whitebread

5.30.2006

It could use some simpsons questions

but it’s not a bad metric:
http://students.washington.edu/mmccain/nerdtest.html

5.21.2006

rush

“I knew he was different, in his sexuality
I went to his parties, as a straight minority
It never seemed a threat to my masculinity
He only introduced me to a wider reality

As the years went by, we drifted apart”

Congratulations on the masters. You’ll be missed–I hope your new life brings you much joy and happiness.

5.19.2006

pages

Horray, i figured out how to use pages in wordpress. See the buddhism tab at the top? click, read, and (hopefully) feel inspired.

5.18.2006

curse you pdb!

Take that, CSS
($atomtype,$serial,$name,$altLoc,$resName,$chainID,$resSeq,$iCode,$x,$y,$z,$occupancy,$tempFactor,$segID,$element,$charge) = unpack(”Z6Z6Z4Z1Z4Z1Z4Z4Z8Z8Z8Z6Z12Z4Z2Z2″,$lastLine);

5.15.2006

Not good

I may have the strength to break deraileur hangers with my hands, but d managed to blow apart his axel this morning. Also:

kmerString was: 2
got kmersize 2
Reading training prots from ../train-ideals
Reading testing prots from ../idltst
. probabilities loaded.
Loading training proteins with cathclass: -1
0…done
loaded 2 proteins

Loading all testing proteins: cathclass: -1
Checkstruct returns: 1
0…Checkstruct returns: 1
done
loaded 2 proteins
Working with 275 fragments ksize: 9
Initializing extended chain scores…d153l__…d1a1x__done
Getting neighbors…CCCCCCCHHHCCCCCECHHHHHHHCCCCCEHHHHHHHHHHCHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCECCECCCCCEECCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCHHHCCCCCCCCCCCHHHCHHHHHHHHHHHHHHCC
CCCCCCCHH hsize 2
Inserting at position 28
LLL insertion caused chain break CA-CA: 25 29 4.100890
H Inserting at position 32
LLL insertion caused chain break CA-CA: 25 29 4.100890
H CCCCCECHH hsize 2
Inserting at position 68
LLL insertion caused chain break CA-CA: 25 29 4.100890
H Inserting at position 72
LLL insertion caused chain break CA-CA: 25 29 4.100890
H HHHH hsize 2
Inserting at position 88
LLL insertion caused chain break CA-CA: 25 29 4.100890
H Inserting at position 92
LLL insertion caused chain break CA-CA: 25 29 4.100890
H CCCCEHH hsize 2
Inserting at position 120
H HCCC^@±^@^@^G^F^C^S^G^@^N^N^C^H
^Q^S^H^E^F^G ^R^A^C^F^R^E^A^P^Q^S^@^S^S^F^F^F^P^O^M
^A^@^A^S^E^E ^E^S^N
^G^C^@^@^A^N^O^H

^P^O^E
^N
^L^Q^E
^R^N^F^F^A^R^L^C^B^B^O^A
^Q^E ^E^H^H
^L^S^A^G^S^E^F

^K

^N^C^Cq^@ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ^@!^@^@^Y ^@<90>^@q^@ÿ^B^H*ð^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@<91>^@X*^@^@^@^@^@^@^@^@^H^@^@^@^@^@P^@p^@`^@^@^@^@^@À^@^P^@ ^@^@^@q^@ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ^@!^@^@^YÐ^@ ^@!^@^@^Yp^@@^@±^@CCCCCCCCCCEEEEEECCEEEECCCCEEEEEEEECCCCEEEEEECCCCCCCCCCCHH

5.11.2006

“Heisenbugs”

BUGS
assert() is implemented as a macro; if the expression tested has side-effects, program
behaviour will be different depending on whether NDEBUG is defined. This may create
Heisenbugs which go away when debugging is turned on.

5.3.2006

pdb

Let me tell you something about the protein data bank.

It sucks:

fprintf(OUTFP,
“%-6s%5d%1s%4s%1s%3s%1s%1s%4d%1s%3s%8.3lf%8.3lf%8.3lf%6.2f%6.2f%6s%4s%2s%2s\n”,
atom,serial,” “,name,altLoc,resName,” “,chainId,resSeq,iCode,” “,x,y,z,occupancy,tempFactor,” “,segId,element,charge);

You have GOT to be kidding me. CSS can’t even hold it.