Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Conflicting model scale definitions #88

Open
aozalevsky opened this issue Jun 27, 2024 · 1 comment
Open

Conflicting model scale definitions #88

aozalevsky opened this issue Jun 27, 2024 · 1 comment

Comments

@aozalevsky
Copy link
Contributor

aozalevsky commented Jun 27, 2024

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
Copy link

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?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants