User:Wayne Decatur/Sandboxmangai
From Proteopedia
m |
|||
| (4 intermediate revisions not shown.) | |||
| Line 4: | Line 4: | ||
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/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 too.<br> | + | Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9cmorph2h9dplusside/1'>here</scene> to see sidechains in the morph too.<br> |
| Line 14: | 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> | ||
Current revision
Isochorismate-Pyruvate Lyase
| |||||||
Isochorismate-Pyruvate Lyase: apoenzyme to open conformation with pyruvate bound
made by chains A and B of 2h9c morphed to A and B of 2h9d
Click .
Click to see sidechains in the morph too.
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.
View the too.
Found out about PyMol's alter command at http://pymol.sourceforge.net/newman/ref/S1000comref.html. Ran sort command after each altering.
