2005年7月24日

Hacker們,準備好大震盪了嗎?

Windows XP 的繼承人 Windows Vista 來了
完整支援 新型CPU的 "NX" (No-Execute) 功能
使得未來hacker常用的buffer overflow 技巧將無法使用
呵呵 這可好玩了
我猜大概下個月 應該網路上就會有beta版流出來了

其他詳情請見 Windows Vista

2005年7月22日

駭客雜誌隨筆

今天在做我的routing時 看到兩篇好玩的paper

  • 一篇是利用IE的FTP client當smtp client使用
    當user連到你的網頁的時候
    IE會照網頁裡面的一個FTP URL去download圖片
    img src="ftp://..."
  • 另一篇是討論怎麼干擾GPS運作
    基本原理是用高斯訊號蓋台 比較不容易被filter掉
    paper嘛~當然都要說說可以怎麼運用
    美其名說要先想好怎麼對付GPS飛彈
    後來就扯到最近有賣GPS追蹤手機 可讓父母或配偶追蹤愛人
    這時你就可以用這招蓋台
    我突然想起前兩天看到的新聞
    說追捕張錫銘的時候 有放定位晶片
    我看 下次的歹徒 可能需要買幾台這種裝置
    不過 具我觀察 警方放的 可能只是台手機罷了
    GPS哪有定位誤差差到一兩公里的
    張錫銘的同夥只要去找找他們車子裡 有沒有哪個弟兄『不小心』掉的手機 就知道誰是抓耙子了 嘿嘿

2005年7月21日

幫你的Pocket PC 換Rom, Update Rom, 中文化, 隨便你怎麼叫!

三年前 曾經把我的IPAQ PDA從上玩到下 從下玩到上 連裡面都玩了 (詳見上一篇)
今天 看到網路上有人在問怎麼換ROM 一副不相信ROM可以不用用『燒』的
呵呵 其實IPAQ PDA用的ROM(firmware)是可以軟體更新(update)的啦
我把三年前的筆記貼上來 希望對某些人有用。

  1. Download Rom image from Compaq
    這裡我以我的H3650舉例
    連到http://www.compaq.com/support/files/handhelds/us/locate/48_1230.html
    找”ROMPaqs/BIOS and Firmware”那個section,
    應該可以找到 “iPAQ H3600 Series Pocket PC ROM Update”
    連進去後 選擇你要的語言 (ex:繁體中文版SP20016.exe 英文版SP20010.exe)
    Download後執行
    裡面的檔案解開後 找一個檔 NK_XXX###XXX.nbf
  2. 想辦法download到host11.exe
    http://www.ipaq.com.ua/files/host11.exe
  3. 把Rom image的前32bytes 去掉
    可以用ultraedit把前32bytes cut 掉
    如果你用linux, 可以用dd (參考ref2)
    把此檔rename成nk.nb0
  4. 把host11.exe跟我們剛剛做好的nk.nb0放在同一個目錄下
  5. 把PDA設定成 Remote USB Update 模式
    按住2+4+power 三個按鈕, 並按下reset
    此時螢幕應該如圖所示
  6. 執行 host11.exe
  7. 等host11執行完, 切斷PDA內部電池迴路, 方法如下:
    按住1+4+power三個按鈕 並按下reset, 一直按住, 直到螢幕慢慢變不見
  8. 耐心的等60秒, 讓記憶體裡的東西消失…
  9. 叫醒你的PDA
    把你的PDA放到底座上充電, PDA就會自動把內部電池迴路接上並開機

Have Fun!

不保證以大家的技術都能成功 請自行斟酌
中文ROM比英文ROM大 所以記得先確認你的記憶體夠用
PS:換ROM將使您失去保固 (所以送修前記得把ROM換回來喔!)

Reference:
http://www.cewindows.net/reviews/image016.jpg
http://www.handhelds.org/z/wiki/HosT11
http://ipaq.com.ua/ipaq_usb_pop.html
http://www.ipaq.com.ua/files/host11.exe

三年前 因為工作的關係 把我的IPAQ PDA翻過來玩
研究怎麼把他換成linux系統 研究怎麼把她換成中文的ROM
兩年前 我不小心把我的IPAQ摔壞了 送去美國的HP跟台灣的HP 他們都跟我說面版壞了 換一個面版要US$700~800 台灣也跟我說要一萬八左右
靠!那我不如買個新的!
結果 好死不死 我那有錢的房東 留下了一個他不要的PDA 我看都是IPAQ的 也都是彩色面版
想說那我把她面版換到我的PDA上面 說不定就能動了
所以我就回台灣拿了我的機司 回美國準備幫我的PDA動手術
結果 摸了一個小時 終於小心翼翼的把她們拆開了 就在準備要換臉的時候
才發現 靠 他們的主機板規格是不一樣的 面版規格從內部看也不一樣
他的面版根本塞不進我的PDA裡面 會卡到我的PDA的主機板
只好通通重新裝回去 認輸了
結果 好死不死 就在裝回去後 順手按了一下開關 沒想到...
我愛死你了 老天爺 Oh, God, I love you!
我的PDA死而復生 完全看不出曾經死掉過
耶!我竟然修好了死掉兩年的PDA...

2005年7月20日

看到有人用google map api 寫了一個像 mygmaps 的東西
http://www.flashanywhere.net/map.cfm
至於資料 他是用這樣的方法放進去的
http://www.flashanywhere.net/mapjs.cfm

2005年7月19日

When I have time, I might try running linux on my wireless router.
You can run linux on it, run a web server on it, OR, run a snort on it...
http://www.batbox.org/wrt54g-linux.html
or, run a portal on it

2005年7月16日

無線網路侵入法

STEPS:

  1. Kismet:用來掃描整個區域內的WLAN,找到實驗用的目標WLAN,收集相關數據(SSID值、頻道、AP及與之相連接的客戶端的MAC位址等);
  2. Airodump:對目標WLAN進行掃描並捕獲其產生的數據包到一個文件中;
  3. Void11:從目標AP中驗証某台計算機,並強製這個客戶端重新連接到到目標AP,以使其一個ARP請求;Aireplay:接受這些ARP請求並回送到目標AP,以一個合法的客戶端身分來截獲這個ARP請求;
  4. Aircrack:接受Airodump生成的捕獲文件並從中提取WEP密鑰。
ref:
http://biz.chinabyte.com/159/2027659_3.shtml
http://soft.yesky.com/security/hkjj/318/2030318.shtml
http://soft.yesky.com/2/2032502_3.shtml
http://soft.yesky.com/408/2033408.shtml
英文版
如何攻擊?
如何防守?

2005年7月13日

link to get lat lon from www.map.com.tw
PS: it will check ref, so you can't just click and go there.
you have to copy paste the link.

2005年7月9日

Just tried Google's Map API
http://www.google.com/apis/maps/

Maybe I'll check Yahoo's Map API
http://ws1.inf.scd.yahoo.com/maps/

and check MSN's Virtual Earth

Thank you
for signing up for a Google Maps API key. Your key
is:



ABQIAAAAVMbuegtOpYPpbJgxBw6T3xT0EyVsxfSpbdrKS-8Sa2Ocoxm2QxTd_U0pkKXMPKjOULzG15CrCUTRkA



This key is good for all URLs in
this directory:



http://mmap.no-ip.info/



Here is an example web page to
get you started on your way to mapping glory:



<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
  <head>
    <script src="http://maps.google.com/maps?file=api&v=1&key=ABQIAAAAVMbuegtOpYPpbJgxBw6T3xT0EyVsxfSpbdrKS-8Sa2Ocoxm2QxTd_U0pkKXMPKjOULzG15CrCUTRkA" type="text/javascript"></script>
  </head>
  <body>
    <div id="map" style="width: 500px; height: 400px"></div>
    <script type="text/javascript">
    //<![CDATA[
    
    var map = new GMap(document.getElementById("map"));
    map.addControl(new GSmallMapControl());
    map.centerAndZoom(new GPoint(-122.1419, 37.4419), 4);
    
    //]]>
    </script>
  </body>
</html>


Check out the API documentation for
more information.





Then, I made This

2005年6月16日

housing info using google map
http://housingmaps.com/
you can search by city and price range, and it will show on google's map.

gas price info using google map
http://www.ahding.com/cheapgas/

crime info for chicago using google map
http://www.chicagocrime.org/map/

crime info for florida using google map
http://www.floridasexualpredator.com/

traffic
http://supergreg.hopto.org/google-yahoo/

flickr photos using google map
http://www.thickey.co.uk/gmaps/

2005年6月15日

Tried to find Text to Speech software, but nothing good.
I've tried SmartRead from China, but it read word by word.
the best one I've tried is from ITRI, but there's only online version, no SAPI on market yet.
the second one is from NTU. the advantage is they also support Taiwanese.

2005年6月14日

有人反應我的地址轉經緯度有BUG
我查了一下 演算法及答案基本上沒有問題
但是有些偏遠地方 或者地址寫法不同時 或地址找不到時會有問題
如: 台北縣淡水鎮中正路251號
所以我另外查了兩個地址轉經緯度的source
http://hipages.hinet.net/
http://maps.yam.com/yam/search.asp
但是這兩個需要先把地址parse開

2005年6月5日

2005年5月31日

finally I found a freeware which can do "undelete" for me.
restoration
it's small, 192k, doesn't need installation, and it's free.

2005年5月27日

There's a student wana pay $1000 for a hello-world type 8051 program.
After I did some research, I think
"SimLab 8051" is pretty good for beginner.
"PROTEUS's VSM for 8051" is better if you want to use your own circuit layout.

2005年5月24日

the alignment algorithm used for my MMusic & MMovie might be modified from this perl code:
code1
code2

2005年5月14日

my mom's email software (outlook express) out of work
the reason is because there's email which has only headers but not body.
when use dos to telnet to port 110 and use retr to get those emails, the connection will be disconnected.
but you can use "top 24 10" to check email#24.
then use "dele 24" to delete it.
I think it's because she didn't have outlook express patched.

the debug info is as follow:


top 24 10
+OK
Return-Path:
Received: from [63.168.128.101] (63.168.128.101) by pu05.cathaylife.com.tw (NPlex 5.1.956)
id 41E20B0200684240 for cwchiang@cgh.org.tw; Tue, 10 May 2005 14:38:16 +0800
Sender: ReyesArroyo@invinciblemonkey.com (derived from envelope by postmaster@pu05.cathaylife.com.tw)
Date: Tue, 10 May 2005 14:38:16 +0800 (added by postmaster@pu05.cathaylife.com.tw)
Message-ID: <41e20b0200684240@pu05.cathaylife.com.tw> (added by postmaster@pu05.cathaylife.com.tw)
Received: from FO09@localhost by C[3

.

2005年5月5日

according to this paper and this paper
you can use pxe pdk 2.0
to boot machine into windows' Remote Desktop.

2005年4月29日

電線桿座標換經緯度的algorithm
http://www.csie.nctu.edu.tw/~jjyang/ppc2003/TaiPower_To_TM2.xls

I just find someone create a website I just wana to create.
custumized maps.google.com,
you can put information you want on the map
I create one too.

2005年3月24日

I used to use rainbow to implement a text categorizer for AT&T
http://www-2.cs.cmu.edu/~mccallum/bow/rainbow/
but I was interestedin using weka, and I saw a simple one today
http://www.hakank.org/weka/TextClassifierApplet.html

#!/usr/bin/perl
use SOAP::Lite;

$str="> t1 asdf
ASDF

> t2 asdf
ASDDF

> t3 asdf
SDFF";


printf SOAP::Lite -> service('http://xml.nig.ac.jp/wsdl/ClustalW.wsdl')
-> analyzeSimple($str);
printf("\n");

#!/usr/bin/perl
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::LocatableSeq;

my $seq1=new Bio::LocatableSeq(
-seq=>"ABCDEFG-",
-id=>"t1",
-start=>1,
-end=>8
);

my $seq2=new Bio::LocatableSeq(
-seq=>"BCZEFGIH",
-id=>"t2",
-start=>1,
-end=>8
);
my $seq3=new Bio::LocatableSeq(
-seq=>"KBCDEGH-",
-id=>"t3",
-start=>1,
-end=>8);


$aln=Bio::SimpleAlign->new();
$aln->add_seq($seq1);
$aln->add_seq($seq2);
$aln->add_seq($seq3);


#$factory= Bio::Tools::Run::Alignment::Clustalw->new();
#$aln=$factory->align(\@seq_array);

#$threshold=50;
$str=$aln->consensus_string($threshold);
#printf $aln->length,"\n";
#printf $aln->no_residues,"\n";
#printf $aln->no_sequences,"\n";
#printf $aln->percentage_identity,"\n";
printf $seq1->seq(),"\n";printf("\n");
printf $seq2->seq(),"\n";printf("\n");
printf $seq3->seq(),"\n";printf("\n");
printf("$str\n");
printf $aln->match_line(),"\n";
printf $aln->match(),"\n";

2005年3月20日

for search protein by 3D structure
Protein Structure Similarity Search http://mbs.cbrc.jp/papia-cgi/str_menu.pl
you can also query it by protein fragment (residue numbers), c-alpha coordinates

2005年3月18日

if you are impressed by maps.google.com, and you are interested about how they do that,
you can check this website.

http://jgwebber.blogspot.com/2005/02/mapping-google.html

2005年3月16日

2005年3月13日

2005年3月12日

miniGPS is pretty interesting, it use GSM network to know your location,
not like GPS, miniGPS can only know the places you've been before.
ex: when you sleep on bus to your school, you can use it to alarm you when your bus is arrived to your school's station.

you can get new york's webcam image here
http://207.251.86.248/
simple, just jpg images. ex: http://207.251.86.248/cctv20.jpg

code for Symbian OS cellular phone
http://crschmidt.net/symbian/traffic/

my NOKIA from AT&T can also go into field test mode by using *3001#12345#
detail http://www.geckobeach.com/cellular/secrets/nokia_secrets_6188.asp

SGH-E315 with t-mobile you will have to make your own wap settings

enter this in your phone, *#87927# you will then get a screen saying settings voicestream, voicestream, gprs preferred, profile4 info, profile5 info...go down to profile4 info and you will then get another screen, this is where it all comes...type this is for the following...

Profile name...waptunnel
Homepage URL...http://wap.crjt.net
Security...non-secure
Bearer...data
IP address...24.3.27.144
Login name...guest
Password...password
Dial-up number 3604692000
Data call type...Analog

your all done...exit out and connect to t-zones or just start sending ringtones to your phone by e-mail like this yournumber@tmomail.net you should be receving them at pic messages...GOOD LUCK.

ps...login in to you t-zones with the new settings will charge you by the minute so watch out...to change them again to its original settings just go the the setting screen and choose the original settings and there no harm done...

if the code does not work try this one...
Profile name...waptunnel
Homepage URL...http://wap.yahoo.com
Security...non-secure
Bearer...data
IP address...12.25.203.11
Login name...guest
Password...password
Dial-up number 3604692000
Data call type...Analog

Default:

Profile name...GPRS Preferred
Homepage URL...http://wap.myvoicestream.com
Security...non-secure
Bearer...GPRS
IP address...216.155.165.50
Login name...anonymous
Password...
APN...wap.voicestream.com

My cell phone from T-Mobile is SAMSUNG's "SGH-E315"
I just tried to enter the Engineering-Mode of it.

Success entering:
*#06# Displays phones IMEI No.
*#9999# SW Version
*#8888# HW Version
*#0842# Vibrator
*#0289# Buzzer
*#0228# Battery Stat
*#0782# RTC Display (???)
*#0523# LCD Contrast
*#0778# Sim Size
*#0638# SIM network ID
*#0746# SSMS memory
*#4357# This screen (the actual help screen)
*#9324# Netmon (press the hangup key to exit)

2005年3月11日

if you want to try color the protein using chime, you can use this webpage to execute chime command.

http://www3.sympatico.ca/diane.demers/moi/example2/index.htm

2005年3月7日

old pdb file can be find by this way
ex: 1FB3 now is 1SM4, but if you want old pdb file you can get it this way
http://pdbobs.sdsc.edu/cgi/parse.cgi?id=1FB3

old pdb file can be find by this way
ex: 1FB3 now is 1SM4, but if you want old pdb file you can get it this way
http://pdbobs.sdsc.edu/cgi/parse.cgi?id=1FB3

2005年2月24日

sniffer for wireless network,
I was using Network Stumbler, but it can only do very simple stuff.
I think I'll try AirSnort for WEP and AiroPeek NX or kismet for packets.

2005年2月17日

forget admin's password in xp
press F8 while booting, select safe mode with command line.
select administrator account to login (don't need password)
use "net user owner 123456 /add" to change owner's password to 123456
"net user abcdef 123456 /add" to add a user
"net localgroup administrators abcdef /add" to make abcdef an administrator
reboot, then abcdef has administrator's privilege.
now you can use abcdef as administrator to assign a new password for anyone.

to use gcg through VNC
instructions

change vnc password: vncpsswd
start vnc server: vncserver
You should see "New 'X' desktop is siriusC:y"
ex: New 'X' desktop is siriusC:1
connect to http://gcgserver.umdnj.edu:5800+y/
ex: http://gcgserver.umdnj.edu:5801/
fill in your vnc password.
gcg
seqlab

to translate GB2BIG5, usually use a translate table
you can find it here

for code, 1.PHP 2.PHP

2005年2月15日

2005年2月7日

A power point file explain what's WordNet in Chinese
Chinese version WordNet

What do stars means for hotel?
I got an answer from Taiwan's government
or you can search google by keyword: 旅館等級評鑑制度
sorry, it's in chinese.

2005年2月5日

for online multiple text alignment, you can use this one
http://prodes.toulouse.inra.fr/multalin/multalin.html

if you want to use bioperl to align sequences, you have to install ClustalW first, and also the Lib for ClustalW.
the AlignIO::ClustalW only read ClustalW files, it will not do alignment.
RUN::ClustalW...will only work if you installed ClustalW.

#!/usr/bin/perl
use SOAP::Lite;

$str="> t1 asdf
ASDF

> t2 asdf
ASDDF

> t3 asdf
SDFF";


printf SOAP::Lite -> service('http://xml.nig.ac.jp/wsdl/ClustalW.wsdl') -> analyzeSimple($str);
printf("\n");

2005年2月4日

To know which process listen on which port on windows (tested on XP)
use "netstat -ano" to list all the information (includes ports and PIDs),
then use windows task manager(Ctrl-Alt-Del/ taskmgr.exe) to check the name of that PID. (active: Porcesses, View, select columes, PID)

2005年2月2日

mark


mark
Originally uploaded by markchiang.
test flickr
test chinese 中文

2005年1月27日

2005年1月20日

http://www.archive.org/
waybackmachine
can let you see a website in each year.
ex: www.yahoo.com in 1999
I saw this in google's corn speach.

2005年1月7日

After AGTC's presentation,
I think this field is too late for me to start, then already did part of it.
they identify active compounds in Chinese Herbs by using there HerboChip & HerboLink plate form.
they got several patents for it, ex: microarray on plastic, microarray using unknown probes, microarray using natural compounds as probes, etc.
But, they need target to start.

they proved it works, already have products, already have sale lines.
can scan 400000 compounds / human day.

2005年1月6日

sort table in client side, data from xml, chart to svg, image in data, tree.

2004年12月19日

when typeing in msn messenger, I got lot of error message says my message can't reach my partner.
two way to solve it.
1. use webmessenger.msn.com
2. update "Windows" Messenger

2004年12月7日

in Google (in English version)
You can query

145 Myrtle Ave. APT#BSMT. Fort Lee, NJ 07024

and it will give you a link to Yahoo! Maps & MapQuest

You can also query
145 Mertal Ave. APT#BSMT. Fort Lee, NJ 07024
it will correct it to
145 Myrtle Ave. APT#BSMT. Fort Lee, NJ 07024
for you.

mail address correction
http://www.semaphorecorp.com/cgi/form.html
MapQuest supports address correction.

simple mail address parser
http://www.cedar.buffalo.edu/adserv.html

Google 計算機
直接在google打下面的字串查詢 就會自動跳google計算機
(中文需使用中文Google)(括號為註解,不要打)
30C=?F 三十度攝氏度等於多少華氏度
1day=?seconds 一天等於多少秒
1cm=?inch (中文還沒玩出來)
1gal=?l 1加侖等於多少升
1W/1V^2= (電阻)
1S*1V^2= (功率)
一瓦*一秒 (能量)
一磅等於多少公斤

2004年12月4日

use wget as another browser
wget -U "user-agent=Mozilla/2.01Gold > (Win95;I)" http://images.google.com/images?q=men+in+black

use lynx to get html source
lynx -source http://images.google.com/images?q=men+in+black

tested two "text to speech" / "text to voice" service

rhetorical

2004年12月3日

to install tomcat on knoppix, you'll need to install Java JDK first.
but Phoebe found a package for JDK, Tomcat...
you can just use bunzip2 to unzip it, un-tar it, and use it.

ref: http://talk.org/archives/000323.html

you can get aligned sequences for families or superfamilies in scop from here

2004年11月30日

test free audio blogger
http://www.audioblogger.com/

this is an audio post - click to play

Express NewsPictures 還可以用用看
Diiva 好像還不錯 不過在vmware裡面滑鼠不太能控制上下拉
AutoPix 不能跑 有error message
Kuro 收錢了 爛
muper 只能在簡體中文版的windows上跑
8la 跟 threedegrees 概念很像 都是朋友之間一起聽 有點不合我的習慣

2004年11月24日

mysql on knoppix

files in /var/lib/mysql/mysql are read only.
rm *
cp from /Knoppix/....

after copy the owner will become root.
chown mysql *

then, you can
GRANT ALL PRIVILEGES ON *.* TO mark@localhost
GRANT ALL PRIVILEGES ON *.* TO mark@Knoppix

2004年11月22日

How to use Oracle? compare to mysql.
ref: http://www.weiw.com/article/list.asp?id=605

select * from tab;
select * from cat;

How to install Oracle 8i client on XP?

(Windows XP Pro or Windows 2000 with Pentium 4 only)

Copy all the files/folders from the oracle 8i CD on to a folder on your c: drive.
Do NOT name this folder Oracle.
Change the name of the symcjit.dll file.
For Windows XP: Change from symcjit.dll to symcjit_disc.dll
For Windows 2000: Change the symcjit.dll to symcjit.dll.ori
The path to this file is:
C:\stage\components\oracle.swd.jre\1.1.7.30\1\Data Files\Expanded\jre\win32\bin
Now go back to your main c: drive directory and run the setup file.

Alternatively the 1507768 patch reference on Metalink will do the trick.
also, see http://www.intel.com/support/processors/pentium4/sb/cs-001674-prd483.htm

ref:

----------------------------

after installed the Oracle 8i client, you can use this command in command line to get into Oracle.

SQLPLUS SYSTEM@(DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=binfs.umdnj.edu)(PORT=1521))(CONNECT_DATA=(SERVICE_NAME=binfs">SYSTEM/binfs4lab@(DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)(HOST=binfs.umdnj.edu)(PORT=1521))(CONNECT_DATA=(SERVICE_NAME=binfs)))

2004年11月21日

Kister gave me this pattern
[IMFV]-x(3)-E-x(7,9)-[LVI]-x(2)-[ILVF]-x(8,10)-[VILA]-x-[YF]-x-[LVI]-x-G-x(4,9)-[IVL]-F-x-[IV]-x(3)-[TS]-G-x-[LVIM]-x(5)-[LMI]-x(7)-[YF]-x-L

I got this pattern using PRATT
G-x-[ILMV]-x(5)-[ILM]-D-R-E-x(15)-[AGT]-x(4)-[DEGNS]-[PQST]
with -PL 40 -PX 30 -FN 3 -FL 5 -FP 100

when I use 3motif to see the proteins matched these patterns,
I found my pattern is very interesting!
it target four points, two for sandwich's interlock, two for active sites.

Also, I found Shibata's idea is also interesting when I check interlocks with 3motif
1tf4: Y-x-F-x(10)-I-x-V-x(22)-V-x-I-x(20)-F-x-I

2004年11月19日

Chime tutorial
http://www.clunet.edu/BioDev/omm/scripting/molmast.htm

I can't delete a file on my windows' desktop.
I've tried several ways, use DOS filename, use del \\?\C:\..., change name, etc. DIDN'T WORK!!!
finally, I delete it using a software, JRTS Delete FXP Files to delete it.

2004年11月17日

use PRATT or advPRATT to generate pattern
use ScanProsite or 3motif to scan that pattern in Swiss-Prot, PDB, etc.

[EQ]-x-L-Y-[DQSTE]-x(3,12)-[LIV]-[ST]-Y-x-R-[ST]-[DEQS]
[eq].ly[dqste]{0,1}.{3,12}[liv][st]y.r[st][deqs]

2004年11月10日

try signed and encrypt email in outlook express

I got free Personal Certificates from

https://www.thawte.com/cgi/enroll/personal/step1.exe
AND
http://certs.ipsca.com/CSB1Free/

first one not working.
second works fine.

umdnj sig works but enc not working.
yahoo, gmail, hotmail not working.

2004年11月7日

Usually people use firewall to block the ports to prevent hackers.
But I think we can try an opposite way.

在武俠小說裡 真正厲害的人 你是看不出他在防守的

1. Imaging that when you scan a computer's ports, every ports from 1 to 9999999... are all opened.

2. When you want to test each port, you'll fire the alarm.

2004年10月23日

2004年10月6日

Biological graph layout and display
http://home.comcast.net/~natgoodman/Biological_Graph_Software.htm

for piping the output of one program in unix to another program's command line, (instead of input)
ls only files contents "test", (for checking the size of the file)
ls -al `grep -L test *`
or
str=`grep -L test *`
ls $str

2004年9月29日

maybe we can use http://i.moltalk.org/
instead of CSU
cause, sometimes CSU is not working.

Also, Moltalk will be quicker and more details.

choose "Find interface between two chains of a structure" in http://i.moltalk.org/
enter the pdb code,
when select chains, just select the same chain twice.

Done.

use
http://balabio.dcs.gla.ac.uk/tops/
to generate
http://www3.ebi.ac.uk/tops/ExplainDetailed.html
and you can easily compare things like

1bia

1gh4

2004年9月15日

For calculating Hydrogen Bond

HBPLUS, which is distributed with LIGPLOT: http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html

There's also HBOND, which comes with the JOY package:
http://www-cryst.bioc.cam.ac.uk/~joy/

they are free, but they all need Academic License which I can't apply individually, has to apply by UMDNJ.

for example, I want to know the H-Bonds in protein 1a2p, I go to

http://bioportal.weizmann.ac.il/oca-bin/csu?PDB_ID=1a2p

I found there's four sheet strands for each chain.
I click on "Strand 1" on "A sheet" (residue 96-99)
I'll go to this page
from this page, if there's a "+" sign under HB colume, I know there's a H-Bond.

2004年9月5日