Proteopedia talk:Development - Revision history

Angel Herraez: Focus on ligands and sites - proposals for improvement

Angel Herraez — Sun, 25 Jun 2017 18:35:52 GMT

Focus on ligands and sites - proposals for improvement

←Older revision		Revision as of 18:35, 25 June 2017
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	* '''Proposal C:''' additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script.		* '''Proposal C:''' additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script.
		+	:This does not seem necessary in full model display, since the contacting sidechains make the group larger, but in simplified display the ligand is alone. Zn has a volume of 4 (or 11?), sulphate has a volume of 70.
		+	<pre>
		+	select (ligOne , ligContact);
		+	if ( {selected}.volume.sum > 100 ) { zoomTo 0.5 {selected} 0 0.8; } else { zoomTo 0.5 {selected} 0 0.5; }
		+	</pre>

Angel Herraez: Focus on ligands and sites - proposals for improvement

Angel Herraez — Sun, 25 Jun 2017 17:53:36 GMT

Focus on ligands and sites - proposals for improvement

←Older revision		Revision as of 17:53, 25 June 2017
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	Focus on ligands and sites when their green links are clicked.		Focus on ligands and sites when their green links are clicked.

-	* '''Current state:''' the selected entity becomes the center of rotation, and the molecule is zoomed onto it (80% of the JSmol panel). Residues within 4 Â are highlighted with ~~sidechains in~~ sticks and ~~C_beta labeled~~.	+	* '''Current state:''' the selected entity becomes the center of rotation, and the molecule is zoomed onto it (80% of the JSmol panel). Residues within 4 Â are highlighted with sticks for sidechains and labels for beta carbons. (The script is applied by pdbligand.php)
	<pre>define ligContact within(4.0, [HEM]) and protein;		<pre>define ligContact within(4.0, [HEM]) and protein;
	define ligContact within(group,ligContact);		define ligContact within(group,ligContact);
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	select all;		select all;
	</pre>		</pre>
-	* '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one.

-	* Proposal A: select only the first ligand of the set, by looking for first chain and first residue in it. Then, label and focus on that one as before.	+	* '''Problem:''' when there are several ligands of the same name, the focus acts on their geometric center, with a not too helpful result. Example: 4 heme groups in hemoglobin, center is on the whole model. It would be better to focus on just the first heme group.
		+
		+	* '''Proposal A:''' select only the first ligand of the set, by looking for first chain and first residue in it. Then, label and focus on that one as before.
	<pre>nc = {[HEM]}.chainNo.min;		<pre>nc = {[HEM]}.chainNo.min;
	define ligOne [HEM] and chainNo=nc;		define ligOne [HEM] and chainNo=nc;
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	</pre>		</pre>

-	* Proposal B: label all but zoom in on the first one.	+	* '''Proposal B:''' label all but zoom in on the first one.
	<pre>define ligContact within(4.0, [HEM]) and protein;		<pre>define ligContact within(4.0, [HEM]) and protein;
	define ligContact within(group,ligContact);		define ligContact within(group,ligContact);
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	zoomTo 0.5 {selected} 0 *0.8;		zoomTo 0.5 {selected} 0 *0.8;
	select all;		select all;
-	</pre>
	</pre>		</pre>

-	* Proposal C: additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script.	+	* '''Proposal C:''' additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script.

Angel Herraez: Focus on ligands and sites - proposals for improvement

Angel Herraez — Sun, 25 Jun 2017 15:36:31 GMT

Focus on ligands and sites - proposals for improvement

←Older revision		Revision as of 15:36, 25 June 2017
Line 10:		Line 10:
	background label yellow; color labels black;		background label yellow; color labels black;
	zoomTo 0.5 { ([HEM] , ligContact )} 0 *0.8;		zoomTo 0.5 { ([HEM] , ligContact )} 0 *0.8;
		+	select all;
	</pre>		</pre>
	* '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one.		* '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one.
Line 26:		Line 27:
	background label yellow; color labels black;		background label yellow; color labels black;
	zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;		zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;
		+	select all;
	</pre>		</pre>

Line 44:		Line 46:
	define ligContact within(group,ligContact);		define ligContact within(group,ligContact);
	zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;		zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;
		+	select all;
		+	</pre>
		+	or, maybe this end gives a better orientation for focus:
		+	<pre>select (ligOne , ligContact);
		+	rotate best -0.3;
		+	zoomTo 0.5 {selected} 0 *0.8;
		+	select all;
		+	</pre>
	</pre>		</pre>

	* Proposal C: additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script.		* Proposal C: additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script.

Angel Herraez: typo

Angel Herraez — Sun, 25 Jun 2017 15:16:45 GMT

typo

←Older revision		Revision as of 15:16, 25 June 2017
Line 12:		Line 12:
	</pre>		</pre>
	* '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one.		* '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one.
		+
	* Proposal A: select only the first ligand of the set, by looking for first chain and first residue in it. Then, label and focus on that one as before.		* Proposal A: select only the first ligand of the set, by looking for first chain and first residue in it. Then, label and focus on that one as before.
	<pre>nc = {[HEM]}.chainNo.min;		<pre>nc = {[HEM]}.chainNo.min;
-	define ligOne [HEM] and chainNo=~~{[HEM]}.chainNo.min~~;	+	define ligOne [HEM] and chainNo=nc;
	nc = {ligOne}.resNo.min;		nc = {ligOne}.resNo.min;
	define ligOne ligOne and resNo=nc;		define ligOne ligOne and resNo=nc;
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	zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;		zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;
	</pre>		</pre>
		+
	* Proposal B: label all but zoom in on the first one.		* Proposal B: label all but zoom in on the first one.
	<pre>define ligContact within(4.0, [HEM]) and protein;		<pre>define ligContact within(4.0, [HEM]) and protein;
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	nc = {[HEM]}.chainNo.min;		nc = {[HEM]}.chainNo.min;
-	define ligOne [HEM] and chainNo=~~{[HEM]}.chainNo.min~~;	+	define ligOne [HEM] and chainNo=nc;
	nc = {ligOne}.resNo.min;		nc = {ligOne}.resNo.min;
	define ligOne ligOne and resNo=nc;		define ligOne ligOne and resNo=nc;

Angel Herraez: Focus on ligands and sites - proposals for improvement

Angel Herraez — Sun, 25 Jun 2017 15:14:27 GMT

Focus on ligands and sites - proposals for improvement

New page

== Focus on ligands and sites ==
Focus on ligands and sites when their green links are clicked.

* '''Current state:''' the selected entity becomes the center of rotation, and the molecule is zoomed onto it (80% of the JSmol panel). Residues within 4 Â are highlighted with sidechains in sticks and C_beta labeled.
<pre>define ligContact within(4.0, [HEM]) and protein;
define ligContact within(group,ligContact);
select ligContact and sidechain; color cpk;
select ligContact and (sidechain,alpha); wireframe 0.3;
select ligContact and *.CB; label %m%r;
background label yellow; color labels black;
zoomTo 0.5 { ([HEM] , ligContact )} 0 *0.8;
</pre>
* '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one.
* Proposal A: select only the first ligand of the set, by looking for first chain and first residue in it. Then, label and focus on that one as before.
<pre>nc = {[HEM]}.chainNo.min;
define ligOne [HEM] and chainNo={[HEM]}.chainNo.min;
nc = {ligOne}.resNo.min;
define ligOne ligOne and resNo=nc;

define ligContact within(4.0, ligOne) and protein;
define ligContact within(group,ligContact);
select ligContact and sidechain; color cpk;
select ligContact and (sidechain,alpha); wireframe 0.3;
select ligContact and *.CB; label %m%r;
background label yellow; color labels black;
zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;
</pre>
* Proposal B: label all but zoom in on the first one.
<pre>define ligContact within(4.0, [HEM]) and protein;
define ligContact within(group,ligContact);
select ligContact and sidechain; color cpk;
select ligContact and (sidechain,alpha); wireframe 0.3;
select ligContact and *.CB; label %m%r;
background label yellow; color labels black;

nc = {[HEM]}.chainNo.min;
define ligOne [HEM] and chainNo={[HEM]}.chainNo.min;
nc = {ligOne}.resNo.min;
define ligOne ligOne and resNo=nc;

define ligContact within(4.0, ligOne) and protein;
define ligContact within(group,ligContact);
zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;
</pre>

* Proposal C: additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script.