User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods: Difference between revisions
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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. | ||
* To add sulfate ion from 1ig8 back to first frame of "1ig8TO3b8a.pdb":<br/> | * To add sulfate ion from 1ig8 back to first frame of "1ig8TO3b8a.pdb":<br/> | ||
First made file of just first frame of "1ig8TO3b8a.pdb", then loaded that into Jmol.<br/> | **First made file of just first frame of "1ig8TO3b8a.pdb", then loaded that into Jmol.<br/> | ||
Then used open with append option to open the original 1ig8 pdb fle. | **Then used open with append option to open the original 1ig8 pdb fle. | ||
Then issued in the console:<br/> | **Then issued in the console:<br/> | ||
compare {2.1}{1.1} rotate translate; | compare {2.1}{1.1} rotate translate; | ||
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", renumbered atoms by adding another 20 so don't overlap with heteroatoms in last frame, 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.) | **Opened that new file and copied sulfate ion and pasted into the morph file "1ig8TO3b8aplusheteroatomstolastframe.pdb", renumbered atoms by adding another 20 so don't overlap with heteroatoms in last frame, 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.)<br/> | ||
**I added the glucose I had from frame 10 of "1ig8TO3b8aplusheteroatomsto10thru12frames.pdb" to the end of frame 1 of "1ig8TO3b8aplusheteroatomsto10thru12frames.pdb", renumbered to be after sulfate ion aton numbers I had there already, and saved as "1ig8TO3b8aplusglucose.pdb ". | |||
