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

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
mNo edit summary
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
mNo edit summary
Line 85: Line 85:
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.)<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 aton 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
set dragSelected ON;
set PICKING select molecule;
set allowRotateSelected ON;
select model=11 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.
 
Then issued in the console:
select all;
write COORDS PDB "1ig8TO3b8aplusglucose.pdb";
Retrieved from "https://proteopedia.org/User:Wayne_Decatur/1ig8_to_3b8a_(hexokinase)_morph_methods"