Proteopedia talk:Wishlist

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<td></td>
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<td colspan='2'>'''Nucleic residues'''</td>
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<td>''but we can remove this altogether'' </td>
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<td>dA</td>
<td>dA</td>
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<td>dA</td>
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<td>A</td>
<td>A</td>
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<td>A</td>
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<td>A</td>
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<td>dC</td>
<td>dC</td>
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<td>dC</td>
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<td>dC</td>
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<td>C</td>
<td>C</td>
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<td>C</td>
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<td>C</td>
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<td>dG</td>
<td>dG</td>
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<td>dG</td>
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<td>dG</td>
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<td>G</td>
<td>G</td>
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<td>G</td>
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<td>G</td>
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<td>dI</td>
<td>dI</td>
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<td>dI</td>
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<td>dI</td>
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<td>I</td>
<td>I</td>
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<td>I</td>
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<td>I</td>
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<td>purine</td>
<td>purine</td>
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<td>dT</td>
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<td>dT</td>
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<td>pyrimidine</td>
<td>pyrimidine</td>
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<td>T</td>
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<td>T</td>
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<td>dT</td>
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<td>dU</td>
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<td>dU</td>
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<td>T</td>
<td>T</td>
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<td>U</td>
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=== More tools in "selections" tab ===
=== More tools in "selections" tab ===
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Add <code>pick from selection</code> to do "select selected and *".
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*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)
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Add <code>clear form</code> to set all text boxes to "all"
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==== 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:
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=== More tools in "representations" tab ===
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: <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
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: <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)
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Add <code>clear form</code> to uncheck all check boxes (next to <code>hide selection</code> button?)
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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.
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Combine the following items in a new area between the two existing ones: |
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=====Example=====
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<code>center selected atoms</code> |
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<code>center visible atoms</code> |
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<code>zshade on/off</code> |
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and the existing slab from above.
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 +
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.
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=== Suggestions for under the Jmol panel ===
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<jmol><jmolButton><text>replace selection</text></jmolButton></jmol> all histidines selected
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Either:
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<jmol><jmolButton><text>add to selection</text></jmolButton></jmol> all histidines selected, plus the neighbors of iron
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number of atoms selected _______
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Or: after "Show Selected with Halos", just show the number in parentheses as done in the Jmol right-click menu
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<jmol><jmolButton><text>remove from selection</text></jmolButton></jmol> neighbors of iron selected, except for histidines
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<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 ===
 +
 +
*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: <code>center selected atoms</code> <code>center visible atoms</code> <code>zshade on/off</code> and the existing slab from above.
 +
 +
 +
=== 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)
 +
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
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"

Current revision

Contents

To-Do

Some redesign of the options in the SAT:

List of items in "selections" tab of the SAT

heading current
submenu		 current
command		 proposal
submenu		 proposal
command
all all all all
protein Protein
all protein protein all protein
alpha carbon alpha alpha carbon
backbone/mainchain backbone backbone/mainchain protein and backbone
helix helix sidechain protein and sidechain
sheet sheet helix
sidechain sidechain sheet
turn turn turn
non-protein Nucleic acid
base base RNA rna
carbohydrate carbohydrate DNA dna
dna dna bases base
hetero hetero purines purine
ions ions pyrimidines pyrimidine
ligand ligand backbone/mainchain nucleic and backbone
nucleic nucleic
rna rna Other
solvent solvent all ligands ligand
water water solvent/water solvent
carbohydrate carbohydrate
protein residues all hetero hetero
acidic/negative acidic ions ions
acyclic acyclic
aliphatic aliphatic
all residues amino Protein residues
aromatic aromatic Amino acid properties maybe "by amino acid property"
basic/positive basic acidic/negative acidic
buried buried basic/positive basic
charged charged charged charged
cyclic cyclic polar polar
hydrophobic hydrophobic hydrophobic hydrophobic
large large aromatic aromatic
medium medium
neutral neutral
polar polar
small small
surface surface
nucleotides
dA dA
A A
dC dC
C C
dG dG
G G
dI dI
I I
purine purine
pyrimidine pyrimidine
dT dT
T T
dU dU
U U

More tools in "selections" tab

  • Add pick from selection to do "select selected and *".
  • Add clear form to set all text boxes to "all" Done 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:

Clears current selection and selects (constraints)
Adds (constraints) to selection
Removes (constraints) from selection
or 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. --Angel_Herraez 08:34, 29 October 2020 (UTC)

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.

all histidines selected

all histidines selected, plus the neighbors of iron

neighbors of iron selected, except for histidines

just the histidines that are neighbors of the iron, nothing else

--Karsten Theis 13:04, 29 October 2020 (UTC)

More tools in "representations" tab

  • Add clear form to uncheck all check boxes (next to hide selection button?) Done Jaime Prilusky 04:15, 29 October 2020 (UTC)
  • Combine the following items in a new area between the two existing ones: center selected atoms center visible atoms zshade on/off and the existing slab from above.


Suggestions for under the Jmol panel

  • Display updated number of selected atoms on SAT. Done Jaime Prilusky 04:15, 29 October 2020 (UTC)

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 Suggestion: "___ atoms currently selected", right after "Select Atoms ALL NONE" or inside the box under "currently loaded file" --Angel_Herraez 13:39, 28 October 2020 (UTC)

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. --Karsten Theis 13:04, 28 October 2020 (UTC)

Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez, Jaime Prilusky, Karsten Theis

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