夞愜僨乕僞偺張棟偐傜棫懱峔憿偺寛掕傑偱

揳捤棽巎乮搶嫗擾岺戝妛戝妛堾墳梡惗柦壔妛愱峌乯


儅僯儏傾儖廤堦棗偵栠傞

 

亂侾亃僨乕僞張棟偺棳傟

 

 

寁嶼偺棳傟偼戝懱埲壓偺偲偍傝

(1) 寢徎妛揑側惈幙偺寛掕丅

(2) 夞愜僀儊乕僕偺悢抣壔丅

(3) 寢徎妛揑懳徾扨埵偵暘巕偑偄偔偮偁傞偐尒愊傕傞丅

(4) 悢抣壔偟偨夞愜僨乕僞傪堦偮偵傑偲傔傞丅

(5) 摼傜傟偨僨乕僞傪傕偲偵埵憡傪寛掕丅

(6) 儌僨儖傪惛枾壔丅

(7) 儌僨儖偺峔抸丅

 

偙偙偱偼丄僯儚僩儕棏敀儕僝僠乕儉偺夞愜僨乕僞傪幍柺捁棏敀儕僝僠乕儉偺棫懱峔憿偐傜暘巕抲姺朄傪梡偄偰埵憡傪寛掕偟丄儌僨儖偺夵椙傪峴偭偰傒傞丅椉僞儞僷僋幙偲傕129傾儈僲巁巆婎偐傜峔惉偝傟丄堎側傞傾儈僲巁巆婎偼埲壓偺7巆婎偱偁傞丅

 

巆婎斣崋

僯儚僩儕

幍柺捁

3

Phe

Tyr

15

His

Leu

41

Gln

His

73

Arg

Lys

99

Val

Ala

101

Asp

Gly

121

Gln

His

 

 側偍丄杮儅僯儏傾儖偼丄徻嵶側愝掕側偳偺婰弎傗寢徎妛揑側尨棟偺愢柧偼徣棯偟偰偄傑偡丅偛梕幫偔偩偝偄丅

 

 

亂俀亃Mosflm 偵傛傞夞愜僨乕僞偺張棟

 

1. R-AXIS II C 梡偺弶婜愝掕僼傽僀儖偺曇廤

揔摉側僥僉僗僩僄僨傿僞乮Linux 側傜 gedit丄Mac 側傜 mi 僄僨傿僞側偳乯偱丄壓恾偺偲偍傝丄弶婜愝掕僼傽僀儖偺僼傽僀儖柤偲怳摦妏傪曇廤偟丄raxis.inp 側偳偺柤慜偱曐懚偡傞丅愒偱埻傫偩僼傽僀儖柤偲怳摦妏傪曇廤偡傞丅偁偲偼偙偺傑傑偱傛偄丅Mac 偺応崌丄夵峴僐乕僪偼昁偢 Unix 偵偡傞丅

 

 


 

2. Mosflm 偺婲摦

僔僃儖偺僐儅儞僪儔僀儞偐傜 ipmosflm 偲僞僀僾偡傞丅僾儘僌儔儉偑婲摦偟偨傜愭傎偳曇廤偟偨僼傽僀儖柤偵 @ 傪偮偗偨傕偺傪僞僀僾偡傞丅偙偙偱偼 @raxis.inp 偲僞僀僾偡傞丅

 

 


師偺儁乕僕偺傛偆側夋柺偑昞帵偝傟傞丅儊僯儏乕偼偨偔偝傫暲傫偱偄傞偑丄婎杮揑偵偼 Find spots 仺 Autoindex 仺 Predict 仺 Integrate 偺弴偱恑傓丅傑偢Find spots 傪僋儕僢僋偡傞丅

 

 

 


偄傠偄傠恞偹偰偔傞偑丄婎杮揑偵偼僨僼僅儖僩偺傑傑丄偦偺傑傑儕僞乕儞僉乕傪墴偟偰恑傔傞偲僗億僢僩傪扵偟偰偔傞丅搑拞 Threshold 偵偮偄偰恞偹傜傟偨応崌丄偦偺傑傑 OK 儃僞儞傪僋儕僢僋偟偰恑傔傞丅

 

 

3. 寢徎妛揑側僷儔儊乕僞偺寛掕

 

 


Autoindex 傪僋儕僢僋偡傞丅婎杮揑偵偼僨僼僅儖僩偺傑傑丄偦偺傑傑儕僞乕儞僉乕傪墴偟偰恑傔傞丅

 

 

 

嬻娫孮偍傛傃寢徎奿巕偺僷儔儊乕僞偺岓曗儕僗僩偑昞帵偝傟傞丅PENALTY 偼掅偄傎偳妋偐傜偟偄偑丄摨偠傛偆側 PENALTY 偱偁傟偽丄婯懃惈偺傛傝崅偄嬻娫孮傪嵦梡偡傞丅偙偙偱偼PENALTY 偼庒姳崅偄偑丄Suggested Solution 偲偟偰 Primitive Tetragonal 偑偁偘傜傟偰偍傝丄幚嵺偼 P43212 偱偁傞偙偲偑曬崘偝傟偰偄傞偺偱 10 p43212 偲僞僀僾偡傞丅

 

 


Predict 傪僋儕僢僋偟丄寛掕偟偨寢徎偺僷儔儊乕僞偑偁偭偰偄傞偐偳偆偐妋擣偡傞丅幚嵺偺僗億僢僩偲梊應偝傟偨僗億僢僩偺埵抲偑堎側傞応崌偼丄Autoindex 傪傗傝捈偡丅

 

 

 


4. 夞愜僨乕僞偺悢抣壔

丂Integrate 傪僋儕僢僋偡傞丅夞愜僨乕僞僼傽僀儖偺枃悢傪恞偹偰偔傞偺偱1枃栚偐傜31枃栚側傜 1,31 偲擖椡偡傞丅偁偲偼婎杮揑偵偼僨僼僅儖僩偺傑傑儕僞乕儞僉乕傪墴偟偰恑傔偰偄偔偲僀儞僥僌儗乕僔儑儞偑巒傑傞丅

 

搑拞偺夋柺

 

5. Mosflm 偺廔椆

丂Save/Exit 傪僋儕僢僋偡傞丅僷儔儊乕僞傪曐懚偡傞偐側偳偄偔偮偐恞偹偰偔傞偑丄捠忢偼偦偺傑傑儕僞乕儞僉乕傪墴偟偰恑傔傞丅

 

 


僐儅儞僪偺夋柺偵栠偭偨傜丄偝傜偵 stop 偲擖椡偡傞偲廔椆偡傞丅

 

 


 亂俁亃CCP4 偵傛傞僨乕僞偺張棟

 丂偙偙偱偼丄僼傽僀儖偼 Full path 仺 Browse 偵傛傝捈愙撉傒崬傫偱偄傑偡偑丄Project directory 偲偟偰巜掕偡傞偙偲傕偱偒傑偡丅傗傝曽偺儖乕儖偼僐儞僺儏乕僞偺娗棟幰偵恞偹偰偔偩偝偄丅

 

1. CCP4i乮CCP4interface乯偺婲摦

僔僃儖偺僐儅儞僪儔僀儞偐傜ccp4i 偲僞僀僾偟偰婲摦偝偣傞丅

 

2. 寢徎妛揑旕懳徧扨埵偵懚嵼偡傞暘巕偺悢偺尒愊傕傝

丂

1. CCP4i 儊僀儞僂傿儞僪僂傛傝嵍忋墿怓偄僞僽傪僋儕僢僋 仺 Molecular Replacement

 

 


2. 嵍懁偺僞僽 仺 Cell Content Analysis

 

3. MTZ File 仺 Full path 仺 Browse 仺 mtz 僼傽僀儖傪巜掕

Mosflm 偺寢壥傛傝摼傜傟偨 mtz 僼傽僀儖傪庢傝崬傒丄寢徎妛揑側僷儔儊乕僞傪擖椡偡傞丅傑偨偼僷儔儊乕僞傪捈愙庤擖椡偟偰傕傛偄丅

 

 


丂4. OK傪僋儕僢僋

5. Molecular weight of protein 仺 暘巕検傪擖椡

僯儚僩儕棏敀儕僝僠乕儉偺応崌 14300丄堦師峔憿傛傝偁傜偐偠傔寁嶼偟偰偍偔丅

6. Run Now

 

% solvent 偺抣偼捠忢 40乣50 掱搙偱偁傞丅

 

 


僯儚僩儕棏敀儕僝僠乕儉偺応崌丄寢徎妛揑旕懳徧扨埵拞偵1暘巕偲尒愊傕傜傟傞丅

 

7. 埲忋廔椆偟偨傜丄Cell Content Analysis 僂傿儞僪僂偼僋儘乕僘偟偰傛偄丅

Close 傪僋儕僢僋

 

 

3. 夞愜僨乕僞偺儅乕僕偲僗働乕儕儞僌

 

1. CCP4i 儊僀儞僂傿儞僪僂傛傝嵍忋墿怓偄僞僽傪僋儕僢僋 仺 Data Reduction

2. 嵍懁偺僞僽 仺 Scale and Merge Intensities

 

 

 

3. Ensure unique data & add Free R column for ... 偵僠僃僢僋擖傟傞丅

4. MTZ in 仺 Full path 仺 Browse 仺 Mosflm 偱惗惉偟偨 mtz僼傽僀儖傪巜掕

丂5. MTZ out 仺 Full path 仺 僼傽僀儖柤偑彑庤偵擖傞偑丄岲偒側柤慜偵曄峏偟偰傕傛偄丅

丂6. Estimated muber of residues in the asymmetric unit 偵巆婎悢傪擖椡

丂丂僯儚僩儕棏敀儕僝僠乕儉偺応崌 129

丂丂傕偟丄寢徎妛揑旕懳徧扨埵偑2暘巕偱偁傟偽巆婎悢偼2攞傪丄3暘巕側傜3攞偟偨悢傪擖椡偡傞丅

丂7. belonging to Project 偍傛傃 Dataset name 偵揔摉側柤慜傪擖椡

丂8. Run 仺 Run Now

 

 


9. 寢壥傪僠僃僢僋偡傞丅CCP4i 偺儊僀儞偺僂傿儞僪僂偺塃懁偺僞僽傛傝

View Files form Job 仺 View Log File

丂10. 僗僋儘乕儖僶乕傪僗僋儘乕儖偡傞偲丅拞墰晅嬤偵師儁乕僕偺傛偆側摑寁抣偑偁傞

丂丂Rmrg丄I/sigma丄%poss 側偳傪僠僃僢僋偟偰暘夝擻傪寛掕偡傞丅

11. Scale and Merge Intensities 僂傿儞僪僂偵栠傝丄Excede data less than ... Angstrom or greater than ### Angstrom 偺 ### 偺晹暘偵寛掕偟偨暘夝擻傪擖椡偟丄摨偠梫椞偱傕偆堦搙寁嶼傪峴偆丅

12. 埲忋廔椆偟偨傜丄Scale and Merge Intensities 僂傿儞僪僂偼僋儘乕僘偟偰傛偄丅

Close 傪僋儕僢僋


 

 

4. 暘巕抲姺朄偵傛傞埵憡偺寛掕

丂1. 拻宆偲側傞暘巕儌僨儖偺梡堄

丂丂丂Protein Data Bank 乮http://www.rcsb.org/乯傛傝丄拻宆偲側傞暘巕儌僨儖傪僟僂儞儘乕僪偡傞丅偙偙偱偼丄幍柺捁棏敀儕僝僠乕儉 1JEF 傪巊梡偡傞丅

丂2. 拻宆偲側傞暘巕儌僨儖偺惍宍

丂拻宆偲側傞暘巕儌僨儖傪丄揔摉側僥僉僗僩僄僨傿僞乮Linux 側傜 gedit丄Mac 側傜 mi 僄僨傿僞側偳乯偱丄惍宍傪峴偆丅

偙偺応崌丄PDB 僼傽僀儖偺嵟屻偺曽偵婰嵹偝傟偰偄傞悈暘巕丄儕僈儞僪暘巕丄摐嵔傪嶍彍偡傞乮壓恾偺斀揮偟偰偄傞売強乯丅END 偼巆偟偰偍偔丅

丂3. 揔摉側柤慜偱曐懚偡傞丅偙偙偱偼 1jef-template.pdb 偲偟偨丅

 


4. CCP4i 儊僀儞僂傿儞僪僂傛傝嵍忋墿怓偄僞僽傪僋儕僢僋 仺 Molecular Replacement

5. 嵍懁偺僞僽 仺 Molrep -auto MR

 

 

6. MTZ in 仺 Full path 仺 Browse 仺 Scale and Merge Intensities偱惗惉偟偨 mtz僼傽僀儖傪巜掕

 

7. Model in 仺 Full path 仺 Browse 仺 僄僨傿僞偱惍宍偟偨拻宆儌僨儖傪巜掕

丂丂偙偙偱偼 1jef-template.pdb

丂8. Coords out 仺 Full path 仺

僼傽僀儖柤偑彑庤偵擖傞偑丄岲偒側柤慜偵曄峏偟偰傕傛偄丅

丂9. Run 仺 Run Now

10. 寢壥傪僠僃僢僋偡傞丅CCP4i 偺儊僀儞偺僂傿儞僪僂偺塃懁偺僞僽傛傝

View Files form Job 仺 View Log File

丂偙偺応崌丄Rotation function乮RF乯丄Translation funcion乮TF乯偲傕1偮偩偗桳堄偵戝偒偔側偭偰偄傟偽傛偄丅寢壥偼師偺偲偍傝偲側傞丅

11. 埲忋廔椆偟偨傜丄Molrep 偺僂傿儞僪僂偼僋儘乕僘偟偰傛偄丅

 

 


 

 

5. 暘巕儌僨儖偺惛枾壔乮儕僼傽僀儞儊儞僩乯亅偦偺侾丂Rigid Body Refinement

1. CCP4i 儊僀儞僂傿儞僪僂傛傝嵍忋墿怓偄僞僽傪僋儕僢僋 仺 Refinment

2. 嵍懁偺僞僽 仺 Run Refmac5

3. Do 偺僞僽傛傝 rigid body refinement 傪慖戰

4. MTZ in 仺 Full path 仺 Browse 仺 Scale and Merge Intensities偱惗惉偟偨 mtz僼傽僀儖傪巜掕

丂5. MTZ out 仺 Full path 仺

僼傽僀儖柤偑彑庤偵擖傞偑丄岲偒側柤慜偵曄峏偟偰傕傛偄丅

6. PDB in 仺 Full path 仺 Browse 仺丂Molrep 偺寢壥摼傜傟偨儌僨儖傪巜掕

丂7. PDB out 仺 Full path 仺

僼傽僀儖柤偑彑庤偵擖傞偑丄岲偒側柤慜偵曄峏偟偰傕傛偄丅

 

 


丂8. Run 仺 Run Now

 

9. 寢壥傪僠僃僢僋偡傞丅CCP4i 偺儊僀儞偺僂傿儞僪僂偺塃懁偺僞僽傛傝

View Files form Job 仺 View Log Graps 仺 怴偟偄僂傿儞僪僂偑尰傟傞

丂丂壓偵僗僋儘乕儖 仺 Rfactor analysis, stats vs cycle 傪僋儕僢僋

丂丂Rfactor 偍傛傃 Rfree 傪僠僃僢僋偡傞

 

 

 


6. 暘巕儌僨儖偺惛枾壔乮儕僼傽僀儞儊儞僩乯亅偦偺俀 Restrained Refinement

1. Refmac5 偺僂傿儞僪僂偑奐偄偰偄側偐偭偨傜奐偔

2. Do 偺僞僽傛傝 restrained refinement 傪慖戰

3. MTZ in 仺 Full path 仺 Browse 仺 Scale and Merge Intensities偱惗惉偟偨 mtz僼傽僀儖傪巜掕

丂4. MTZ out 仺 Full path 仺

僼傽僀儖柤偑彑庤偵擖傞偑丄岲偒側柤慜偵曄峏偟偰傕傛偄丅

偡偱偵摨柤偺僼傽僀儖偑偁傝慜偺僼傽僀儖偑忋彂偒偝傟偰偟傑偆帪偼棑偑擹偄墿怓偲側傞偺偱丄暿偺僼傽僀儖柤偵偡傞丅

5. PDB in 仺 Full path 仺 Browse 仺 rigid body refinement 偺寢壥摼傜傟偨儌僨儖傪巜掕

6. PDB out 仺 Full path 仺

僼傽僀儖柤偑彑庤偵擖傞偑丄岲偒側柤慜偵曄峏偟偰傕傛偄丅

偡偱偵摨柤偺僼傽僀儖偑偁傝慜偺僼傽僀儖偑忋彂偒偝傟偰偟傑偆帪偼棑偑擹偄墿怓偲側傞偺偱丄暿偺僼傽僀儖柤偵偡傞丅

7. Use weighting term 偺崁偼丄儕僼傽僀儞儊儞僩偺嵺倃慄偺夞愜僨乕僞傪偳偺偖傜偄廳帇偡傞偐偲偄偆崁栚偱偁傞丅僨僼僅儖僩偱偼彮偟崅偡偓傞偺偱丄偙偙偱偼 0.1 掱搙偺抣傪擖椡偡傞丅捈偝側偄偲儌僨儖偵備偑傒偑惗偠傞応崌偑偁傞丅

8. Run 仺 Run Now

 

 

 

9. rigid body refinement 偺帪偲摨條偵

View Files form Job 仺 View Log Graps 仺

怴偟偄僂傿儞僪僂 仺 壓偵僗僋儘乕儖 仺

Rfactor analysis, stats vs cycle

 

偵傛傝Rfactor丄Rfree 傪僠僃僢僋偡傞丅 

 

 

亂係亃Coot 偵傛傞暘巕儌僨儖偺峔抸

 

 

 


1. Coot 偺婲摦偲儌僨儖偺撉傒崬傒

丂1. 僔僃儖偺僐儅儞僪儔僀儞偐傜coot 偲僞僀僾偟偰婲摦偝偣傞丅

 

丂2. File 仺 Open Coordinates 仺 CCP4 偺儕僼傽僀儞儊儞僩偺寁嶼偺寢壥摼傜傟偨儌僨儖乮柤慜偼1jef_molrep1_refmac2.pdb 側偳偲側偭偰偄傞乯傪撉傒崬傓丅

 

2. 儅僂僗偺巊偄曽

嵍儃僞儞偺僪儔僢僌丗儌僨儖傪夞揮

拞儃僞儞傪僋儕僢僋丗僋儕僢僋偟偨応強傪拞墰偲偟偰忋壓嵍塃偵堏摦

ctrl + 嵍儃僞儞偺僪儔僢僌丗儌僨儖傪忋壓嵍塃偵堏摦

塃儃僞儞偺僪儔僢僌丗儌僨儖傪奼戝弅彫

 

3. 儌僨儖偍傛傃儅僢僾偺撉傒崬傒

1. File 仺 Auto Open MTZ 仺 CCP4 偺儕僼傽僀儞儊儞僩偺寁嶼偺寢壥摼傜傟偨 mtz 僼傽僀儖乮柤慜偼lyso_refmac2.mtz 側偳偲側偭偰偄傞乯傪撉傒崬傓丅

丂丂偙傟偵傛傝丄2庬椶偺儅僢僾偑撉傒崬傑傟傞丅

 

 


2. Coot 偱偼僐儞僣傾乕偺僨僼僅儖僩抣偑 1.5 sigma 偲側偭偰偄傞丅偦偙偱丄僉乕儃乕僪偺儅僀僫僗僉乕傪5夞墴偟偰 1 sigma 掱搙偵壓偘傞丅儂僀乕儖儅僂僗偺応崌丄儂僀乕儖偱傕挷愡偱偒傞丅

 

3. 偙偙偱偼丄偲傝偁偊偢僆儈僢僩儅僢僾偼巊傢側偄偺偱丄Display Manager 傪僋儕僢僋偡傞丅僆儈僢僩儅僢僾偼 ... DELFWT ... 偲昞帵偝傟偰偄傞偺偱丄偙偺 Display 偺僠僃僢僋傪僋儕僢僋偟偰偼偢偡丅

 

 


4. 儌僨儖偺廋惓

丂偙偙偱偼椺偲偟偰丄巆婎斣崋俁斣傔偺 Tyr 傪 Phe 偵捈偟偰傒傞丅

 

丂1. 傑偢俁巆婎傔偺 Tyr 傪昞帵偝偣傞丅Draw 仺 Go To Atom 偱Go To Atom僂傿儞僪僂傪奐偔丅

丂2. Chain A 傪僋儕僢僋偟巆婎斣崋偺儕僗僩傪昞帵偝偣傞丅

丂3. 3 TYR 傪僋儕僢僋偡傞偲俁巆婎傔偺 Tyr 偑昞帵偝傟傞丅

 

 


4. Calculate 仺 Model/Fit/Refine 傛傝 Model/Fit/Refine 僂傿儞僪僂傪奐偔丅

5. Mutate & Auto Fit 傪僋儕僢僋偡傞偲丄偳偺儅僢僾傪巊偆偐暦偄偰偔傞丅偙偙偱偼... FWT ... 偲昞帵偝傟傞儅僢僾傪巊偆偺偱丄偦偺傑傑 OK 傪僋儕僢僋丅

 

 

 


6. 傕偆堦搙 Mutate & Auto Fit 傪僋儕僢僋偡傞偲丄儃僞儞偑墴偟崬傑傟偨忬懺偵側傞丅

7. 偙偺忬懺偱傾儈僲巁巆婎偺庬椶傪曄峏偟偨偄巆婎乮偙偙偱偼俁斣傔偺 Tyr乯傪僋儕僢僋偡傞丅

 

 

8. 怴偟偄僂傿儞僪僂偑億僢僾傾僢僾偟丄偳偺傾儈僲巁巆婎偵曄峏偟偨偄偐恞偹偰偔傞丅偙偙偱偼 PHE(F) 傪僋儕僢僋偡傞丅

 

 


9. 巆婎偑 Phe 偵曄峏偝傟傞丅

10. File 仺 Save Coordinates 傛傝丄峔抸偟偨儌僨儖傪曐懚偡傞丅僼傽僀儖柤偼彑庤偵擖傞偑丄岲偒側柤慜偵曄峏偟偰傕傛偄丅

11. 摨條偺庤弴偱丄巆傝偺俇偮偺傾儈僲巁巆婎傕慡偰廋惓偡傞丅

12. CCP4 偱丄峔抸偟偨儌僨儖偺 restrained refinement 傪峴偆丅