User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods: Difference between revisions

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Wayne Decatur (talk | contribs)
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Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
mNo edit summary
Line 96: Line 96:
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";
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