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User:Wayne Decatur/Sandboxmangai
From Proteopedia
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Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2'>here to initiate the animation showing morph of open conformation with pyruvate bound morphing to closed conformation with pyruvate bound</scene>.<br> | Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2'>here to initiate the animation showing morph of open conformation with pyruvate bound morphing to closed conformation with pyruvate bound</scene>.<br> | ||
Morph uses all 8 models obtained from editing sets of chains A and B and chains C and D to be submitted to Yale Morph server.<br> | Morph uses all 8 models obtained from editing sets of chains A and B and chains C and D to be submitted to Yale Morph server.<br> | ||
| - | + | Copied C and D and pyruvates to new files. For chains A and B file, I deleted C and D and CA heteroatom. Used alter command (example for chain c= select chain C; alter (chain C),chain='A') in pymol to change names of C and D chains in file to A and B. Then removed some residues with gaps to match better but seemed unnecessary because one worked before doing that but I thought it failed because went to spam.<br> | |
| - | Copied C and D and pyruvates to new files. For chains A and B file, I deleted C and D and CA heteroatom. Used alter command (example for chain c= select chain C; alter (chain C),chain='A') in pymol to change names of C and D chains in file to A and B. Then removed some residues with gaps to match better but seemed unnecessary because one worked before doing that but I thought it failed because went to spam. | + | |
| + | <scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/3'>Morph from open to closed with sidechains shown.</scene> | ||
<br> | <br> | ||
Found out about alter command at http://pymol.sourceforge.net/newman/ref/S1000comref.html. Ran sort command after each altering. | Found out about alter command at http://pymol.sourceforge.net/newman/ref/S1000comref.html. Ran sort command after each altering. | ||
Revision as of 19:47, 27 November 2008
Isochorismate-Pyruvate Lyase
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Isochorismate-Pyruvate Lyase: apo enzyme to open conformation with pyruvate bound
made by chains A and B of 2h9c morphed to A and B of 2h9d
Isochorismate-Pyruvate Lyase: open conformation with pyruvate bound morphing to closed conformation with pyruvate bound
made by chains A and B of 2h9d morphed to chains C and D
Click .
Morph uses all 8 models obtained from editing sets of chains A and B and chains C and D to be submitted to Yale Morph server.
Copied C and D and pyruvates to new files. For chains A and B file, I deleted C and D and CA heteroatom. Used alter command (example for chain c= select chain C; alter (chain C),chain='A') in pymol to change names of C and D chains in file to A and B. Then removed some residues with gaps to match better but seemed unnecessary because one worked before doing that but I thought it failed because went to spam.
Found out about alter command at http://pymol.sourceforge.net/newman/ref/S1000comref.html. Ran sort command after each altering.
