User:Wayne Decatur/3fpn Morph methods
From Proteopedia
(Difference between revisions)
(→Morph from normal 3fpn structure to view in Figure 3 of article describing the structure) |
(→Morph from normal 3fpn structure to view in Figure 3 of article describing the structure) |
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| - | <scene name='3fpn_Morph_methods/Monitoranim/ | + | <scene name='3fpn_Morph_methods/Monitoranim/5'>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/Animpalindrome/ | + | <scene name='3fpn_Morph_methods/Animpalindrome/5'>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 08:15, 24 October 2009
Moving 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 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 Image: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 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
