User:Wayne Decatur/3fpn Morph methods: Difference between revisions
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Moving to match Figure 3
Morph from normal 3fpn structure to view in Figure 3 of article describing the structure
Paper on the structure
| Line 39: | Line 39: | ||
Then draw measurements between using menu | Then draw measurements between using menu | ||
select | select 173:a and sidechain and 1.8; wireframe 0.55; color cpk; | ||
select 196:b and sidechain and 1.8; wireframe 0.55;color cpk; | select 196:b and sidechain and 1.8; wireframe 0.55;color cpk; | ||
Then draw measurements between using menu | Then draw measurements between using menu | ||
select | select 176:a and sidechain and 1.8; wireframe 0.55; color cpk; | ||
select 222:b and sidechain and 1.8; wireframe 0.55;color cpk; | select 222:b and sidechain and 1.8; wireframe 0.55;color cpk; | ||
select 215:b and sidechain and 1.8; wireframe 0.55;color cpk; | select 215:b and sidechain and 1.8; wireframe 0.55;color cpk; | ||
| Line 50: | Line 50: | ||
Then draw measurements between using menu | Then draw measurements between using menu | ||
select | select 206:a and sidechain and 1.8; wireframe 0.55; color cpk; | ||
select 216:b and sidechain and 1.8; wireframe 0.55;color cpk; | select 216:b and sidechain and 1.8; wireframe 0.55;color cpk; | ||
select 198:b and sidechain and 1.8; wireframe 0.55;color cpk; | select 198:b and sidechain and 1.8; wireframe 0.55;color cpk; | ||
| Line 70: | Line 70: | ||
select 185:a and sidechain; wireframe 0.55; color cpk; | select 185:a and sidechain; wireframe 0.55; color cpk; | ||
select 223:b and sidechain; wireframe 0.55;color cpk; | select 223:b and sidechain; wireframe 0.55;color cpk; | ||
select | select 173:a and sidechain; wireframe 0.55; color cpk; | ||
select 196:b and sidechain; wireframe 0.55;color cpk; | select 196:b and sidechain; wireframe 0.55;color cpk; | ||
select | select 176:a and sidechain; wireframe 0.55; color cpk; | ||
select 222:b and sidechain; wireframe 0.55;color cpk; | select 222:b and sidechain; wireframe 0.55;color cpk; | ||
select 215:b and sidechain; wireframe 0.55;color cpk; | select 215:b and sidechain; wireframe 0.55;color cpk; | ||
select | select 206:a and sidechain; wireframe 0.55; color cpk; | ||
select 216:b and sidechain; wireframe 0.55;color cpk; | select 216:b and sidechain; wireframe 0.55;color cpk; | ||
select 198:b and sidechain; wireframe 0.55;color cpk; | select 198:b and sidechain; wireframe 0.55;color cpk; | ||
| Line 87: | Line 87: | ||
--> | --> | ||
<scene name='3fpn_Morph_methods/ | <scene name='3fpn_Morph_methods/Monitoranim/1'>Test 1.8 wireframe and measures</scene> | ||
<scene name='3fpn_Morph_methods/Testmeasureanimwo18/1'>back and forth with wireframe and only monitors on 1.8 maybe?</scene><br> | <scene name='3fpn_Morph_methods/Testmeasureanimwo18/1'>back and forth with wireframe and only monitors on 1.8 maybe?</scene><br> | ||
<scene name='3fpn_Morph_methods/ | <scene name='3fpn_Morph_methods/Animpalindrome/1'>TextToBeDisplayed</scene> | ||
<nowiki>[</nowiki>Control the animation with the 'animation' submenu on the menu that comes up if you click on the Jmol frank in the bottom rigth corner. Also, if the animation seems to be stuck, scroll in the bar on the right of your browser.<nowiki>]</nowiki> | <nowiki>[</nowiki>Control the animation with the 'animation' submenu on the menu that comes up if you click on the Jmol frank in the bottom rigth corner. Also, if the animation seems to be stuck, scroll in the bar on the right of your browser.<nowiki>]</nowiki> | ||
==Paper on the structure== | ==Paper on the structure== | ||
<ref group="xtra">PMID:19287003</ref><references group="xtra"/> | <ref group="xtra">PMID:19287003</ref><references group="xtra"/> | ||
Revision as of 10:48, 24 October 2009
Moving to match Figure 3Moving to match Figure 3
Using Pymol and the 3fpn file, I moved so interface is perpendicular to y axis:
translate [10,0,0], chain b
rotate y, 65, chain b
Saved molecule.
Morph from normal 3fpn structure to view in Figure 3 of article describing the structureMorph from normal 3fpn structure to view in Figure 3 of article describing the structure
|
Took the two files and submitted them. Since the structures didn't have nucleic acids, I took the advice here and used the Yale Morph Server for morphing complexes.
Uploaded to Proteopedia File:3fpntorotatedversion.pdb.
loaded '3fpntorotatedversion.pdb' in Scene Authoring Tools.
[Control the animation with the 'animation' submenu on the menu that comes up if you click on the Jmol frank in the bottom rigth corner. Also, if the animation seems to be stuck, scroll in the bar on the right of your browser.]
Paper on the structurePaper on the structure
- ↑ Pakotiprapha D, Liu Y, Verdine GL, Jeruzalmi D. A structural model for the damage-sensing complex in bacterial nucleotide excision repair. J Biol Chem. 2009 May 8;284(19):12837-44. Epub 2009 Mar 13. PMID:19287003 doi:10.1074/jbc.M900571200