Proteopedia talk:Wishlist
From Proteopedia
(Difference between revisions)
(more suggestions for SAT) |
(→Example) |
||
| (11 intermediate revisions not shown.) | |||
| Line 246: | Line 246: | ||
<td>aromatic</td> | <td>aromatic</td> | ||
<td colspan="2">'''Amino acid properties'''</td> | <td colspan="2">'''Amino acid properties'''</td> | ||
| - | <td></td> | + | <td>''maybe "by amino acid property"''</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 348: | Line 348: | ||
<td></td> | <td></td> | ||
<td></td> | <td></td> | ||
| - | <td | + | <td></td> |
<td></td> | <td></td> | ||
</tr> | </tr> | ||
| Line 356: | Line 356: | ||
<td>dA</td> | <td>dA</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 364: | Line 364: | ||
<td>A</td> | <td>A</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 372: | Line 372: | ||
<td>dC</td> | <td>dC</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 380: | Line 380: | ||
<td>C</td> | <td>C</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 388: | Line 388: | ||
<td>dG</td> | <td>dG</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 396: | Line 396: | ||
<td>G</td> | <td>G</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 404: | Line 404: | ||
<td>dI</td> | <td>dI</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 412: | Line 412: | ||
<td>I</td> | <td>I</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 420: | Line 420: | ||
<td>purine</td> | <td>purine</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 428: | Line 428: | ||
<td>pyrimidine</td> | <td>pyrimidine</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 436: | Line 436: | ||
<td>dT</td> | <td>dT</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 444: | Line 444: | ||
<td>T</td> | <td>T</td> | ||
<td></td> | <td></td> | ||
| - | <td> | + | <td></td> |
| - | <td> | + | <td></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 465: | Line 465: | ||
</table> | </table> | ||
| - | == More tools in "selections" tab == | + | === More tools in "selections" tab === |
| - | 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" '''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: | ||
| + | : <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?? | ||
| + | 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. '''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 === | |
| - | + | ||
| + | *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 | 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== | ||
| + | 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) | ||
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 selectionto do "select selected and *". - Add
clear formto 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 formto uncheck all check boxes (next tohide selectionbutton?) Done Jaime Prilusky 04:15, 29 October 2020 (UTC) - Combine the following items in a new area between the two existing ones:
center selected atomscenter visible atomszshade on/offand 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)
