salilab / IHMValidation

Validation software for integrative models deposited to PDB
MIT License
2 stars 2 forks source link

Conflicting model scale definitions #88

Open aozalevsky opened 1 week ago

aozalevsky commented 1 week ago

The most obvious way to retrieve model scale (atomic/coarse-grained/multiscale (a mix of atomic and coarse-grained)) is from the _ihm_model_representation_details table. However, the scale is also explicitly defined in _ihm_modeling_protocol_details.multi_scale_flag.

It causes a conflict for PDBDEV_00000093:

According to the representation table, the model is purely atomic:

loop_                                                                                                                                                                                                                                                                                                                         
_ihm_model_representation_details.id                                                                                                                                                                                                                                                                                          
_ihm_model_representation_details.representation_id                                                                                                                                                                                                                                                                           
_ihm_model_representation_details.entity_id                                                                                                                                                                                                                                                                                   
_ihm_model_representation_details.entity_description                                                                                                                                                                                                                                                                          
_ihm_model_representation_details.entity_asym_id                                                                                                                                                                                                                                                                              
_ihm_model_representation_details.entity_poly_segment_id                                                                                                                                                                                                                                                                      
_ihm_model_representation_details.model_object_primitive                                                                                                                                                                                                                                                                      
_ihm_model_representation_details.starting_model_id                                                                                                                                                                                                                                                                           
_ihm_model_representation_details.model_mode                                                                                                                                                                                                                                                                                  
_ihm_model_representation_details.model_granularity                                                                                                                                                                                                                                                                           
_ihm_model_representation_details.model_object_count                                                                                                                                                                                                                                                                          
_ihm_model_representation_details.description                                                                                                                                                                                                                                                                                 
1 1 1 'N4BP1 CUE domain' A 1 atomistic 1 rigid by-atom . .                                                                                                                                                                                                                                                                    
2 1 2 'Ubiquitin' B 2 atomistic 2 rigid by-atom . .                                                                                                                                                                                                                                                                           
3 1 1 'N4BP1 CUE domain' A 3 atomistic 1 flexible by-atom . .                                                                                                                                                                                                                                                                 
4 1 1 'N4BP1 CUE domain' A 4 atomistic 1 flexible by-atom . .                                                                                                                                                                                                                                                                 
5 1 1 'N4BP1 CUE domain' A 5 atomistic 1 flexible by-atom . .                                                                                                                                                                                                                                                                 
6 1 2 'Ubiquitin' B 6 atomistic 2 flexible by-atom . .                                                                                                                                                                                                                                                                        
7 1 2 'Ubiquitin' B 7 atomistic 2 flexible by-atom . .                                                                                                                                                                                                                                                                        
8 1 2 'Ubiquitin' B 8 atomistic 2 flexible by-atom . .                                                                                                                                                                                                                                                                        
9 1 2 'Ubiquitin' B 9 atomistic 2 flexible by-atom . .                                                                                                                                                                                                                                                                        
10 1 2 'Ubiquitin' B 10 atomistic 2 flexible by-atom . .                                                                                                                                                                                                                                                                      
11 1 2 'Ubiquitin' B 11 atomistic 2 flexible by-atom . .  

at the same time _ihm_modeling_protocol_details.multi_scale_flag is set to YES.

Thus, on the website it's rendered as 'multiscale' : multi-scale )

I think structural model scale should be inferred using only _ihm_model_representation_details. @brindakv @jaredsagendorf what do you think?

jaredsagendorf commented 1 week ago

This table is populated during deposition, correct? Seems like the deposition system just needs a consistency check. Or maybe just make this field not editable and automatically populate it for the user?