Proteopedia talk:Wishlist - Revision history

Karsten Theis: /* Example */

2020-10-29T13:04:30Z

Example

←Older revision		Revision as of 13:04, 29 October 2020
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	<jmol><jmolButton><text>replace selection</text></jmolButton></jmol> all histidines selected		<jmol><jmolButton><text>replace selection</text></jmolButton></jmol> all histidines selected
		+
	<jmol><jmolButton><text>add to selection</text></jmolButton></jmol> all histidines selected, plus the neighbors of iron		<jmol><jmolButton><text>add to selection</text></jmolButton></jmol> all histidines selected, plus the neighbors of iron
		+
	<jmol><jmolButton><text>remove from selection</text></jmolButton></jmol> neighbors of iron selected, except for histidines		<jmol><jmolButton><text>remove from selection</text></jmolButton></jmol> neighbors of iron selected, except for histidines
		+
	<jmol><jmolButton><text>limit selection</text></jmolButton></jmol> just the histidines that are neighbors of the iron, nothing else		<jmol><jmolButton><text>limit selection</text></jmolButton></jmol> just the histidines that are neighbors of the iron, nothing else

Karsten Theis: /* Renaming selection buttons */

2020-10-29T13:04:04Z

Renaming selection buttons

←Older revision		Revision as of 13:04, 29 October 2020
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	Action: Changes the selection to just the (constraints) that were also in the previous selection. '''Example please''', it looks to me identical to "replace selection", unless you clear the tab in between.		Action: Changes the selection to just the (constraints) that were also in the previous selection. '''Example please''', it looks to me identical to "replace selection", unless you clear the tab in between.
		+
		+	=====Example=====
		+
		+	We selected atoms in the neighborhood of myoglobin's iron atom. The selection includes the heme, the iron, and different protein residues. In the selection box, we choose Residue type: His.
		+
		+	<jmol><jmolButton><text>replace selection</text></jmolButton></jmol> all histidines selected
		+	<jmol><jmolButton><text>add to selection</text></jmolButton></jmol> all histidines selected, plus the neighbors of iron
		+	<jmol><jmolButton><text>remove from selection</text></jmolButton></jmol> neighbors of iron selected, except for histidines
		+	<jmol><jmolButton><text>limit selection</text></jmolButton></jmol> just the histidines that are neighbors of the iron, nothing else
		+
		+	--[[User:Karsten Theis\|Karsten Theis]] 13:04, 29 October 2020 (UTC)

	=== More tools in "representations" tab ===		=== More tools in "representations" tab ===

Jaime Prilusky at 09:20, 29 October 2020

2020-10-29T09:20:53Z

←Older revision		Revision as of 09:20, 29 October 2020
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	I think the "to" is not good since the new selection has already been chosen, it will not be chosen after pressing the button. --[[User:Angel Herraez\|Angel_Herraez]] 08:34, 29 October 2020 (UTC)		I think the "to" is not good since the new selection has already been chosen, it will not be chosen after pressing the button. --[[User:Angel Herraez\|Angel_Herraez]] 08:34, 29 October 2020 (UTC)

-	Action: Changes the selection to just the (constraints) that were also in the previous selection.	+	Action: Changes the selection to just the (constraints) that were also in the previous selection. '''Example please''', it looks to me identical to "replace selection", unless you clear the tab in between.

	=== More tools in "representations" tab ===		=== More tools in "representations" tab ===

Angel Herraez: discard entries for nucleic residues

2020-10-29T08:50:52Z

discard entries for nucleic residues

←Older revision		Revision as of 08:50, 29 October 2020
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	<td></td>		<td></td>
	<td></td>		<td></td>
-	<td ~~colspan='2'~~>~~'''Nucleic residues'''~~</td>	+	<td></td>
-	<td>~~''but we can remove this altogether''~~ </td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>dA</td>		<td>dA</td>
	<td></td>		<td></td>
-	<td>dA</td>	+	<td></td>
-	<td>dA</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>A</td>		<td>A</td>
	<td></td>		<td></td>
-	<td>A</td>	+	<td></td>
-	<td>A</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>dC</td>		<td>dC</td>
	<td></td>		<td></td>
-	<td>dC</td>	+	<td></td>
-	<td>dC</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>C</td>		<td>C</td>
	<td></td>		<td></td>
-	<td>C</td>	+	<td></td>
-	<td>C</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>dG</td>		<td>dG</td>
	<td></td>		<td></td>
-	<td>dG</td>	+	<td></td>
-	<td>dG</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>G</td>		<td>G</td>
	<td></td>		<td></td>
-	<td>G</td>	+	<td></td>
-	<td>G</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>dI</td>		<td>dI</td>
	<td></td>		<td></td>
-	<td>dI</td>	+	<td></td>
-	<td>dI</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>I</td>		<td>I</td>
	<td></td>		<td></td>
-	<td>I</td>	+	<td></td>
-	<td>I</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>purine</td>		<td>purine</td>
	<td></td>		<td></td>
-	<td>dT</td>	+	<td></td>
-	<td>dT</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>pyrimidine</td>		<td>pyrimidine</td>
	<td></td>		<td></td>
-	<td>T</td>	+	<td></td>
-	<td>T</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>dT</td>		<td>dT</td>
	<td></td>		<td></td>
-	<td>dU</td>	+	<td></td>
-	<td>dU</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>
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	<td>T</td>		<td>T</td>
	<td></td>		<td></td>
-	<td>U</td>	+	<td></td>
-	<td>U</td>	+	<td></td>
	</tr>		</tr>
	<tr>		<tr>

Angel Herraez at 08:34, 29 October 2020

2020-10-29T08:34:11Z

←Older revision		Revision as of 08:34, 29 October 2020
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	: <jmol><jmolButton><text>remove from selection</text></jmolButton></jmol> Removes (constraints) from selection		: <jmol><jmolButton><text>remove from selection</text></jmolButton></jmol> Removes (constraints) from selection
	: <jmol><jmolButton><text>pick from selection</text></jmolButton></jmol> or <jmol><jmolButton><text>restrict selection to</text></jmolButton></jmol> This is a new button. What's the unique action??		: <jmol><jmolButton><text>pick from selection</text></jmolButton></jmol> or <jmol><jmolButton><text>restrict selection to</text></jmolButton></jmol> This is a new button. What's the unique action??
		+	How about "reduce selection"?
		+	I think the "to" is not good since the new selection has already been chosen, it will not be chosen after pressing the button. --[[User:Angel Herraez\|Angel_Herraez]] 08:34, 29 October 2020 (UTC)
		+
		+	Action: Changes the selection to just the (constraints) that were also in the previous selection.

	=== More tools in "representations" tab ===		=== More tools in "representations" tab ===

Jaime Prilusky at 05:01, 29 October 2020

2020-10-29T05:01:49Z

←Older revision		Revision as of 05:01, 29 October 2020
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	=== More tools in "selections" tab ===		=== More tools in "selections" tab ===

-	Add <~~jmol~~>~~<jmolButton><text>restrict~~ selection to</~~text></jmolButton></jmol~~> to do "select selected and *".	+	Add <code>pick from selection</code> to do "select selected and ".
		+	*Add <code>clear form</code> to set all text boxes to "all" '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)

-	~~Add <code>~~clear ~~form</code> to set all text boxes to "all" '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15~~, ~~29 October 2020~~ (~~UTC~~)	+	==== Renaming selection buttons ====
		+	We need a clear and consistent naming for the buttons in the selection pannel. These are the names and actions of the current and proposed additional button, combined with the (constraints) above the buttons:

-	~~=== More tools in "representations" tab ===~~	+	: <jmol><jmolButton><text>replace selection</text></jmolButton></jmol> Clears current selection and selects (constraints)
		+	: <jmol><jmolButton><text>add to selection</text></jmolButton></jmol> Adds (constraints) to selection
		+	: <jmol><jmolButton><text>remove from selection</text></jmolButton></jmol> Removes (constraints) from selection
		+	: <jmol><jmolButton><text>pick from selection</text></jmolButton></jmol> or <jmol><jmolButton><text>restrict selection to</text></jmolButton></jmol> This is a new button. What's the unique action??

-	~~Add <code>clear form</code> to uncheck all check boxes (next to <code>hide selection</code> button?) '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)~~	+	=== More tools in "representations" tab ===

-	Combine the following items in a new area between the two existing ones: \|	+	*Add <code>clear form</code> to uncheck all check boxes (next to <code>hide selection</code> button?) '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)
-	<code>center selected atoms</code> \|	+	*Combine the following items in a new area between the two existing ones: <code>center selected atoms</code> <code>center visible atoms</code> <code>zshade on/off</code> and the existing slab from above.
-	<code>center visible atoms</code> \|	+
-	<code>zshade on/off</code> \|	+
-	and the existing slab from above.	+


	=== Suggestions for under the Jmol panel ===		=== Suggestions for under the Jmol panel ===

-	Display updated number of selected atoms on SAT. '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)	+	*Display updated number of selected atoms on SAT. '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)
	Either: number of atoms selected _______		Either: number of atoms selected _______
	Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu		Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu

Jaime Prilusky at 04:28, 29 October 2020

2020-10-29T04:28:15Z

←Older revision		Revision as of 04:28, 29 October 2020
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	=== More tools in "selections" tab ===		=== More tools in "selections" tab ===

-	Add <~~code~~>~~pick from~~ selection</~~code~~> to do "select selected and *".	+	Add <jmol><jmolButton><text>restrict selection to</text></jmolButton></jmol> to do "select selected and *".

	Add <code>clear form</code> to set all text boxes to "all" '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)		Add <code>clear form</code> to set all text boxes to "all" '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)

Jaime Prilusky at 04:15, 29 October 2020

2020-10-29T04:15:22Z

←Older revision		Revision as of 04:15, 29 October 2020
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	Add <code>pick from selection</code> to do "select selected and *".		Add <code>pick from selection</code> to do "select selected and *".

-	Add <code>clear form</code> to set all text boxes to "all"	+	Add <code>clear form</code> to set all text boxes to "all" '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)

	=== More tools in "representations" tab ===		=== More tools in "representations" tab ===

-	Add <code>clear form</code> to uncheck all check boxes (next to <code>hide selection</code> button?)	+	Add <code>clear form</code> to uncheck all check boxes (next to <code>hide selection</code> button?) '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)

	Combine the following items in a new area between the two existing ones: \|		Combine the following items in a new area between the two existing ones: \|
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	=== Suggestions for under the Jmol panel ===		=== Suggestions for under the Jmol panel ===

-	~~Either~~:	+	Display updated number of selected atoms on SAT. '''Done''' [[User:Jaime Prilusky\|Jaime Prilusky]] 04:15, 29 October 2020 (UTC)
-	number of atoms selected _______	+	Either: number of atoms selected _______
-		+
	Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu		Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu
-
	Suggestion: "___ atoms currently selected", right after "Select Atoms ALL NONE"		Suggestion: "___ atoms currently selected", right after "Select Atoms ALL NONE"
	or inside the box under "currently loaded file"		or inside the box under "currently loaded file"

Angel Herraez at 13:39, 28 October 2020

2020-10-28T13:39:46Z

←Older revision		Revision as of 13:39, 28 October 2020
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	Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu		Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu
		+
		+	Suggestion: "___ atoms currently selected", right after "Select Atoms ALL NONE"
		+	or inside the box under "currently loaded file"
		+	--[[User:Angel Herraez\|Angel_Herraez]] 13:39, 28 October 2020 (UTC)

	==Karsten's comments==		==Karsten's comments==
	Thanks for posting this here, Angel. I vote for removing the Nucleic residues from the group selections because it is redundant. We could consolidate the "protein" and the "amino acid properties" into a single category. I did not do this because then the next category is not visible at first glance.		Thanks for posting this here, Angel. I vote for removing the Nucleic residues from the group selections because it is redundant. We could consolidate the "protein" and the "amino acid properties" into a single category. I did not do this because then the next category is not visible at first glance.
	--[[User:Karsten Theis\|Karsten Theis]] 13:04, 28 October 2020 (UTC)		--[[User:Karsten Theis\|Karsten Theis]] 13:04, 28 October 2020 (UTC)

Karsten Theis at 13:04, 28 October 2020

2020-10-28T13:04:49Z

←Older revision		Revision as of 13:04, 28 October 2020
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	Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu		Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu
		+
		+	==Karsten's comments==
		+	Thanks for posting this here, Angel. I vote for removing the Nucleic residues from the group selections because it is redundant. We could consolidate the "protein" and the "amino acid properties" into a single category. I did not do this because then the next category is not visible at first glance.
		+	--[[User:Karsten Theis\|Karsten Theis]] 13:04, 28 October 2020 (UTC)