User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods: Difference between revisions
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1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47 | 1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47 | ||
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3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470 | 3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470 | ||
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**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/> | **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 atom numbers I had there already, and saved as "1ig8TO3b8aplusglucose.pdb ". | **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 atom numbers I had there already, and saved as "1ig8TO3b8aplusglucose.pdb ". | ||
**Opened "1ig8TO3b8aplusglucose.pdb " and set so viewing first frame (model) and issued following commands in console | **Opened "1ig8TO3b8aplusglucose.pdb " and set so viewing first frame (model) and issued following commands in console:<br/> | ||
set dragSelected ON; | set dragSelected ON; | ||
set PICKING select molecule; | set PICKING select molecule; | ||
set allowRotateSelected ON; | set allowRotateSelected ON; | ||
select model= | select model=1 and [BGC]; | ||
AND AFTER THAT COMMAND TO PICK GLUCOSE held down alt and shift and clicked on glucose molecule and pulled molecule out of active site. | AND AFTER THAT COMMAND TO PICK GLUCOSE held down alt and shift and clicked on glucose molecule and pulled molecule out of active site. | ||
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select all; | select all; | ||
write COORDS PDB "1ig8TO3b8aplusglucose.pdb"; | write COORDS PDB "1ig8TO3b8aplusglucose.pdb"; | ||
RENAMED file to "1ig8TO3b8aplusglucoseENDPT.pdb" since glucose only at end points. | |||
*Now that I had glucose at end points, thought I'd see how it looked adding glucose back to each frame. Going back to "1ig8TO3b8aplusheteroatomsto10thru12frames.pdb" where I had added sulfate ion to frame 1, I continued the process of adjusting glucose in higher number frames, copying to previous frame and adjusting successively to be further from active site. Due to sulfate ion in frame 1, I had to re-adjust each of earlier frames to keep glucose away from it. Did this by using buttons in Jmol application to click through to frame I needed to adjust glucose in and issued command like used above with that model number and adjusted. For frame 1, I found in fact I needed to temporarily remove sulfate ion atoms from pdb file while I was working on glucose or Jmol was connecting glucose and sulfate because they were so close. Eventually seemed to be away from that area and so placed sulfate ion back in frame 1 and saved file as "1ig8TO3b8aplusglucoseALLframes.pdb" with: | |||
select all; write COORDS PDB "1ig8TO3b8aplusglucoseALLframes.pdb"; | |||
