Templates¶
VLab4Mic ships with pre-configured templates for common structures, probes, virtual samples, and imaging modalities. These are ready to use in both notebooks and Python scripts.
Structures¶
Any atomic structure in PDB or CIF format can be used with VLab4Mic. The package
includes YAML templates and example IDs for the structures below; the
corresponding CIF files are downloaded on first use and cached in
~/.vlab4mic/structures unless VLAB4MIC_STRUCTURE_DIR is set.
| Structure ID | Description | Database | Format |
|---|---|---|---|
| 1XI5 | Clathrin D6 coat with auxilin J-domain | RCSB | CIF |
| 7R5K | Human nuclear pore complex (constricted) | RCSB | CIF |
| 3J3Y | Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers) | RCSB | CIF |
| 8GMO | Bacteriophage T4 capsid shell | RCSB | CIF |
Probes¶
Probes are configuration files that model a specific type of fluorescent labelling. Pass the probe name as probe_template in image_vsample.
Structure-Independent Probes¶
These probes work with any atomic structure. Specify your target using probe_target_type and probe_target_value.
| Probe name | Description | Probe model |
|---|---|---|
| NHS_ester | Direct label targeting lysine (LYS) residues | — |
| Linker | Indirect label modelled as a rigid spacer | — |
| Antibody | Indirect label based on an IGG antibody (anti-HIV-1) | 1HZH |
| Nanobody | Indirect label based on a synthetic nanobody | 7MFV |
| GFP | Indirect label based on GFP crystal structure | 6YLQ |
| GFP_w_nanobody | Indirect label based on a nanobody–eGFP complex | 6XZF |
| mMaple | Indirect label based on the mTFP1 fluorescent protein | 2HQK |
| SNAP-tag | Indirect label based on SNAP-tag with conjugated fluorophore | 6Y8P |
Structure-Specific Probes¶
Pre-configured probes tuned to particular structures.
| Probe name | Description | Target | Probe model | Structure |
|---|---|---|---|---|
| CCP_heavy_chain_Cterminal | Direct probe for C-terminal of Clathrin Heavy Chain | EQATETQ |
— | 1XI5 |
| NPC_Nup96_Cterminal_direct | Direct probe for C-terminal of Nup96 in the NPC | ELAVGSL |
— | 7R5K |
| HIV_capsid_p24_direct | Direct probe for HIV-1 Capsid monomer (p24) | SPRTLNA |
— | 3J3Y |
| anti-p24_primary_antibody_HIV | Antibody targeting HIV-1 Capsid monomer (p24) | SPRTLNA |
1HZH | 3J3Y |
Virtual Sample Templates¶
| Template name | Description |
|---|---|
| square1x1um_randomised | Square field of view with a single particle placed in the centre |
Modalities¶
| Modality | Description | PSF shape XYZ (nm) | Pixel size (nm) |
|---|---|---|---|
| Widefield | Widefield epifluorescence | 130 × 130 × 400 | 100 |
| Confocal | Laser scanning confocal | 100 × 100 × 300 | 70 |
| AiryScan | Zeiss AiryScan detector | 61 × 61 × 230 | 40 |
| STED | Stimulated emission depletion | 20 × 20 × 20 | 15 |
| SMLM | Single-molecule localisation (effective image model) | 8 × 8 × 8 | 2 |
| Reference | Idealised diffraction-limited reference | 5 × 5 × 5 | 5 |
Thevathasan 2019 Variants¶
Modality configurations (the *_Thev2016 config family) tuned to the experimental parameters reported in Thevathasan et al. 2019, for use in article figure reproductions.
| Modality | Description | PSF shape XYZ (nm) | Pixel size (nm) |
|---|---|---|---|
| Widefield_Thev2016 | Widefield — Thevathasan 2019 parameters | 94 × 94 × 331 | 100 |
| Confocal_Thev2016 | Confocal — Thevathasan 2019 parameters | 94 × 94 × 331 | 70 |
| AiryScan_Thev2016 | AiryScan — Thevathasan 2019 parameters | 61 × 61 × 230 | 40 |
| STED_Thev2016 | STED — Thevathasan 2019 parameters | 15 × 15 × 20 | 15 |
| STORM_Thev2016 | STORM/SMLM — Thevathasan 2019 parameters | 8 × 8 × 8 | 5 |