changes to server

Adam tell me the server is not running,
so I've made following changes to the server

cd /etc/rc3.d
ln -s /opt/xampp/xampp S99xampp
ln -s /opt/xampp/xampp K01xampp

server

xampp on binfs


installed "XAMPP for Solaris" ver 0.8.1
on binfs
under /opt/xampp

it seems there's a firewall block outside traffic to binfs,
but traffic inside umdnj should be fine.
tested by using ssh tunneling, works fine.

Apache (web server) runs on port 80 by root
MySQL (database)
PHP (pulling data from MYSQL)
phpMyAdmin (let you modify database through browser)

password, same as binfs.

Have to ask Adam to whom I should contact for opening the firewall.

test BETApro result

1i8lc
our = betapro
33 1:[2-4]:[1-3]
34 2:[8-10]:[4-6]
35 3:[17-24]:[7-14]
36 4:[31-39]:[15-23]
37 5:[44-52]:[24-32]
6:[57-57]:[33-33]
7:[59-59]:[34-34]
8:[66-71]:[35-40]
38 9:[74-79]:[41-46]
39 10:[88-98]:[47-57]
40 11:[103-106]:[58-61]
41 12:[110-113]:[62-65]

I 33 35 38
II 34 41 39 36 37
II 40


1 3 9 8
2 12 10 4 5
11


當score達到多少以上 會有百分之百的true positive rate？
2.0?

still interested in why first strand and last strand close to each other?

If this simulation from theory.med.buffalo.edu is correct,
Why, the first strand will always fold close to the last strand?
Why cyclic order applied?
651 of 703 ~= 92% follow the rule. (RULE: first strand close to last strand)

paper for supersecondary structure prediction

I think this one is pretty similar to our's.

http://contact.ics.uci.edu/betasheet.pdf

I've tried the service BETApro
but the accuracy is about half of it.
so, even combine with our rules, it's hard to get the correct motif.

example of different domain definition in scop and cath

1o7d

in SCOP
d1o7d.2 C:488-585,D:603-875,E:885-1007

in CATH
1o7dC02 2.60.40.1180
1o7dC01 1.10.287.530
1o7dE00 2.60.40.1360

1B should be 1A

strand#7 should devide to two (7 and 7')

an additional strandon rule I found

Is it possible to say, the first or last strandon might not exist or might be too short so sometimes it's hard to detect.
so
I III
IV II
might become
I III
II
OR
SM6 become SM7
this can also explain why the direction is not correct.

SM4 become SM10
SM8 become SM11