Difference between revisions of "AtomSets/Popup Menu"
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AngelHerraez (talk | contribs) (→Selection of atom sets from the pop-up menu) |
AngelHerraez (talk | contribs) m (formatting) |
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= Selection of atom sets from the pop-up menu = | = Selection of atom sets from the pop-up menu = | ||
| − | + | Pop-up menu (as of Jmol 11.9.19): | |
[[File:Popup_select_submenu.gif]] | [[File:Popup_select_submenu.gif]] | ||
| − | * Select | + | * '''Select''' |
| − | ** Element | + | ** '''Element''' |
| − | *** | + | *** (list of elements present) |
| − | + | ** '''Protein''' (disabled for non-pdb files) | |
| − | |||
| − | |||
| − | ** Protein | ||
*** By residue name | *** By residue name | ||
| + | **** (list of amino acid residues present) | ||
*** (protein subsets) | *** (protein subsets) | ||
| − | ** Nucleic | + | ** '''Nucleic''' (disabled for non-pdb files) |
*** By residue name | *** By residue name | ||
| + | **** (list of nucleotide residues present) | ||
*** (nucleic subsets) | *** (nucleic subsets) | ||
| − | ** Hetero | + | ** '''Hetero''' (disabled for non-pdb files)<br />Proposed change to other more friendly term - which one? |
| − | *** By HETATM | + | *** By HETATM<br />Proposed change to 'By group name' |
| − | *** All PDB "HETATM" | + | **** (list of hetero groups present) |
| − | *** All solvent | + | *** All PDB "HETATM" - applies script <code>select hetero</code><br />Proposed change to 'All hetero' |
| − | *** All water | + | *** All solvent - applies script <code>select solvent</code> |
| − | *** Ligand | + | *** All water - applies script <code>select water</code> |
| − | *** Nonaqueous HETATM | + | *** Ligand - applies script <code>select ligand</code>, which is the same as <code>select hetero and not solvent</code> |
| − | *** Nonaqueous solvent | + | *** Nonaqueous HETATM - applies script <code>select hetero and not water</code><br />Proposed change to 'Nonaqueous hetero' |
| − | ** Carbohydrate | + | *** Nonaqueous solvent - applies script <code>select solvent and not water</code> |
| + | ** '''Carbohydrate''' (disabled for non-pdb files) | ||
*** By residue name | *** By residue name | ||
| − | *** All | + | **** (list of monosaccharide residues present) |
| − | ** None of the above | + | *** All - applies script <code>select carbohydrate</code> |
| + | ** '''None of the above''' (disabled for non-pdb files) - applies script <code>select not(hetero,protein,nucleic,carbohydrate)</code> | ||
Latest revision as of 19:46, 26 July 2012
Pop-up menu (as of Jmol 11.9.19):
- Select
- Element
- (list of elements present)
- Protein (disabled for non-pdb files)
- By residue name
- (list of amino acid residues present)
- (protein subsets)
- By residue name
- Nucleic (disabled for non-pdb files)
- By residue name
- (list of nucleotide residues present)
- (nucleic subsets)
- By residue name
- Hetero (disabled for non-pdb files)
Proposed change to other more friendly term - which one?- By HETATM
Proposed change to 'By group name'- (list of hetero groups present)
- All PDB "HETATM" - applies script
select hetero
Proposed change to 'All hetero' - All solvent - applies script
select solvent - All water - applies script
select water - Ligand - applies script
select ligand, which is the same asselect hetero and not solvent - Nonaqueous HETATM - applies script
select hetero and not water
Proposed change to 'Nonaqueous hetero' - Nonaqueous solvent - applies script
select solvent and not water
- By HETATM
- Carbohydrate (disabled for non-pdb files)
- By residue name
- (list of monosaccharide residues present)
- All - applies script
select carbohydrate
- By residue name
- None of the above (disabled for non-pdb files) - applies script
select not(hetero,protein,nucleic,carbohydrate)
- Element
