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
New page: ==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 ... |
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| Line 25: | Line 25: | ||
select 219:a and sidechain and 1.8; wireframe 0.55; color cpk; | select 219:a and sidechain and 1.8; wireframe 0.55; color cpk; | ||
select 183:b and sidechain and 1.8; wireframe 0.55;color cpk; | select 183:b and sidechain and 1.8; wireframe 0.55;color cpk; | ||
Then draw measurements between using menu | |||
select 170:a and sidechain and 1.8; wireframe 0.55; color cpk; | |||
select 231:b and sidechain and 1.8; wireframe 0.55;color cpk; | |||
Then draw measurements between using menu | Then draw measurements between using menu | ||
| Line 36: | Line 42: | ||
--> | --> | ||
<scene name='3fpn_Morph_methods/Testmeasureanim/ | <scene name='3fpn_Morph_methods/Testmeasureanim/2'>Test 1.8 wireframe and measures</scene> | ||
==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 07:39, 23 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'.
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