User:Wayne Decatur/Sandboxmangai: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
mNo edit summary |
||
| (7 intermediate revisions by the same user not shown) | |||
| Line 3: | Line 3: | ||
'''Isochorismate-Pyruvate Lyase: apoenzyme to open conformation with pyruvate bound'''<br> | '''Isochorismate-Pyruvate Lyase: apoenzyme to open conformation with pyruvate bound'''<br> | ||
made by chains A and B of 2h9c morphed to A and B of 2h9d<br> | made by chains A and B of 2h9c morphed to A and B of 2h9d<br> | ||
Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9cmorph2h9d/2'>here to initiate the animation showing morph of aopenzyme to pyruvate bound to the open confirmation</scene>.<br> | |||
Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9cmorph2h9dplusside/1'>here</scene> to see sidechains in the morph too.<br> | |||
'''Isochorismate-Pyruvate Lyase: open conformation with pyruvate bound morphing to closed conformation with pyruvate bound'''<br> | '''Isochorismate-Pyruvate Lyase: open conformation with pyruvate bound morphing to closed conformation with pyruvate bound'''<br> | ||
| Line 9: | Line 14: | ||
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 | Copied C and D and pyruvates to new files. For chains A and B file, I deleted C and D and CA heteroatom. <b>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.</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> | ||
<scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/3'> | View the <scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/3'>morph from open to closed conformation with sidechains shown</scene> too. | ||
<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 <b>PyMol's alter command at http://pymol.sourceforge.net/newman/ref/S1000comref.html. Ran sort command after each altering</b>. | ||
<scene name='User:Wayne_Decatur/Sandboxmangai/Test/1'>Test later</scene> | |||
