Preparing proteins
To quickly prepare a protein structure in SAMSON (remove alternate locations, ligands, water and monatomic ions, and add hydrogens), click on Home > Prepare, select the steps you would like to include, and click Ok.
Category: Modeling
Freezing atoms positions
To control atoms mobility during minimization or simulation, use the Freeze (shortcut F) and Unfreeze (shortcut U) commands. Frozen atoms have a dark blue overlay in the viewport.
Snapping molecules
To position molecules precisely, you can use translational and angular snapping. You can also choose any atom as rotation center.
Generating symmetric replicas
To quickly add symmetric replicas in SAMSON, use the Symmetry Mate Editor. This free extension lets you interactively generate symmetry mates of a protein based on the crystallographic information from a PDB file.
Editing side-chain conformations
To edit protein side-chain conformations in SAMSON, use the Rotamers editor extension based on Roland Dunbrack’s famed library. Select a residue, then choose the rotamer you want to use from the corresponding table. Potential clashes will be automatically detected and…
Quick geometry optimization using the FIRE minimizer
To perform very fast geometry optimization, use the FIRE minimizer. When this carbon nanotube is sliced, it quickly relaxes to a mostly flat graphene sheet.
Creating a nanopore
To build a carbon nanopore, draw a graphene sheet and a nanotube, remove some atoms and use the Brenner reactive force field during interactive minimization to meld them. The Brenner potential (Brenner et al., Journal of Physics: Condensed Matter, Volume…
Building with atoms and fragments
To build molecules, use A to add atoms and fragments, B to edit bonds, and C to edit charges. Combine this with interactive minimization (shortcut Z) to build physically-based structures.
Rotating fragments around bonds
To rotate a molecular fragment around a bond, use the Local Move Editor (shortcut M) and just click on the bond. The editor will automatically select the shortest fragment and will show the move widgets. Combine this with interactive minimization…
Freezing atoms positions
To control atoms mobility during minimization or simulation, use the Freeze (shortcut F) and Unfreeze (shortcut U) commands. Frozen atoms have a dark blue overlay in the viewport.
Snapping molecules
To position molecules precisely, you can use translational and angular snapping. You can also choose any atom as rotation center.
Generating symmetric replicas
To quickly add symmetric replicas in SAMSON, use the Symmetry Mate Editor. This free extension lets you interactively generate symmetry mates of a protein based on the crystallographic information from a PDB file.
Editing side-chain conformations
To edit protein side-chain conformations in SAMSON, use the Rotamers editor extension based on Roland Dunbrack’s famed library. Select a residue, then choose the rotamer you want to use from the corresponding table. Potential clashes will be automatically detected and…
Quick geometry optimization using the FIRE minimizer
To perform very fast geometry optimization, use the FIRE minimizer. When this carbon nanotube is sliced, it quickly relaxes to a mostly flat graphene sheet.
Creating a nanopore
To build a carbon nanopore, draw a graphene sheet and a nanotube, remove some atoms and use the Brenner reactive force field during interactive minimization to meld them. The Brenner potential (Brenner et al., Journal of Physics: Condensed Matter, Volume…
Building with atoms and fragments
To build molecules, use A to add atoms and fragments, B to edit bonds, and C to edit charges. Combine this with interactive minimization (shortcut Z) to build physically-based structures.
Rotating fragments around bonds
To rotate a molecular fragment around a bond, use the Local Move Editor (shortcut M) and just click on the bond. The editor will automatically select the shortest fragment and will show the move widgets. Combine this with interactive minimization…