 0        0         2213149 Jun 01  1998 plotutils-2.1.1.tar.gz
-rw-r--r--    1 0        0         2301517 Jul 24  1998 plotutils-2.1.4.tar.gz
-rw-r--r--    1 0        0         2341836 Aug 22  1998 plotutils-2.1.5.tar.gz
-rw-r--r--    1 0        0         2360867 Oct 07  1998 plotutils-2.1.6.tar.gz
-rw-r--r--    1 0        0         2189094 Apr 25  1998 plotutils-2.1.tar.gz
-rw-r--r--    1 0        0         2819122 Mar 18  1999 plotutils-2.2.tar.gz
-rw-r--r--    1 0        0         3124258 Oct 07  1999 plotutils-2.3.tar.gz
-rw-r--r--    1 0        0         3316030 Jul 04  2000 plotutils-2.4.1.tar.gz
-rw-r--r--    1 0        0         3304075 Jun 26  2000 plotutils-2.4.tar.gz

still, not too bad, good dedication, good gradual increase in size, fairly well spaced apart, with a bugfix coming soon after the release. the api looks cool too.


I want to make scientific graphs that are to the standards of Tufte. Is that too much to ask for?

grep -A4 Resl ~/CrankTests/generated-feb0805/jia*/run/1-shelx/logfile | less