Proteopedia:Development/2024-09
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Development August-Sept. 2024
Flowchart of loading and initialview
Proteopedia Page Contributors and Editors (what is this?)
Angel Herraez
Development August-Sept. 2024Development August-Sept. 2024
- Update of initialview script for seeded pages.
- Combined initialview01.spt, initialview02.spt, initialview02v4.spt into a single initialview03.spt
- Hardcoded calls to initialview01.spt are kept, but initialview01.spt is now a duplicate of initialview03.spt
- Modularisation of initialview contents by creating several functions.
- Fixed the rendering of multimodel files (which had been broken at some previous stage)
- Introduced conditionalLoad function for deciding to skip simplified view, based on molecular weight of biological unit (all models added, in case of multimodel files). Cutoff set inside the function (currently 200 kDa)
- Data to detect ca_p_only, number of models and MW are retrieved from PDBe REST API and stored in a Jmol variable pdb_features.
- Many utility functions combined into functions.spt (including conditionalLoad)
- General review of dealing with all cases:
- Files that have only Calpha and P coordinates vs. normal all-atom models.
- Files with one or more models (not just NMR, also other exp.methods).
- Loaded as simplified or as full.
- Special cases like very few residues.
- Need to display [load full] button only in relevant cases.
- New buttons [model 1][all models] in relevant cases. All models are displayed by default.
- Review of ConSurf coloring on/off scripts to be valid for all cases considering the revision in loading and display scripts.
Pending:
- Apply similar renderings to files that do not match the data at PDBe. Right now, they get a basic rendering (shortScript) that, for example, does not offer alternative displays for multimodel files.
- Some examples: MET.pdb, 8XH1.pdb, 1crn_test.pdb, 1nns_box_251-253.pdb, UPL8H1D.pdb (10 models)
Flowchart of loading and initialviewFlowchart of loading and initialview
| atoms? | only Calpha & P | only Calpha & P | all atoms | all atoms | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| multimodel? | 1 model | N models | 1 model | N models | ||||||
| MW? | small | large | small | large | small | large | small | large | ||
| PDB id example (kDa/Mda) | 1ae4(36k) | 2rec(228k) | 1w2r(93k) | 1jq2(722k) | 1buu(56k) | 1flo(235k) | 2dan(133k) | 8h1d(251k) | ||
| conditionalLoad() | ca_p_only | read from API | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 |
| number_of_deposited_models | read from API | 1 | 1 | N | N | 1 | 1 | N | N | |
| load | full (not filtered) | filtered | full (not filtered) | filtered | full (not filtered) | filtered | full (not filtered) | filtered | ||
| numModelsLoaded | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | ||
| initialview03.spt | initVars() | numModelsLoaded | 1 (read iin Jmol) | N, read iin Jmol | 1 (read iin Jmol) | N, read iin Jmol | ||||
| startClean() | ||||||||||
| "modelnumberbuttons" span | hidden | hidden | hidden | hidden | hidden | hidden | hidden | hidden | ||
| renderMultiModel() | no | no | yes | no | no | no | yes | no | ||
| needsFullScript | false | false | ||||||||
| renderSingleModel() | yes | yes | no | yes | yes | yes | no | yes | ||
| needsFullScript | true | true | true | true | true | true | ||||
| isSimplified | true | true | true | false | true | true | ||||
| useFullScript | false | false | false | true | false | false | ||||
| needsFullScript | false | false | false | |||||||
| applyFullScript() | yes | |||||||||
| isSimplified | false | |||||||||
| warningSimplified() | ||||||||||
| echo simplified | no | |||||||||
| applyShortScript() | yes | yes | yes | yes | yes | |||||
| isSimplified | false | false | true | |||||||
| numModelsLoaded | 0 | 0 | 0 | 0 | 0 | |||||
| warningSimplified() | ||||||||||
| echo simplified | yes | yes | ||||||||
| "Load Full" btn | hidden | hidden | visible | hidden | visible | visible | ||||
| after click on [load full] | <== | <== | <== | |||||||