User:Wayne Decatur/Sandboxmangai: Difference between revisions
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==Isochorismate-Pyruvate Lyase: open conformation with pyruvate bound morphing to closed conformation with pyruvate bound | ==Isochorismate-Pyruvate Lyase== | ||
<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='2h9dmorph8.pdb' size='390' frame='true' align='right' scene='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Isochorismate-Pyruvate Lyase: open to closed morph''' (2h9dmorph8.pdb), resolution XXXÅ (<scene name='scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2'>initial scene</scene>).</center></td></tr></table> | |||
'''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> | |||
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> | |||
made by chains A and B of 2h9d morphed to chains C and D | made by chains A and B of 2h9d morphed to chains C and D | ||
Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/ | 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> | ||
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 | 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. <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> | |||
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> | |||
