Refine cryo-EM SPA and crystallographic models with reciprocal-space refinement and Fo-Fc maps.
npx skills add https://github.com/farnunglab/benchaid --skill servalcat
Please help me install this Agent Skill. Skill: servalcat Source: https://github.com/farnunglab/benchaid/tree/main/skills/servalcat Command: npx skills add https://github.com/farnunglab/benchaid --skill servalcat
Servalcat enables reciprocal-space refinement and map calculation for cryo-EM SPA and crystallography, delivering properly weighted Fo-Fc difference maps and refined models.
Install Servalcat and run a basic SPA refinement with your model.pdb and half-maps to generate a refined structure.
High-intent search queries and answers about installing and using this skill.
Reciprocal-space refinement for cryo-EM SPA data is performed by fitting a model against half-maps. This Skill refines the input model pdb or mmCIF and outputs refined models along with diagnostic maps.
Fo-Fc difference maps for cryo-EM models are calculated automatically during reciprocal-space refinement. This process applies properly weighted Fo-Fc map calculations against input half-maps to validate model fitting.
Yes, you can generate omit maps for ligands and other applications. The Fo-Fc map calculation workflows support omit-map scenarios to validate specific structural features against cryo-EM and crystallographic data.
Yes, reciprocal-space refinement supports external restraints and NCS/symmetry expansion. It includes utility commands for map trimming and symmetry expansion to facilitate precise model fitting and validation.
Cryo-EM refinement and map calculation require a model pdb or mmCIF, half-maps, and masks. You also need to specify refinement options to generate refined models and diagnostic maps properly.
Reciprocal-space refinement is used when you need properly weighted Fo-Fc difference maps and precise model fitting against half-maps. It is suited for structure-determination workflows requiring validation through difference maps.
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