User:Wayne Decatur/1ig8 to 3b8a (hexokinase) morph methods - Revision history

Wayne Decatur at 05:07, 14 December 2018

2018-12-14T05:07:41Z

← Older revision		Revision as of 05:07, 14 December 2018
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	<small><font face = 'courier'>		<small><font face = 'courier'>
	<~~nowiki~~>		<pre>
	1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47		1ig8 1 ---DVPKELMQQIENFEKIFTVPTETLQAVTKHFISELEKGLSKKGGNIP 47
	\|\|\|\|\|\|\|.:\|...\|.:\|\|\|.:\|\|\|:.\|.\|\|\|\|.\|\|.\|\|\|:\|\|\|\|\|\|\|		\|\|\|\|\|\|\|.:\|...\|.:\|\|\|.:\|\|\|:.\|.\|\|\|\|.\|\|.\|\|\|:\|\|\|\|\|\|\|
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	\|\|\|\|\|\|::\|\|\|\|\|\|\|\|:\|\|\|\|\|		\|\|\|\|\|\|::\|\|\|\|\|\|\|\|:\|\|\|\|\|
	3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470		3b8a 449 AVIAALSEKRIAEGKSLGIIGA 470
	</~~nowiki~~>		</pre>
	<br>		<br>
	</font></small><br/>		</font></small><br/>

Wayne Decatur at 04:53, 15 January 2012

2012-01-15T04:53:53Z

← Older revision		Revision as of 04:53, 15 January 2012
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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";

Wayne Decatur at 03:37, 15 January 2012

2012-01-15T03:37:30Z

← Older revision		Revision as of 03:37, 15 January 2012
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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=11 and [BGC];		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.

Wayne Decatur at 03:23, 15 January 2012

2012-01-15T03:23:38Z

@@ Line 85: / Line 85: @@
 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/>
-**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 ".

Wayne Decatur at 02:32, 15 January 2012

2012-01-15T02:32:45Z

← Older revision		Revision as of 02:32, 15 January 2012
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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 ".

Wayne Decatur at 02:25, 15 January 2012

2012-01-15T02:25:29Z

← Older revision		Revision as of 02:25, 15 January 2012
Line 77:		Line 77:
	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.
	* 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.)

Wayne Decatur at 02:05, 15 January 2012

2012-01-15T02:05:55Z

← Older revision		Revision as of 02:05, 15 January 2012
Line 84:		Line 84:
	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 . (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.)

Wayne Decatur at 01:57, 15 January 2012

2012-01-15T01:57:06Z

← Older revision		Revision as of 01:57, 15 January 2012
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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.
Line 84:		Line 84:
	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.)

Wayne Decatur at 01:50, 15 January 2012

2012-01-15T01:50:05Z

← Older revision		Revision as of 01:50, 15 January 2012
Line 84:		Line 84:
	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 .

Wayne Decatur at 01:44, 15 January 2012

2012-01-15T01:44:56Z

← Older revision		Revision as of 01:44, 15 January 2012
Line 77:		Line 77:
	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.
			* 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>
			Then used open with append option to open the original 1ig8 pdb fle.
			Then issued in the console:</br>
			compare {2.1}{1.1} rotate translate;
			select 2.1;
			write COORDS PDB "heteroatomsforfirstframeof1ig8TO3b8a.pdb";