Difference between revisions of "Normal Mode Analysis of ARSA"

From Bioinformatikpedia
(oGNM – Gaussian network model)
(All-atom NMA of 1BPT)
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|}
 
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=== All-atom NMA of 1BPT ===
+
=== NMA of 1BPT ===
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
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|mode 11
 
|mode 11
 
|-
 
|-
| ''600K''
+
| ''600K (all-atom)''
 
|[[Image:nomadgr_arsa7.gif|200px]]
 
|[[Image:nomadgr_arsa7.gif|200px]]
 
|[[Image:nomadgr_arsa8.gif|200px]]
 
|[[Image:nomadgr_arsa8.gif|200px]]
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|[[Image:nomadgr_arsal11.gif|200px]]
 
|[[Image:nomadgr_arsal11.gif|200px]]
 
|-
 
|-
| ''2000K ''
+
| ''2000K (all-atom)''
 
|[[Image:nomadgr_arsa7_2000.gif|200px]]
 
|[[Image:nomadgr_arsa7_2000.gif|200px]]
 
|[[Image:nomadgr_arsa8_2000.gif|200px]]
 
|[[Image:nomadgr_arsa8_2000.gif|200px]]
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|[[Image:nomadgr_arsal10_2000.gif|200px]]
 
|[[Image:nomadgr_arsal10_2000.gif|200px]]
 
|[[Image:nomadgr_arsal11_2000.gif|200px]]
 
|[[Image:nomadgr_arsal11_2000.gif|200px]]
  +
|-
  +
| ''Elastic Network''
  +
|[[Image:nomad_1bpt7.gif|200px]]
  +
|[[Image:nomad_1bpt8.gif|200px]]
  +
|[[Image:nomad_1bpt9.gif|200px]]
  +
|[[Image:nomad_1bpt10.gif|200px]]
  +
|[[Image:nomad_1bpt11.gif|200px]]
 
|-
 
|-
 
|}
 
|}

Revision as of 11:53, 26 July 2011

WEBnm@

We used | http://www.lcdf.org/gifsicle/ to generate the animated gifs:

gifsicle --delay=5 --loop --colors 256 *.gif > anim.gif

Mode Motion Vecors Displacement
mode 7 Webnma arsa7.gif Webnma arsa7 vectors.gif Webnma arsa7 dis.png
mode 8 Webnma arsa8.gif Webnma arsa8 vectors.gif Webnma arsa8 dis.png
mode 9 Webnma arsa9.gif Webnma arsa9 vectors.gif Webnma arsa9 dis.png
mode 10 Webnma arsal10.gif Webnma arsal10 vectors.gif Webnma arsa12 dis.png
mode 11 Webnma arsal11.gif Webnma arsal11 vectors.gif Webnma arsa11 dis.png
mode 12 Webnma arsa11.gif Webnma arsa11 vectors.gif Webnma arsa12 dis.png

ElNemo

Mode Pymol animation picture 1 from ElNemo picture 2 from ElNemo picture 3 from ElNemo Fluctuations
Mode 7 Elnemo arsa7.gif Elnemo arsa7 1.gif Elnemo arsa7 2.gif Elnemo arsa7 3.gif Elnemo arsa7 4.gif
Mode 8 Elnemo arsa8.gif Elnemo arsa8 1.gif Elnemo arsa8 2.gif Elnemo arsa8 3.gif Elnemo arsa8 4.png
Mode 9 Elnemo arsa9.gif Elnemo arsa9 1.gif Elnemo arsa9 2.gif Elnemo arsa9 3.gif Elnemo arsa9 4.png
Mode 10 Elnemo arsa10.gif Elnemo arsa10 1.gif Elnemo arsa10 2.gif Elnemo arsa10 3.gif Elnemo arsa10 4.png
Mode 11 Elnemo arsa11.gif Elnemo arsa11 1.gif Elnemo arsa11 2.gif Elnemo arsa11 3.gif Elnemo arsa11 4.png

Anisotropic Network Model web server

for file in *.png; do convert "$file" "$(basename $file .png).gif";done

mode 1 mode 2 mode 3 mode 4 mode 5
Motion Anm arsa1.gif Anm arsa2.gif Anm arsa3.gif Anm arsa4.gif Anm arsa5.gif
Distance Dist arsa1.gif Dist arsa2.png Dist arsa3.png Dist arsa4.png Dist arsa5.png
Fluctuations Fluct arsa1.gif Fluct arsa2.gif Fluct arsa3.gif Fluct arsa4.gif Fluct arsa5.gif

oGNM – Gaussian network model

http://ignm.ccbb.pitt.edu/ognm/1960654514/temp/index.htm

mode 7 mode 8 mode 9 mode 10 mode 11
Motion Ognm arsa1.png Ognm arsa2.png Ognm arsa3.png Ognm arsa4.png Ognm arsa5.png
Fluctuations Ognmfluct arsa1.png Ognmfluct arsa2.png Ognmfluct arsa3.png Ognmfluct arsa4.png Ognmfluct arsa5.png


Fluctuations of mode 7-11
Correlation of mode 1-20
Correlation of mode 7-11

NOMAD-Ref

NMA of ARSA

mode 7 mode 8 mode 9 mode 10 mode 11
Motion Nomad arsa1.gif Nomad arsa2.gif Nomad arsa3.gif Nomad arsa4.gif Nomad arsa5.gif
Distance Nomaddist arsa1.png Nomaddist arsa2.png Nomaddist arsa3.png Nomaddist arsa4.png Nomaddist arsa5.png

NMA of 1BPT

Temperature mode mode 8 mode 9 mode 10 mode 11
600K (all-atom) Nomadgr arsa7.gif Nomadgr arsa8.gif Nomadgr arsa9.gif Nomadgr arsal10.gif Nomadgr arsal11.gif
2000K (all-atom) Nomadgr arsa7 2000.gif Nomadgr arsa8 2000.gif Nomadgr arsa9 2000.gif Nomadgr arsal10 2000.gif Nomadgr arsal11 2000.gif
Elastic Network Nomad 1bpt7.gif Nomad 1bpt8.gif Nomad 1bpt9.gif Nomad 1bpt10.gif Nomad 1bpt11.gif