Studio

Step by step

1. Find your way

   The module bar along the top runs in working order: Studio · Build, Polymer cell, Packing · Force field, Minimise, Equilibrate, Dynamics, React · Analyze, Export · Jobs, Bench. The gear opens Settings.

   Press ⌘K (Ctrl+K) to find any page, builder or command by name.

2. Follow the pipeline strip

   Structure → Made by → Force field → Minimise → Equilibrate → Dynamics → Export. A step turns green when done; click any step to go to its page. Minimise, Equilibrate and Dynamics are optional.

3. Look and edit

   Click an atom to pick it, drag to rotate, ⇧-drag to pan. The toolbar selects, moves, rotates, draws bonds, adds hydrogens and rings, measures and colours.

   Each open structure has its own tab; + opens another.

4. Use the project tree

   Every structure in the project, with Edit (reopens the builder that made it, with its settings), Delete (twice to confirm; files on disk stay) and Copy structure to try a change on a duplicate.

5. Check and save

   Validation › All checks… lists every file check. The File tab saves as LAMMPS data, PDB, XYZ, mol2, CIF or a VASP POSCAR.

6. Quick analysis

   The bottom tabs analyse the frame shown: g(r), Minimisation, Thermo, Molecules, Network, Around atom, Chains.

The same without the Studio

Every Studio page calls the same core as the caps command and the caps Python package, so a step you clicked can be repeated in a script.

caps check cell.data --report checks.md
caps render cell.data -o cell.png --style ball --colour molecule
caps convert cell.data cell.pdb

import caps

d = caps.open("cell.data")
print(d.checks())
d.render("cell.png", style="ball_and_stick")
d.save("cell.pdb")

Where to go next

BuildPolymer builder114 repeat units and 21 copolymers, or your own SMILES; architecture, sequence, composition, tacticity and end groups.PrepareForce fieldType every atom from SMARTS rules, set charges, fill any missing term and give each part of a composite its own force field.