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
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Then draw measurements between using menu | Then draw measurements between using menu | ||
select 185:a and sidechain and 1.8; wireframe 0.55; color cpk; | |||
select 223:b and sidechain and 1.8; wireframe 0.55;color cpk; | |||
Then draw measurements between using menu | |||
select 173a 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 | |||
select 176a 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; | |||
Then draw measurements between using menu | |||
select 206a 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; | |||
Then draw measurements between using menu | |||
then in console: | then in console: | ||
Revision as of 07:33, 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
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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