User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods: Difference between revisions
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write COORDS PDB "1ig8TO3b8aplusheteroatomsto10thru12frames.pdb" | write COORDS PDB "1ig8TO3b8aplusheteroatomsto10thru12frames.pdb" | ||
Opened 1ig8TO3b8aplusheteroatomsto10thru12frames.pdb" in text editor and copied the molecule of glucose from frame 11 to 10. | Opened "1ig8TO3b8aplusheteroatomsto10thru12frames.pdb" in text editor and copied the molecule of glucose from frame 11 to 10. | ||
Now I need to repeat the pulling and rotating of the glucose molecule in frame 10 so looks a little more like drifted out of active site relative next two frames. | Now I need to repeat the pulling and rotating of the glucose molecule in frame 10 so looks a little more like drifted out of active site relative next two frames. | ||
REALIZED AFTER STARTING THIS APPROACH THAT ALTHOUGH IT WOULD PRODUCE A COOL ANIMATION, IT MIGHT NOT BE VERY CHEMICALLY ACCURATE AND SO MAYBE FOR NEEDS I HAVE BETTER TO HAVE GLUCOSE AND SULFATE ION JUST AT ENDPOINTS, WITH AN UNBOUND REPRESENTATION OF GLUCOSE FOR 1ig8. | REALIZED AFTER STARTING THIS APPROACH THAT ALTHOUGH IT WOULD PRODUCE A COOL ANIMATION, IT MIGHT NOT BE VERY CHEMICALLY ACCURATE AND SO MAYBE FOR NEEDS I HAVE BETTER TO HAVE GLUCOSE AND SULFATE ION JUST AT ENDPOINTS, WITH AN UNBOUND REPRESENTATION OF GLUCOSE FOR 1ig8. | ||
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select 2.1; | select 2.1; | ||
write COORDS PDB "heteroatomsforfirstframeof1ig8TO3b8a.pdb"; | write COORDS PDB "heteroatomsforfirstframeof1ig8TO3b8a.pdb"; | ||
Opened that new file and copied sulfate ion and pasted into the morph file "1ig8TO3b8aplusheteroatomstolastframe.pdb" and saved as 1ig8TO3b8aplusheteroatomstofirstnlastframe.pdb . | Opened that new file and copied sulfate ion and pasted into the morph file "1ig8TO3b8aplusheteroatomstolastframe.pdb" and saved as 1ig8TO3b8aplusheteroatomstofirstnlastframe.pdb . (Actually added this sulfate ion to the first frame of the last intermediate I made, "1ig8TO3b8aplusheteroatomsto10thru12frames.pdb", because may end up using those at some point.) | ||
