16

BLAST-EXER C ISE ·
J. Poi::i 1 your brow:,er to t he X C · · - -"o. I
PQA(:T\CA<-- 6 · I) ( BLAST scn·cr. 11 ,. , ·
· .
2. Jn 1he B :i.s rc lll:ts 1 scc ii on, click th . .· · · - Al\•1 ncb1.nlm.:D.!I'•_Q O'J{~~~T .
3 . .Enter accession num be r( ) e protein BL.-\ST (b la~1p) fin k.
E3LRST: nBLAST I f6lflS-T

A-\ W To s-tt..ld'f
h
BLRST-toir sEOtr i~
- -~
. -
8'XPS ~ ol.o.--fo~ c.~~ •
------ .
s , or FA....CTA sequence(s) in :t Qu e Se
You h3·,·e two ways to pas 1e., ~
~ s ~quencc to ihc bla~1p Serve r·
• Jf ::,our sequence rs airc:idy in a d:Jtab:isc ·o u e;i . . .
bl aslp. For ou r ex.,m 1 ·)
.
.
ry quc ncc "me.Jo".

· n g i\'t.: !Is ID nu mber 1.c a:u:;:;ion nu;-nber iO

. - p e, \\' C use lhc h:i n~ s1cr nucleoli11 . - . . " .
-- accessiu:i number is po, _ • :l pro 1.:rn !rnm S•.•. ,s~-. ro t ,,. n.,s:.:
c/.v CO ,-,D1r+er \n ~ : c...n1: htt-p : //6/as-1:-. ~ , : ;~ 94 0 -· ro use th e nu c lc 1·
J
R-~~EN T- ~ - I - - - - - - -
• if your sequence is not in "' o in. enter P0 9-l05 in the.: c;..:qu•:nc,: CO'..
3
d.,.::ibas<'. , yc u must prov·,.,.. 1• • , • l• .••, '> ·f". fr,rm ·.,. TIH:
u~ t in Inc
n ih -a,av/ BLost-- C'} · sequence you g ive to bbs1 .
p ,s lhc q1,e1y seq 111:nc<.:.
FA.ST A format of P09405
THEOR'i - ~~aJ 9 riry,enfs pmvlde o. ~ ~ >
!.fVKLA_KAGKTI-!G E,\K K..'.l'\PPPKEVEEDS Fo •: " •
cr-e~_ ,E•;!·'.FOl;llll~~GLI
PTP,':\(~AAVTPG!C KAV,'.'l h\K;(Nffl',\KVJiri'1 LVVll'Q~:,:c.,;:;: .\TTT ,•,\;.;. ·. ·. •. 'Q".l i..:.A·•
cornpait2 r,ENet s ~«>C€'S (..A.Ji+{,-, p,e--t/Gu~l'f cl,,-,co-Qc-+€,1zEci EDEEDEDDSDEDED OE:-EDE FEPP IVKGVK I' . . G"KC.,\ /\ lh\_K/1 1.V f•TPG KKG1\J\TP,\ KG,W.;,;(,f'.:
.;, ;.Kf:D;Jl " ~

eo+n ...func.-+tonal o.f'UI ~u+i.·o ra f0j frrfo"6TY"JO-HOn a::::v") be i ~ • ~~~~~~~~~~,~~i-~~~~-~~l~t~~i°-~~:;?.~?~~/~!;;~~~;i~- l~E~~~t?,e~:~l:.gt~1~?r⇒~;,·~•;:~~~r~r0

NEI KLEKPKGRl>SK K VR,\,,\Jnu_;\K!•--J S;'N~~~;~~~~IJ(.,\ ~ v FI:.SJ\E0!.1·
_ov1nGT}.l(J.;fGYVDGIJ\ U,i_fl ,r,,_ ,:, ,C.
Y/Ef!-,'.~ t- ', D,\ t:f(:,LJ ;::;..Q
-&c,v, l..l.€,(. 1 o(esi9~ Cf---'e-r,'es and o.1,·9 n ~ - BLAST ~-a,C~ ~ G1\ Efl)GRSVSL YYTG EKGOR()FRTGKTS T• 1 • ;_KL VI· f: OH t,lf-lf{ I.VSQIJGK SK
11
£;=11sFE D,\KE AL:,sc.,:K :.1r:rEG.RTlf{LFLn~ f ~i,s~, ; \:L~S L; ~•c; ,\ :KFT1_EEVFEf:,-.. -,,
1xv1-c,~,;,, :,, i-:r,.rT,-,.,:

At'90men- S-Et\rc-h lCx:>l), f?DV /d~ o.~ool ~~

GFGFVOFNSEE fJAK,\,\K E.-\ ,\ 1!:.DGE JI) ·· :--:· . . ( ~If ;'·',ru \ f,G I. Sl: Dn [ E'JI.K E<;f-[G",Vf/
--,\ KJ\,"TORE l (-S~'-
(c,m.t - FGGRGGFRGGRGG GG D!'f'.i 'QGK KTK g K Vfl.O\, AKPf, Gf:GG FGGJ (GGGKGGFGGi<GG 0FU;GRGGFG<;?0~ CG

~~;~ of ()LcC'IECrHde ard -p-nnein ck:l::tabas-e, F\ BLAS'l'" ~eaa-ch A

4. Choose Swiss-Pro! fro111 pull <l ow n menu (from Cho ose Search Seti
enobles- a. '">E'SeCCYchrE-Y -to c-omp::ne o ~~ ~E=t,(f= LJ...JtH, °' 5. Selec t bl:l s tp from Program Selection (Algorithm)
11 1pz::,Y'f cn- eta.ta~ of- se q,u EY>C<?s, arc:i rctf'rl-t-{fy \t'o-rony
6. Click BLAST button
SBt)JerT~ -+'>"1C& ')-c'~b1e .....+--v-i.e qµ.ery ~ n<R q_k:,Q\JE' o..
Sequences s imi l:!r to th..: query that b!as ip r<.:turn s ar..: the hits or 111u tch ,•~ - -rn..: d:n,,b:!s .: ) ou
cea-tain -+h'J-€5'hDlol .
search is the targt.!I dtd//b u .)C.

7. Go to print prc\·ic \1· ;.?n u pri:ii page u o. :i~ per tir e i11 s !r u1.: 1i on of c:\:!mi:l(:r.
TI PES OF BL AST
1· Nucta:>+<de &.AST (blos+u)
- OTHE R £ X,-\J,1PLES for BLAST - in sulin , h :i cmog lubin e tc.
2 · P'YOtein 8LAST(lo los+p)
3. r:bs-i-HGn - ~ c i-Pi'C. lcerwve 8LAST (BP5I - BLAST) - __,

~ · N u.c.J..eo+.icte b - -frame -tro.nsxa..tron _ p, 0 ~ -n ( 1o I ost- x) _ _ _ - ~

Q. \1/hich bars in d icate hcst/ wurs t m a tches '!

5· Nu..c(eo+rd.e 6 --ha~ +-cansla:Hcn - f)uc teo-Hde 6 - -f-ro(Y)€

-f-r-~s/cr.HOn (t blmf-x)
► 'I I
l

n ( {:- blo s+n )

6· P(o 4€\n -nu cte o+« :,te 6 - -ho me ---w ons \~o
(tvi eqo - BL AS ,)
1 · LOK9e num ber - of-. 9- '~ seq,,u-ence;-

~ CTtiO DO LOG.-'/

A· OA 1A Ac ~s H- lon
AS ,.
I· Ge -tO NC B\ he me po.9e one ). Clr'c-f;=_ Cf'\ ~L
2. - En-\-e'Y acc ~ss -lcn 0u -
m ~ af-. 'fC} jy ~€ r'l ce o-P-- i ~ .i{")
- -

FAS'TA -fu'lrrn :tl- 1r-i o 9,,D-:'6'1 s.e ~e nc

~ ~~ nct a w . _ _
pw~ dO UJn f'YV2nu. a _ro( p ~ afYi seA.ec+furi _~
3 · Ch oo se -th e ~

l-i· Ch'ct::: or, BL AS T -+-e ono..l'•-fse -44 ie

,-,. esw +.

-------
 J8
PRAC'11C'A-L- '1-
M SA E\T l{C!Sr:-1

fV) l) LT\f' le S E(v U8'! CE- 00 G-N M fi'--IT

2. Lt::l\'C th,: F il e N:i mc field lil :rnk , o th ~ brm\\a r c111rn, lhc ,c qucnces cli rect l_, .

- - - - - - - ciJ ·d --1-<rie r-nuf+t'p1.e seo,1...J. (?n<:8 a.!r'9 nrnen+--of---+0e_

---
A1N : lD
-=>TU- 'i _ ~ - -- ----- - i 3. E ntC'r llir a ecc-ss ion nu ,nber~ of yo ur s equ ence~ i11 1l1 c Un,Prot iden 11fic r~ ,.-nn,Jo .·,

'T 'A?n sect,u- ~ . Enter o m; acccss ion number (or scq11cnc1.: 11::i m..:) pa line. f·or our c:-- ::impk, '-'·'-' 1.: ntcrcJ

P20-172 . PS00 79, 1'02626. P026 I 9. P4 3305. PJ2930, Q91 -182 , P02620. P329J0.
11-tEORi - \n b,otnfo"()fY)0.~3 o se~ ence a!t'~nrner"rl- ls o ~ ---·
:t. Click Retrieve
oF olTO.ngin~
~ rro:ry ~ffi<.'E'3 of- ON Ft, RNA- OY pnrtei~-
- - - r'dfn+if-y :::e31onS' of- s\("y')\.lcxY\+-j ~ rno..-.r be con~9U~cE' of- 5. Download FASTA :rnd save the fik (011 desk top)

+urc+rono.J , s+>,u.c+u-c-E> ar-. evotlttfana ~ ~ohbn.sN p s bek.uE'en _ 6. Point your browse r to the EB! Clnsr:i! W scn·cr p:i~c :it ,,w,,.cbi .:ic.us,shi.:J...b.. 7 1..:
-----
--¼e ~ ~ . s . A1 t9~cA ~ '2(')«::;; of- r,uct.e::>-Ho(-e a,, arYr.ir-0 a.o8 Clust:! IW p::igc appears.

're•sfdu f'~ 0."2€ -+-t p t'ca.11_)' -re~ e ~ ~~c...u~ c....or+01n a r n ~·'><'. 6. C li ck Drowse :111d upl o:id the file from the dtsiin:ition whe re you h:i, ~ ~:1, cd lht
Cja.p.s a~ cnS'E'rlEt,! ~ -tt.e. -..eslol<-A.Q.S' so -+{.raj- <)€S'(d ues FASTA format file

- LUi--t-v-1 i d ~'c'a..( O'r .s\rnilOY 0-0.'YOC"tE'Y CJ\'re o...lt'9 neol in COIOul'YV\.S'. 1

7. Set your Pa irwise Alignment Options on Fast.
A sec1µQNR.. o1 ,'9 0 ~
~
-
C'~ol 6'..1 C(us+aJ '-".( bekueen-k.c...:o
-----t
-zinc -firqe,, pm+e1 ris tden-Hft'eol b--( 9t>n e l'.::cu,k o.a:es~ton nut11'bcai-.l S. Click Sub mit

_____ _ _s~ ~~ in on o119nlY')Rrlt- ~ ac-c:,(Y)mcn ar,CEl8toY,

1+=-_-tt.(.,() You r results c:111 be vicm::d in :
1
m.tsrrarrhes Cl::I(') te r~ - ! ed as ro,·nt- ~ C J { ' ) S and 90.,es ~ I . Alignment
o.s 1.--de-ls (-t{,-ccl- f::,, ,ns<214-f'on oY acJdt+ionaJ mu-+-a:t,ons) irrt-rad.u..c:eo.
·, n oneonc,Ht)e• . In ~ ·n ~~ car, be 10+-E='. o( a~ a 2. result summary and

_ u9h rnE'asua-e of- hc:x.u co1>s-e-.n1e°' o

_ _ _')'(J P?::+kwO'Y "rEt:]fan av- .,_ guide tree :
~ ~nce (Y)ofif rs ().fY'O~ ·n ~ . q s . The eons~af'I G7F b~.e.
.· ct limit as pi: r the in strueti on of examiner.
9. View yo ur results. Pi int an su
- - -~ ~., lno/i('a,{e a S'~ it cn--fune+tO()Q,( o-r Slt-n..ictu~ rn:rt~-
. . '
Ve lf'-f ~hen+ a ~ Vf! ~ s frni /a.'Y Sev,<f>~ c~ car-, ~O:{lo/)fd. maf\uoJJI Q wh ich sequence 1s more c Iosc) 1 , rel:itcd to your query sequrncd

Q which sequence is di sl:int ly rel atc:d to yo ur qu.:r:, sequence?

_ _ _6 _ aJ ,'9()1)')~ ~ [~
_ u-t- , h1'qr11 '1 Veh10b1e oy-_ e.~rret_{_ nu~ . . . f lPSOO t 9!PRVA FE LC..\ or IQ91 -IS2!PRV B \_SALSA d e.?
Q. What 1s the distance o - ·
----
~~--"---- Eh
_ C''2::,, ~ mnl)()t- ~ ali:J~ S)le)_ :j by hurnon ef+eJ6T~ .
~~ r ( ) . ~ \s:n~w9e is F rYl0.11'(~ o..pplie:::A 117 (00:::,+n,.Ac+l '4 !
 ,, ,.
J ''

I
3 ~ oJfhy se_~E n< -e cu r9n ~( )t- 5.
oJ qo nW ,rn -to pnx:lu<'e lri1'9W 1
o ~ (:'.Y)<:e o.1 )9'r) me n+ cv~~ aJ ''-f
~I
coMfu+a:Haro .1 Of '~O C: h<? S' --t
·,,,-t o ,..+- u)C ) o:::.t4;€q_~E ? S' .
aJ_!_90i'Y"l~rns, <J-)h,c h ~ -+c a1 9n
i' G io ~ 01 1 9 0 ~ - _G1o_~
'e , o- .e l'Y )() ~ u ~ efu -( LL) her-. --+1
0e.
BJ t?6 , ~9 td Ll2 ·,
0 e. Vf?6'-( S€w -,< f't'X --
---- -
u9 W '( a-f - ~ a ) '3 t-z.E>.
~~
1
n ~ <J,1-'-'2~ _'?e-k ,~ _s,~ Ho.-Y o, rd ¥'O

9 tCJ6?-J at,qr\r•r.en+5 CQ t,Y 10+ er d ,,....., 9a..ps) A-

('T h1S d0 E'S no +- rr. EQ o
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9en0zrcu J lot::aJ_ o
1"c:r'(")(Y")~ ~+ Et :hr uq :,u e ~ rs cnJ ttd ---kre. 1'1E'U..Jt'Y1
i ~ 6?,S'Ed on ,0'-f '2_0 mr 'C rx 4- vo ~ ~ -
_ ulu n8 ch al 9 ' ~ rn on ol
rne h€ ~ sefu.J-R7Y_o f , s-s , ry-,i
!co,,
ca J oJ 1'9 nr ne ~ a-c e
2 · Lo Co l A- \!9 flr ri~ - Lo
n+ o.i n ~ ,ex -is o- f-5 '~i l ~ OY
r l - ~ st.-l~F c« ?o l-t o cc,
59 Ue ~ ~ c
SirY \J.\ O~ 'S ~f '"? _~ _LU ~°"'='~
\+i nin --+ -he .iY IQ ~( ?y s- ~~ e
C c ~-

Tr e sr- nt --¥ h- (J_ _J ~~ 0. cu 9~ (Y ") ,s °'

__3 e ~~ C.K 'al OJ j n'l'Y"Rrrt-

rve +-v -i~ b o ~ c:,n cl'- ('llO

'Yt lc ~~ n 3 LL .J~ S'L (-f. -Rd f?n +{/

di ~ nc e. k::ekU.JE?Pn loc ctl

an :;(
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s\~ i~
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9 \u\coJ aJ
va n~ sei u~ nc :-~ ~
of p6t.u1'.se oJ 1'9 <Y r> ~ -to ~n ~ ma ye _ -+
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_ a±-o.-+-<rf12. Nw -f1 'pte af iC[ nfY

cpu.<?6:f se-+-- Mu J-H pre oJ 1" <= 7n ~ a'r € o+ wn u~

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_
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toe evc,<c...kft<:J()O'/'f I+ r, e l~
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~ ~. s- h·-n:::o+-k2.Sl2Ed --+n 'un c.. ..u ~
.12rce rf"le+-rf:s Co ri be US<?d in (3'.::)ri~
c~ rl 2d ~
eU '-[" \--K
~c d- -tC Jn -to IO Co de --H '\e . ca±
~c -t-u .lS OA arc

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rs ~ CD<'JSTYUC'+i "°1 _P'-"'f ~O~ C'

+r ee s .
 - - -
i - S1" E-P3 \~ \LC, L\/ {?D ---- - -- -
-- --- -
~ \)AT A BC0 U\S\-r \ON :
I. \ '1 N'S A- ~ 6'w ~(2 a,l 1'9 nrr,Qi) t-- ~ rrcre --\--lra n -+u.Jo ~~ ~00

~ dore ~ a +{mQ .
2- R.et')(\'eve arcl SO.'-le ~ ol~t~ ed ~..1.1-\-i'pl.e. ~ €¥)~-tt"~
Uni Prot- Li..R\os r-t-e ir-. f-A.ITA- +erYfY\oJr ·
3 · C.ot"( o 1Jd f?:~ ~
Cl1'ck. ori FASTPr O.<'ld
Qrr::E'S In

suComtt--. onol anoo '-{~~ ~ -

PS\ c.l u. S'-t-oA W u...e~ i+€ wif'CJCJ.u

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

--- - ----
 21

A\ M - -ro pe~~ ?'n'i \°9erie~--lc. 000.A'-i S'(~ b:.de,d or--i ...1..+,2. a v ~

~~
-- J
<;;eq/Jer)C:£ Ord +a d ~ i ~ eva\vHa ra~ reJ eciiGf'\~' P

~e ~ e ~- ---- - -- -----

pR\N~\ Plc - \-\- rum~ ---tD <::~o~·s'n on e'-C\u+-?a flO!', ~ C<\'3" J o --rc:,-o
,,.

'=\~t'~) ruF Q\-(' CJ(\~ , i rd ivk)( w aJs ~ r~ ~ a.mi"{ S( ~ ci- ~ ry-,:. ---:

're,la:t:-Ed. f")ucieic _a.cfd___:__ ~ enc:e ~ s~LU a. -.µ~~r-0 \d tev-0 c..;

S\rnt\C?-~7 b; ~ e_ oJ 1'9 nt'Y)en-\- a-f- rv--cd--ch·, ~ bD-5"?--S ~~ Q~ ')"

ti..-{afY'O\ ~ou ~~ . ~ O'r€ ("1~d -h-arn ColY\~on arx.es', C i'-+-'ra:r

F°~ess 5'V"Y)t\O<Y_ ~c~ O'l5' --KA<'C.4-iCf'I . 7h i s. assu ~ Ed r-x:.rrc ~---s

d~ S On~ _± ~
~OSS'~C'Q:, l;--{C)r) t9S -2 he d ~ l f ' lS b ~ :l

~ -Pov- ~ e _? t ~ o . l Y \ ~ ~ r ~ + c d-f ao cl- {?~ \co~ '-c.. -h ~ _

~CXB:)U f2E-
p. . QA-TR ACC\)O\ST\ ON ·.
1• _Mor:J ~ oJ,·i f'\~ IY)e-+hW ~uC'"~ a.~ c tus+cu O n ~ , i ~
ence
___used-to consrouct- o.. ph:Jl?:--f: ~c. -ttee °f'O~ ttGO'l s ~~L, ~
- -~iT::_'~ ___·____ ____ __
_ 2.... __ Re-h-e,ue ~ 31!.e~ s~~ i n ~ ~S.TA -f'o6,-Y-Xxt .of._.\;re ~~

_Q-f---k--Q ~"9oniSr- ns of- wh1Ch-t1 rl2_ Ph't\OC\e"r \etiC. cv)Cl.l'i -s tS. -h-ee. l""')~

-+o 6e --fcuro(. Turs rs 0e+')(<eved. -P-ro('(\ uri i P>ot- E-6\ \r\0,--:n.2 ~9..~ .
-- - - -
ES\ ~,u~\ O rnQ:f='-- ~
~- Co?-1 ord po.~ ~ e above seqµ~ce tf"'\

---- _O r d ~ ~ NS'A ·
 ♦

~- Se(~ct- o(8"10!~ ~ -tt'OYn --\-v-e 'rE'SW--t- ~-E' .

5. Se.{8:'+ o. 9 u.J'de.-h 'Ee ar-d. bYQ"'c hdis.+o ~ e-to ab\-oJ n~

d.ero ~ rn o.rd--tt-- .e +cree lerq+h-f t'.N' eoctn ~ r ar h--+Hc:, -tr~~ -

& OATI=\ \N\F-f:r\ 2.Effi1lD N

--
H O f'f'G\ D--pUs ~ C')e , o-rl-v'o lSEt1J fu'YOJ9 t , Xf::"lo la9'1 ,~En~~
__-_~s+-,co,€ on O'Ybi-1;-ts-o~ -+v,!1€s'v-ol d l 0,e,( of- slr..-)1\<X>-tt/ olelt'm- ,\~ ~
OJ icf'")~ of- ~ht ~ ~~ O"a-€_4e' <"Y'ed a.~ t{o~\0 9av~ · ~
o~ iritre">1-l-ed --h-arn o.. Cb"0fr'\O f"I oncerle Y -H,cl--' f=>Sses~ 'S\C'Y)i \Ct"Y
- --
5¼'U( 'fu(e,~ 9n-+1r ie st->-uc+ vre of--ive o ~ fY'a'--fbe. ~
---
d~-

HONOLCX&;)VS ARE= 871-<ER . 0 f:!THDL CJ00S, PA-RA-LD Q-S, )(E-NOlC:4-$-

1· ORT1-f0 LOCrS; 1ne---j on-e pmd uc-ed °f s,peo'cl.:HC>n . ' I ~ 're~~em

9-e0e s- de'">1Ved -A-GM a. cornfhO () a~3-t-C Y -+ha:t- d ~ e d d4e~
_ _ oUv~ rce of---¼-Q. CfYCP r\CSmS . ~~ ~f'lol -to ~ve .s/(Y)ilay +urefui

_ ~ Pftt::-IKOaS ·. IY1E'f o.~ f'D~ d °I Cf'r-'12 du p \ fcctl-('c,n · -n---,~ 'tt're~I

_ 9ene d0i11Ed .f'lro(Y) co tnt'Y1Co a ~ 9e~--+hQX o\ u.p1 1'cat(on
wM-h·, n on o is:cpr,iSCY'i ord ~'2..n su.~ ~ , oU~ d • '1Y'e ,-tu..D l

_ CD~ E'S.of---\ +e d ~ ltC£:ti€, q Ere ord-+he rv ~ : t ' f ;Y"'\-+tre. eJalu:fiOr 'O"'J

__\l_n ~ e a~ ~ ~ d - t o OS p cxYOJC4S ·1h~ ...\oerd -to ~ d~+<_ ,({#1
'XENOLO ~s~ ~ ex}€ ptx=tuce d 61 hC>i-zof'")toJ. 9enQ ~n~ ~
.-tt,,o cr-,go"-<.srns • ln Gfh<?r ca~~, shyU\0;y "-BJ''c,r,s tr. 9 eq,ue')(Q S rro-/ "1

v,o.ve o. rornrron a n ~ bu:r rr0j ho..'-fe °'-""-lsen_ h··~~n: Ae-,Hj 't7-j_ ,,,,

-¾.X) eVOlu+ <b~ (.:o:H--i_u.n.,.s' con'J~ l rc:r on ~ e ~o::\1Cf7S',

 RASMOL -E xc-rcis c No. 1
;
1 Doub'c c ,1-. qASWIN ICON

:? <=fLE o 0 E'- 1CO\V.pdbT.\T•\·GO\ S,ria,ng Protein 11' 0P-DNA c1)11lple);)

\GO TO $1 RLICTURE ANO LOOK FOR "1COW pd b FILE)

Put! co,•, '1 the display me/'lu and c-'iange the rende1ing to "ribbons"
\· '3-\-ac:M- SPD~\f
You shoulo t;,e abie to see that} cu l1a, ~ betn-shee t, alµha- hellx, and a short
frag~e~, o' ON.\ 2· cy.J -t-o_?OB oru ~eve I HF\" J.
5 Pu!I oown tile co lors menu and cllange the coloring to "structure". The PDS \1-fe) (oo-+c., - load IHft.-l • pc.A'o(rnenu..fi(-e>c,?e<'I
co'crs ne o show that TSP ,s composed of a-helices and b-s hee ls.
Si->uc-ft.ue Ond, 3e!E'C't- I KEW . pd b)
~· (\ \'Cl::: Clrl -the ¾Ee Ct.('YSOY C -
6 C ick en :ne Rasmol Command V\lindow and typ e. (type th e bold tex t and oM-rol b..ct-to~ O""--f-he -tco\\co.Se Ord
press en:er ~ /l'Ylove/erito9e l½s::.i2....,rre -pl<:+v~.
- :ype- restrict protein (:hrs command cu ts away all atoms except protein 4\ Ope,--l-he C'Qif"Jtn,\ funel (l...(,J/rdo..v f'V\eru')
atoms\
5'·1O pe(') -+Ire A-\(91"'\~J wirdow IYl~) -
S ;; ;>=- select ONA (selects DNA)
---~-
6· saect- cu I
-
r)..J
-,
C \l'ct:1
__
n9 0(\ -+vie l,...,c_
I - C::.' ....lf"'>
~ - ' ><..A'C. G
f- --
O · O- lo'ce.lS i~-+1,,,e
Fu I dc1·.n :.re display menu and set the display to ball and stick. Note that
m s char;;es ,ne rendering only of the selected atoms (in t11is case, the DNA).
~ nttrol f'anel 1~ 9o-ki ~ u '$€.1.e(j- _ > ~1 •
_ _ _1_·,_S_elect- cr'Yi b'oof\' -flror() ~ Cbr)+rnl ~n'2l C
m o::. o l".--01 \u" OI"\ -++<z ~
;Q :ype- color blue chan~es the color oi the selected atoms lo blue. Try green,
·e □ cyar e:c - ' ranQ.( -\-o.b) d
~1 ,ype- select hetero selects non-DNA non-protein atoms _ 8· C'f?lm€ __9(~~m-ca~()')11 (c.PIC, ~ ~C':t<J.&€ ,o.ct~,b\~)
i2 Pull do,·. n ,re display re,"'u and se t the display to "spacefil l". Now you can ard oli'.spa
1 a~~J:.S\--c.J....u CA +m.ce a<'ll.'1 ,.,1,.-ou.;_~~,- ---')(e,~
see the oxygen a:oms irorn 'Naier molecules. In an x-ray diffraction · 7
~rcl<?a- CO\O-.A'Y ar-d. Disp..a
1 ~ s ~--t<',€,l'i; ·
1
e9erimen: h:,c'roge:1 ai0rns are generally not ob servable, so they are lef1 out _ o_,€
of the coordma:e '",le 9 J Click - s19() d- r3\.-,cu.J 1 arid <'std.<?' in co~~'_e._o.0e\ ( S't'Y btA·u....,111

13. type- co lor red changes the water oxygen colo r to red ld1's~ 'Y)
1.1! Lei's take a look at the DNA in the absence of everything else. ~ 8::'t- (t&-- r v , ~ ~~ os-+v'\e 'oU:ttDm o f - ~ cc~\ F<n<?I)
15. rype - res tricl D NA ..µ.,,e NAQ- lnniwttfY 1'-IA&-201 -2..0~
16. Pull down the display menu and sei the display lo " ball an d stick". 11 • Click o.9a.in~ rshCL.u 1 <s id'c'"\ ox)~ \aide C'Qi\Gl..V"""

17. type - select c or g 12· L°O\OY~ 'i.e,1\CUJ(~ ">CJU9V"I cor-rh't.il ~ ~ GI)

18. type- co lor red

19. type- selec t a or t

20. type - color green

 P~A c:-n C Ai._- \0

PRePA-l<--A7lON OF P \C..-k.Fl.

~ M - 1o f7Ef0~ f 1ck~ o+- chil l/ /YV1o ~ a .

-~ E(vU IRE?-MB'-/T- ch~ l'j [rna n5 0, u-ien stls., ~ , sto
.l~, sp t~ °"'"'.d
C D ~ i ~ ,--+ u~c .,ch ill "f pcwdeir CN" pld:: el rnos
ct~~'_rr,u~ )
J'ee m ,IY)e +hi1 oil ,e+c . 1e.--nc,n y..,t.i 'C~~ ~ ~ v ~~
(1.f:.-yG<J.. ~rrt- )_

_ 1· C\eo n o.JI u..+e nsHe s ·a.rd <...LX:)1S'\<..i 13 +o.6 te ~pe

1rl'f -
~- Clea n Chil \ies a.s. u....Ja I OS l€~ '1 u-...,l+ n
--+e:,f u . . . J ~ .
2>· kE?e f' oJ\
S.'pi ces a.Std <2 a.s ~ ( a.s so..t+ - and . Gi(.
~- ctrop-k,-,e CVli !I,~ irrte pcec-es ~ opt-1mL{m s\zE ?_._ _ _ _ __
s~ u-t- on -+he -fiot r.e. orot . k ~ s-\-o Jn \.eSlS ~
fD+" ---A:n-1 heoi {1 .
--TT,e.--f.1orne. sy,0u ..td k:e mod 7Ctl- e -+c \CJu...:>.
(s· TaJ:: e 2.- .spcons- cf- oil Ond hea¼----H--ie o)( on ~-f ior r-e - A~
k::,uo-11 i / of- 0 l_! . --
1 · Add hoJt - .s.p=cn o+-> ~u~-~ -e(~d ~rri h cuf-~ n of c_un-,1 n o._rd. ~ .
_ '8· A::1d --Hre n ~ ak>~ ~ n ~-+< ..nm «~c. _r_oc.udE>a- ard
I f.2SS
8€ol ch~1'l
r°Ll..'.)dQo CJ¥ pie ~ ~asc uo. o.~ p-E>Y 'i~lX Y --+e,, .~.
9 ~ ke~ s-t,1 ~ ?1l-- -l--vl ~ i ~ d i ~_-fua m \C:u.J
+-{O rne c...t.J~ _

· 6u~Nf'9 --\-H?rn _·
___16· Wre n -----tt,,,e 8?\C< 2S ore{ co---:d ', ~ deYe .\O f'
--+t---ez,-e ~~~
oil CAdd CVO fE'd chill / O{rp_ ~f \r")C:-h o+- ~ ~~ rvux 't-\ -~~kk/;,,
 -I

lt · \c~ ~~ a.1 \ -\-he~~ \C"'lc::ped ie~ +\\ \ C h'\\ ''i ? I~ 'oeco«.E'

mode~, S0++-
\2.· \+- ~ ~ k ~ ¼~r"'\~ 't~ p ~roi:i-i<Jri a f\d. a.do s ~(~S' cx(""(j

soi+~ f~lr ~~ .
13·_orx:e -++e c'n,\\\c>s a-ise- ~ ~ ' , sof+ ord, ter-rcf) j u.>.'02 ( 'n().tt- ~(\')

ln ¼e ~ ord tc"I~ -4-he~i~ -¼rMJL9W, ·

\C.. ·To~ ~--the ~ ~ + \ O r r € ard oJ\~-+re ~ n~ a n --te CCI:)\

no:nxol \'f . k:Eef _rn,x1 ~ --+he_ ~ k4 s . \ ~ m H-0. n-\-<'-f ·

\
 P1'2AC1 I CAL - \\ .

\O\e.E1'FH2.R""I ION Ot= 'J F\-M

ft< M - -ro p-,epa tr€' Ja m -P-trom 91,Rt> f1"uJ \-- ·

eECQu! ReMl?N T- Frui+.s 0"'6"'-HIU1+ ju..i02, s u.c:p."' I pEQ·Hn , ~ s I l~ , cy~.,s )
9,t-ove ,·e tc.
~ Jo.r-n is o.. fYOCE'SSE'ct -R:>od p,epo ~ ~ rn~n~ o.-fYl.J.tt- :Ju.lee -thic.J,:::-<:?f- O:fley
addinq s u cp ir ,n+o i"t" · \+ 1S""€r()Oj0 ~ I" cy :,od Cbnd lf-{ari -f'cir a rons-{c(e ~
) ' of-
lO~E'lr -Hn-e 1+ ~.Se.lt\{ 0-{ r'~ e is L.t.SG:U and. +h....ts ln--¼--.e ines-e-n raH00"~ .'
PeOc.FDURE- •Tak:-e on-., f-trw+--- of- 'fC:/J."" c h o ice (~-fe rabt ~esh-, ) .
1
• l"1as h -+he-f'! S'u~ colfefu ll
1 and c~-+h ern tnto .smQ.ll pteCE?~ ('if--~- 1i~
'YE'rn:::N 2 S\-:::i~ o.nd sEEds ) .
• smas h -+<r e~ pl'='CPS and add ~ o:te OrnCil.f( )f--af-- SLACfo' {rrtc l-l_
(the ~ y 0<YO.Jr ,t- (.J...)\\I VQ~-ft ro<'n-t trW+-to -ftn..JJ.t-de .renotl" 9 on
su90 a /ocd O'.Jnt(? ~ of- 4tne -tt't..Jit- •
• l'-'1 fx 'l.Uel \ and lool I t.ue.l l In -+v-18 rY'l l x+u-ce ' n o. ~ on r-ned iu M -fi.0.. rv-e
ard k.e~ ~ "9 corrttn ou c; .
• ~ Ll...)V'Jt0):2 M.l~6 € LL>r'll loo(l and d.evet. q,s b 1~ bublo\ es ,.-,,+<oJ1 LUh!ch
lafE>a on r--re.dLJce ··,n s-ize LUhen m1~1S E' s·\eurt-~ -+!.r,ict::::en'1()9 •
1
• ¼I hen tt- beCGmQS- ~fc~ n l0J...l +tre~a <Y12 orid s-\-l< Cafr+ln ou~\,
.
• \+- ~ ~od d fEC-4f"l-+c h<3p \n SG\ici~ C'cn-fan ~~u cl-- ·
• \.A.lhen-+<re IY)~~ (oe~ -+t,,,c~ cen0-J.9h arid ere+- sett-fe d < r m ~
u..e. co.n ~--¼- e .Jo.rn is ~~po~
TESTS O F- .J-A-N -
• t +-- S hOUld no,+< DLu 1-f----to .~n on -+t,---e '1 l~ f> la.1:€ .
• l+ st,-,ow d hove e ~ h_<......( n 'tt=oirrn -tex+u ise o rd -MOns pa.~r.e e .
• ~'Ir i-\-- 1s coo\i~ a.oe s\.ro~d be. alo\e+ o c~JCA <n-
 PRPC_-t\C Fri.__- \ 2

~M- TC> ~~ sauc e-tto m q iven ¾~ (Ta ~)-

~ff9U\ ~R"'l ~T - larv-a -t-0-k uits , ufE'ns l fes ,onl6() , 91~ ,sat+- ) Qo ~ 1c:: 1

c VI Hl)' _pc>l.l..Jd.~ ete .

----------
Pf0c8 )UR~ -

• C\8:)1") -torr.c::tl-5 ~ (--to YY,()i-e '3r.cu. {d k::e we I ')--j f ~")

• Cu+ --+-6rr-oie,es tntc t''e~ s Of'ci add cur onion ,90--,1,c) saJ+-, 31~ ond
_ c~ pcu.. d~ as pell nB::d cl- 'fCU'6' -+-o* .
• 10.\::12 -+h2 Luhol e m'rxf-u&'Q
____ 10,---thQ. pG+o nd stairt- hea:i-< '19 C() (Y)Ed tum~01€

. • -Meo er-0..t qh C'Co\::::11 +<l ~ l:::eC'Orne ~ ord-~-t- m ,-xed u...., K-h

ock:! ~ i ~ e ~ . --
- - ------------------
-+o_o.."ot i
- - __: ~rl- srras h.5 - + - c ~ ard. k~~ wh:l\e rnix+< J~ S-hi~
_ . __
wYtli "-\ of- .snu_CQ
~ SN"JCSh<~ ~d ~ 0- h~ us slu ~~ of- a.A\ t:91Cb\,E'm-3.

_ · ~ se-H--f ~ of- so.ucQ ( wh2is € SClule becom e ¼ ~ ) 9t-m.i n I+-_

Of'P''-1'7) p->eSS U€ (J.)V1Ch hQfS in sepa ~r::9 SOLl@ -fro<ll +he crl-v\-<?Y

_ _ \ ~ ~ \ik'Q ~ s\<,C\ 1-to.-ro:t-o seeos CS'1" pEei(')1 s OY--fibx:'S a-f-

01"\lcn I Cf: !S'I \C Qf'd 9'i'nq~.

___ _:. Ccci-+v-e ~ c-t, i+- ~~ add P!::~ c r > onol bo-W e+he ~me
-R:; tr" ~ n aro -+u'INV\€'o us.es .

- -- - - - - - - - - - - - - - - - - - - - - - - - - - - -
 C O LCL>U'l7 PD -

fr S1A-Nr)~l)1 z..EQ ,,f>!U...RS

F sQUASK ·
PRE-ffiRAilO N O _ ~6u.l-1 JWCT2 -.:.. 2 .S:/ .

o.SY1 ...frarn ...-w,e 9iven r n ~•OA . A-cid•'~ = l · 11 '/ .

R1M- TC pefOre -fuJ.it" 59)-A
tA.J().;ke6" -::. 2~ -s ·1.
sucp.Y, ci-t->1c oc-1ci1
Rcq}u1ReME'NTS-
R.
.
but- -A ()(Y7 'P rnenno\e,
-T r ) ee-.f-,i-0-c+orn0(-(:'y- ~ d ln °J =- IS
Fl · \ n9'>"0'.:f1err ts- ,pe (both op+(ana.A) .
:x·;. o-f- pwf = 1s ·1. of- pwp
. h l+e a nal -+bod colour
1;:"-rnetalo1.S'L,l,\p .... 1;::1..-<a-e+te' pi~., ~ o.. rH(e.o \ 00 9m s of- -puAp ~ \'S°)f"YIS o.f.. T · S-:
YD1i.JS- Ho nci ~ ( " t e l ' 'cl
~
e, . .
stond , ..funnel ' N1E'O.S'C..,H1n ~ C'-(
(ind~, (;Ll<2i<=fhin
-
3_ b:::t.Jar,ce, IY"ll..tstff) <:\~ ,
2.5 C)'IYlS of- pwp-= ?C. '1= '> o+-- T · S. · <; .

. ·. ~ =-X
beo.keo 1 s+-roin<?r . _ ----- 10 0
. indr'c-cd-O r, O · t N N0-CH-{ . I
c- Chen-i,coJ s - ph<::na'pH->al0 n - -- :x. = 3.75

~OCeDUl2E - _ - - -- -- ~ :. suqo.y -+o \::ie o,,ck.ct~ = '-1'5- 3-,s-

= Yl-2..S~s
i· feel ,Cu be o. rd 9'1'r.d pee{Ebl pioeGfpl.e c:utoes +o °' f u.1.p. __
;/. A-c,ct~::. ,-...IO~o.J.. rt<, (No..0\-f) xBy x IC:Jo x. 6 -06½ vv-el~ Cr+-- pwp
2- The S'fD,-.,qa·x:::Hz.~ VQl u~ of- °' --kui+- ~osi-, o..lf€. 1 iven a.t~~ 9~

on-+<ne f>0-9.e. t -e A- _ _ _ _ __ -=- O· I >c f3."Y x100 xo·6 Y (O sC06bi c o.cid C'oY"is+o 0+-)

~ lnhierrr ~
L
3. fO ~O<, of. T-S'·S ~ nd o.a'a.H)_ t:,.J ~ ..frcivn O'r€

lco:f-ch Cf--frruit--t o Q ~ Q . 'h-er;ce i~ I'S. e~~ oJ -to C'clCu..(~

T s.-;) OIY)O-.lrrr of- Sucp-y ~ ~ cidi:'.:'r_ ~ d add, ~ Y and. a.cfq i

OC'C~d ,·l'"Xj l "(_. '/- A cid ~ : : 0 · 2 .S

: . 10 0 9rv--, o+- ?uJP C'a('-..+a.,it, .Qr -:::.Q . 25cj'n o+ oc i ~

.- _ 2.SqY'Y'ls c.,-t- r'uAf> C'<Jr--.+-oJ0s =- x.~ 3,,1-s

--:: 0- 2.s x. "2..S

\DO

=:. O · O [ ~ of- o.c-,'o',

 23
'\!Ou.> •
ct-t,;c od::" ...L-o 6e odd« i = ,,s - o-o(
::: . J lf OM S

(no+- rnQ1!€ as »- IS .s1t9h\-11 acidi c) .,,+,-rue ~ ? n~ O· \ N No.OH,

rl.,llp .:.s· 2.SG'r(') s = 2..s q ....... · 'The B_: R. is n ~ p1eose. see

_
b End P3i1rt- Ee\a u.n~ ---.,, r=ue p l n'l:::.
~-: uS'f ...1591)'\s = ...., ,. 2..$ 9fY\ . _
-
C
QC(
__ __ _ --_'n_i~'.:LE9 e © -+bY m.!~ GnS '
----'!Oi
1.5 1. 1, vvql'\ "' S'

?,2. 31

100 - :=-a - ,::,- C=

un ,i () ms€ o f - ~~
_ As peo -+v-.e Ql'{) Q_(n f-~i0 €tJ. o.rct ~hoL
:::. 100 - ['2.S-.. .( •2.S+ u4J h. e,'Yi""J -¾a o. bG)\, ('Oat .
-+vie ~as
[67 ·6ct]
9:PY arct ct+rlc acid -tc 1Y)()J; :e
::: C!) -
A:::id. jUJ'C'e ~1 ~ ir\ ~ \ ,z..~ loe{+( e .
_ . -------
po..&"t:5 cf- (..,I.Jo-le-<
M'\ X \ pa.6+- a+- ~a.S h : '?:, Cl'/ I...(
 µ9 n (-'C?v(--1,..., 1 kC\ --f"<v~- \)U-lp : 1 k 9, SLl.l)O. "Y
M El'.1!w'4V) pecH '{") 1...ko., -fc-w-+- 't)u.lp : 7 rn / '?So °i'(Y"\ 'S,l.A.q c.(Y
1ow pec+i,--... 1.k°i -fi-w'+ ?-LJ.\?'. Sc.io9r-n~ su.9qy
P\2.Ef'ARATlON Of J ~L'i
rs w 9 1r, ?£'C-l-( V') --L H l°Jh s u.90.v
l'-1ed. tl..(rn pe c+-< r, - R.'<d..uce su0iov a Mou('rf--
...c, 'el I½ ...f6om--W£ ~ I v<X1 flrt,Jt- . \
HIM- To ~ 0
J , ttt'I \Du.J p-ec.+ ln- LDUJ s w:p-v
-- I I
P?O..An.rr_s-
Rfq>(Jl"-L l' ll:''t '
--

Gt,tovo ju...,., l -
c·
cl,. !'loe ones) , t . . u ~ ' C:

. ' ._~,~ SL-,

~"--',.__J

C: 0.C'fd, ~~.
/-.'>'
; o... n ~ ! l " k
In ....w-,e v-,-e3e rx:e of- 0 1'"'1 o.c1d 0 0 o'- 3-J..°iC('y J p,2C+i (') - rr O ~
0 srnc::lll m,n1 ~ , T"(UJ nE>-c--.
~ \ o.\cohol , ve:s;?}. spoo ' 1
i. · (:;,;u.O..'-I CA ('2...SO C)IYIS.') ~ Cl-lloed (tAJ i4--h S'>=-tr,')
2 · Cover: c...ul+-v, u..lo±e o ·
PROCEDURE- 3 · P-ctd ' / ~ --t-e p c.\-h'\ aclo( .
i . Cube -+ire. --m.~,
"- .u.... a,-u
1 it::OCh'
- - J·~ enou9h u..X:d:€r --to C:Q\R~--+vi€.~lt- - l.-\ · B C\~ -t-n °' 'oOII CJ.rd ~t'Y\IY'ler -fcy l o <Y'll f) .

2 · Pdd 1/4 --to p Clt<iC acid -Ri°" 2..SG cyms- <=jUO.\.O.. C'rt->1C Ocld. ~r>S-to f; · '\"e'6"'t06YY"> o.J. C'O hd -\e"?t-'....+o VE'!"~ ?ro--{ f"'\ e .x;:+YCAcHOri
r:; . 2... ll..LJY\.f' ...foir<Y\Ed, so pecH n CO"<t"E'& ls. cY\~ Um
e~ ~ n oL..rl-- of----tn.J..ifs, espedol1 '1 ---fr'Grn --+hCR.s: -h-u.tt:s wh\~~
1 . -'· ~5 C\'C'r\ o{-- .s~Qv o.d.d 8:J / 10~9 rw :; o+- -ftui-+- p...tl P .
~ 1€ ~ In o.cid. ~~ l'2._ o.n acldic. pH !S. ~~ --fc~r~~,.., '6 ·.·. 2...11 'lm s4a_v odctru ('2...L<.9:9ms cl- 'ca\l~ ~u.i+- e -x--1-~c+
e~c-Ho'2.__wh8'1 ~'J joC'Yl .
9· Boilard "~'1
'V
u., µ+,, y:>\G.:l-€ ~ -f-
3 . Wren --++-e mt)\"\-{.(re comes-to o. loOil, pt.t+- i+-cn S'Gr-ne -Feiir- o.b:lLGt -1
\O rn in s . c oo\ - > stdo-e ir. s+eYt \\sB::,1. k:0\--{-{,€>

C., · Pe ~ m,--+he Cl.lC'OhOl --ie~-+c ('Of\H'fcn ~ n ~C4-/Cn i-€,-Act:;, 1.

dmf ~ above rr, r~K'E' In 9- srna.u ~ C'OrnQinin) ~ I aJ.<::oy,,o\.

f+---l--lrie dmp --¼ams o. luM p ~ f'3 h~h 1n ~ c+ln . i+- 1-1- fS-fc6TnS' 2..-"=> -:ie.111
\n ~ le!A"\S
Q oono.:ke v€::\dect!()n
0ono.H's
lumps , it- i's lei~ in peC't-ln. I+ l's di'S'?E'~ d irrta --+vie su«c.i~no(t) &u.bva -t S-«f<Y -t- cihic adq NOn - v ~ a r , _
N C) preseYVo.,\-h ,
a./ C'Ghcl Nlediurn i+ is v ~ \c.i'.:::1 pe c+!f\ Cc~nt- _ _
2 C D l0 u 'C
s- \..-leire , ~ one \u ~ --foll"~ d.0">ertt ~ ~ ln'9h - ~ ~ n+- •
s. As
PQ I?'
I""' ¼ e "'°""coi'.<a:J vmuf's ~~"':''f<Y o.dldoci du"":J
DYOC+ tctl.l.S , • .--.c- ,....., .,. ,.._ .:.1..
, r -- ~ '--'-" rf'JJ..C'~?-~ -~ -tt,--,e UJ€A'9ht- of- -+he bai\~d-+l!V-1 '
fU:Jp•ln a f'\o+-<r,eir in~rie, ~ ~ e:; c......JE>re u.~e:J.,---4-<rie pec--1-in
COn+E'nt- l.UOS ~ lurr. i' -e --\.-(..,e • -- - ~
. · ~ eiq\--)'?d. ~? \~- Gn-,c ac~ __
'Yl 1X-+u. ~ c....u::)s 2 \S 91'Y) so - ---~-
- - - ) \ 0()0 9Tn f-iru.i+- ~ r =- '6~ m ~ ~
2....\5 = X _.,....---;
7
=- ,i2.. 9yY") of-..su..Gf-
 I
r· I
,1 l

C'cn--\E'rrt-- a nol b ::i,\ --1-i 11.....U,..,e e nd.

po\"+
1
· U~ su cpr as pe r 4v-e f€c+ln
( p,o.ce o. ci mp of- loo \\~ ~X'TT"G
.~
,s- 0
bt-a.l rx? d 0-s:- pe~ -+he plcd€ --K>~ .
d mp, .
on ° C'ald p\Q!e • " \ o ~ sh ow (YI 00 2e o L.tX -fro m ~

_ Cbo fi'c ms ----1+-o:t- -+h e )e( ''1 is kn- mE 'd ar d r e ~ hE1:Xl-'f~

.-n is
~Wd .
.Y ln+ c ~\ \z ed ~e .
~ · S'hGt"' -¾--e -fta rne . COc, \ an d fOu

- - -------
PECT\N

su cpy, J+ -f(T )rnS ' o. N")e~ h f ~6 "k

1

~ el-h,€Y t ~o. ~ l Wi on erf- a_

ock:J( -t-

Luviich T? duaJIJ ~ DS i-t- coo, . Tu ts '1€ -k. uO ~ { s a. 9e1 CA(" )d. -fe r

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