General Changes:
- “connected fragment” inserted into selection cascade between residue and chain
- SMILES-to-3D uses the translator at cactus.nci.nih.gov if the smi23d service does not produce a result
- new volume input format, Amira mesh (scalar)
Tool Changes:
- 2D Labels (Utilities) — existing arrows can be repositioned
- Find Clashes/Contacts (Structure Analysis, Surface/Binding Analysis) — intramolecular interactions can be excluded, where a molecule is defined as a covalently bonded set of atoms
- FindHBond (Structure Analysis, Surface/Binding Analysis) — intramolecular and/or intraresidue H-bonds can be excluded
Command Changes:
- 2dlabels — existing arrows can be repositioned (achange start/end options)
- findclash — intramolecular interactions can be excluded, where a molecule is defined as a covalently bonded set of atoms
- findhbond — intramolecular and/or intraresidue H-bonds can be excluded
- mask — model number of output map can be specified
- measure —
- fieldLines to show electric field lines for potential maps
- vop —
- threshold to reassign values that are below a specified minimum and/or above a specified maximum
Known Bugs:
- surfaces fail for some structures
- Nvidia Quadro graphics on Windows 7 cause ten-second freezes when picking atoms (Ctrl-mouseclick) of large models (20000 atoms). This is caused by the graphics driver "adaptive" power management setting. Using Nvidia Control Panel, Manage 3-D Settings, Global Settings tab to change Power Management to "Prefer maximum performance" solves this problem. Bug report #11315.