Feature List

[trudack]

We can still assign a priority order I am just collecting all ideas of previous issues and discussions I wrote done before I forget.

I would considere the bold ones as most important for now

Rosetta

• [ ] restart option

Modelling

• [x] add fragment file generation with Rosetta
• [x] include Modeller
• [ ] delete and put in non protein molecules before/after rosetta
• [ ] gap finder with sequence

Refinement

• [ ] automated refinement strategies based on cross correlation values
• [ ] automated helix translate and rotate to optimize helix registartions

Analysis

• [ ] Keith Clustering Script
• [ ] Command to cut out a density part based on a structure selection of model
• [ ] Command to color density part based on a structure selection of model
• [ ] Add structure check command
• [ ] adapt clustering model maker selection to VMD atom selections
• [ ] replace gnuplot by VMD shipped plotting tool from Barry when done

Setup MDFF

• [ ] run implicit solvent MDFF
• [ ] add option to solvate and run MDFF for side chain optimization with explizit solvent
• [ ] option to mdff to add a list of different densities and grid scaling factors
• [ ] grid scaling based on local resolution
• [ ] punctuation check script
• [ ] punctuation fix from Xmas-Builder?
• [ ] step flag for iterative refine
• [ ] incorporate a module for resolution exchange mdff
• [ ] incorporate a module for cascade mdff
• [ ] as soon as VMD can write mrc files we can easily automate the cut out of densities to refine only specific areas of the densities or run mdff only on them

iMDFF

• [ ] Command to clear all iMD forces within an interactive VMD iMD
• [ ] Deslect Forces based on on the Atoms/Residues they are on like the lable command for atoms/bonds/angles/dihedrals

Other

• [ ] renaming of chain ID and segname based on txt file with residue range see Issue #14 (double check why some structures only work with -chseg input)
• [ ] have VMD to write out mrc files (John)
• [ ] VMD rigid docking to density followed by short MDFF equilibration (John)
• [ ] VMD density segmentation of "sausages" by mouse click (John)