Monday, February 28, 2005

FORTRAN-2000.com (ha ha!) presents us this wonderful link to setting up cvs via ssh. later, links to abc for def and hkl for xyz.
cool, retro! iviews - Postscript editor.

Sunday, February 27, 2005

wow, a blast from the past: the hitchhikers guide to the galaxy game. like on the apple ][. neato!

the game

and

the walkthrough.

Saturday, February 26, 2005

an indepth review of the ipod shuffle
the grand sofitel demure amsterdam. take my advice, only stay in the presidential suite, you'll thank me later. great neighbourhood as well, right by the dam.



for discriminating guests, you'll want to stay in the maria di medici presidential suite. check the safe for a false bottom, and you'll find a little gift from me.

• To learn the interpretation of a Patterson crossword table, you should read
the following article: G.M. Sheldrick (1997) Meth.Enzym. 276:628
ok kids, ready for this? a bunch of perl+xml links for you (and me!):

The Source page:

Perl and XML

more Perl and XML

xml and sax machines part one and part two

schematron - Web Content Validation with XML::Schematron

XML and modern CGI applications.

XML::LibXML - An XML::Parser Alternative

Transforming XML With SAX Filters.

Writing SAX drivers for non-XML stuff. interesting.
linkfest

gnuplot slides (in pdf).

xmlsh - a shell for interacting with xml

a hack to get barcharts in gnuplot.

why oh why isn't there a free plotting program out there that does graphics worthy of Tufte? Tell me!
ipod shuffle on linux.

Friday, February 25, 2005


Position dependence of non-polar amino acid intrinsic helical propensities1

Michael Petukhov, 1, Victor Muñoz1, Noboru Yumoto2, Susumu Yoshikawa2 and Luis Serrano1

We have interpreted the results from these experiments with the model of the helix/coil transition (AGADIR), that indicates that the intrinsic helical propensity is position dependent. Gly, Val and Ile are more favorable at the first turn than in the middle of the -helix, while for Leu and Met we observe the opposite behavior.

Thursday, February 24, 2005

Wednesday, February 23, 2005

oh dear, lots of good papers, don't even have time to label them correctly. in any case, they are all good, so read them all, my dear smart readaers.

1

2

3

4

5

6
Journal of Grid Computing
5.1. nm command

The nm(1) command can report the list of symbols in a given library. It works on both static and shared
libraries. For a given library nm(1) can list the symbol names defined, each symbol's value, and the symbol's
type. It can also identify where the symbol was defined in the source code (by filename and line number), if
that information is available in the library (see the -l option).
Getting closer:


mistress 41 [~/down/solve-2.08/bin] % setenv LD_LIBRARY_PATH /home/sness/down/solve-2.08/bin
mistress 42 [~/down/solve-2.08/bin] % /lib/ld-linux.so.2 --list --library-path --inhibit-rpath /lib/i686/libc.so.6 . resolve
Program Library Howto
LD_LIBARARY_PATH and LD_PRELOAD

If you want to run a program that needs a different library:

1) ldd programname

This lists the dynamic libary dependencies of the program

2) Copy all those libraries to a directory

3) setenv LD_LIBRARY_PATH /path/to/directory/with/libs

LD_PRELOAD lets you load a different function instead of a libc library call
like if you wanted to make your own testing version of open().

So, so far, I can't override the GLIBC_2.3. If anyone has an idea
email me, please.

Saturday, February 19, 2005

This command line goes through 5gb of files and pulls out the number
of matched residues and atoms from the model building part of Crank.

find . -maxdepth 3 -name 'log' -exec grep -m1 "atoms.*residues" generated/*/log \; | less


and the next one:


find . -maxdepth 3 -name 'log' -exec sh -c "echo -n {} ; grep Rfree {} | tail -1" \; | less


and the synthesis:


find . -maxdepth 3 -name 'log' -exec sh -c "echo -n {} ; grep Rfree {} | tail -1 ; grep -m1 'atoms.*residues' {}" \; | less

Friday, February 18, 2005

Some useful command lines (well, useful for me, at least :)


sftools-compare-phases.sh warp.out.mtz ../../../../jia_mad/jia_mad.phic.mtz FC PHIC FC_1 PHIC_1
compare-arpwarp-solution.tcl ../../../../jia_mad/jia_mad.pdb hand_0_warpNtrace.pdb ../../xml/input.mtz.0.xml -v

Thursday, February 17, 2005

partyflock
Adding a carriage return to a query-replace-string or query-replace-regexp in emacs and xemacs.


You can type a newline into the 'Query replace:' prompt with


C-q C-j

Tuesday, February 15, 2005

Monday, February 14, 2005

roman roads in britain. Like, wow! I cannot believe how many roads there were!
mini mac cluster

Sunday, February 13, 2005

more funky unix command lines:


grep atoms generated*/gilu/log | grep residues
to
grep -m 1 atoms generated*/gilu/log | grep residues
to
grep -m1 "atoms.*residues" generated*/gilu/log


the first one did what i needed it to do. it got me the lines
that said


3375/3152 atoms 323/323.0/341/353 rms=0.402232675761 residues


out of a 18k line logfile. nice.

however, it got both test cases, and the second was a redundant
error checking test case where the wrong hand was run through
ARP/wARP. like this:


mistress 9 [~/cranktestdata] % grep atoms generated*/gilu/log | grep residues
generated-feb0205/gilu/log:3884/3665 atoms 257/257.0/257/387 rms=0.00495389765562 residues
generated-feb0405/gilu/log:3646/3665 atoms 151/151.0/151/387 rms=0.00698162302107 residues
generated-feb0405/gilu/log:3592/3665 atoms 9/9.0/97/387 rms=0.239588154743 residues
generated-feb0504/gilu/log:4023/3665 atoms 380/380.0/380/387 rms=0.00345315304147 residues
generated-feb0504/gilu/log:4639/3665 atoms 9/9.0/141/387 rms=0.248391814632 residues
generated-feb0805/gilu/log:4167/3665 atoms 382/382.0/383/387 rms=0.0697324167629 residues
generated-feb0805/gilu/log:4129/3665 atoms 19/19.0/306/387 rms=0.708511969219 residues
generated/gilu/log:4291/3665 atoms 381/381.0/381/387 rms=0.0807934893814 residues
generated/gilu/log:4142/3665 atoms 18/18.0/313/387 rms=0.713575518255 residues


which wasn't really so bad. however, i wanted just the first match. the second attempt
didn't work, i leave it as an exercise to the reader to figure out why. the third, though
worked great:


mistress 10 [~/cranktestdata] % grep -m1 "atoms.*residues" generated*/gilu/log
generated-feb0205/gilu/log:3884/3665 atoms 257/257.0/257/387 rms=0.00495389765562 residues
generated-feb0405/gilu/log:3646/3665 atoms 151/151.0/151/387 rms=0.00698162302107 residues
generated-feb0504/gilu/log:4023/3665 atoms 380/380.0/380/387 rms=0.00345315304147 residues
generated-feb0805/gilu/log:4167/3665 atoms 382/382.0/383/387 rms=0.0697324167629 residues
generated/gilu/log:4291/3665 atoms 381/381.0/381/387 rms=0.0807934893814 residues


just what i needed. please note for these that i didn't fix the rms calculation yet,
so please disregard it.

Saturday, February 12, 2005

openmms

small flux tubes ccpn
ccp4 and bioxhit

also

bioxhit

i'm back from england. it was a good
conference and I enjoyed being back.
the architecture is very nice. I
will try to post a picture soon, my
camera isn't cooperating with linux.

Tuesday, February 08, 2005

permutations and combinations. A program to generate all of these. I didn't use the program, but found the math on this page useful.

Monday, February 07, 2005

tools for building DNA models

biomer

and

3DNA

Sunday, February 06, 2005

35,000.00 INR India Rupees = 627.945 EUR Euro
ranikhet
According to Ayurveda, Spring is the most recommended season for purification of the body.

Friday, February 04, 2005

a nice awk page.
I had a bunch of run scripts that had line in them "for n in caufd dna360" etc. I wanted to see which ones I had forgotten. Here's what I came up with:


ll generated | cut -c "57-" | cut -f 1 -d "/" | sort > 1

grep for run-all* | awk '{for(i=4;i>=NF;i++){print $i}}' | sort > 2

cat 1 2 | sort | uniq -c | less | grep 1

An improvement on the command shown below to count the number of nodes that have jobs running on them. This greps for "n", to help reduce clutter.


qstat -n | grep node | fold -w 1 | sort | uniq -c | grep n



more cool command lines.
watch (1) rocks.


watch -n 60 "qstat ; echo ; echo ; ls -lrt generated/*/log | wc -l ; echo ; ls -lrt generated/*/log | tail -20 ; "

Thursday, February 03, 2005


mistress 17 [~/cranktestdata/generated] % qstat -n | grep node | fold -w 1 | sort | uniq -c
102
51 -
51 /
18 +
46 0
46 1
23 2
7 3
6 4
5 5
6 6
5 7
5 8
4 9
51 d
51 e
51 g
51 n
51 o
mistress 18 [~/cranktestdata/generated] % qstat -n | tail -10
node-g16/1
27174.mistress. terry dque NaAlH4-2-1 21198 6 1 15gb -- R 03:31
node-g26/1+node-g26/0+node-g24/1+node-g24/0+node-g23/1+node-g23/0+node-g22/1
+node-g22/0+node-g21/1+node-g21/0+node-g02/1+node-g02/0
27218.mistress. terry dque Li-Pnma 18297 1 1 8gb -- R 00:58
node-g28/1+node-g28/0
27227.mistress. girts dque res.pbs 30134 1 1 1gb -- R 00:45
node-g03/1
27228.mistress. terry dque Li-Pnma 28895 1 1 8gb -- R 00:43
node-g27/1+node-g27/0

Wednesday, February 02, 2005

The magic command is "watch"!

I saw this command years ago, but forgot what it was called. Watch is so cool, you can run subcommands periodically and view their output full screen, kind of like a univeral top for unix.

Now, I have found it again!

Tuesday, February 01, 2005

hmmm... interesting. (desk3d)
programming in tk - useful introduction to Tk.