# File PROJECTS # RasMol2, Roger Sayle # Glaxo Research & Development # Last Modified 28/03/95 # Any person (university or company) wishing to help with any # of the projects described below, please e-mail the author at # "ras32425@ggr.co.uk". [A] Machine Independent ======================= [A1] Input Formats ------------------ [1] BioSym's .car format (including polymer extensions). [2] Macromodel format files. [3] Implement STAR file parser for mmCIF,MIF and MODEL files [3] Gaussian (z-matrix) files. [4] DayLight Chemical System's Thor data trees (.tdt) [5] Support for complex parsing of ASN.1 mmdb [A2] Chemistry/Biology Support ------------------------------ [1] Priestle-style Structure Smoothing [2] Define "cisproline" from Omega angles. [3] Crystallographic Symmetry operators. [4] Richardson's `typed' turn definitions (instead of DSSP) [5] "phi" & "psi" properties of amino acid residues. [6] "helix(3)" and "turn(2)" subtypes in expressions. [7] "set dielectric" parameter for potential surfaces. [8] Read default SSBOND from PDB file. [9] Determine charges using "Marselli-Gasteiger" [A3] Output Formats ------------------- [1] Persistance of Vision (POV) ray tracer format [2] Write out secondary structure to PDB files [3] Vector PostScript output of Ribbons (MolScript) [A5] Representations -------------------- [1] Flat Capped Cylinder Representation [2] Full `Connolly' Solvent Accessible Surface [3] Solid Polygonal Solvent Surfaces [like GRASP]. [4] Priestle "Ribbons" for alpha carbon only backbones. [5] Group (Bounding) Spheres Representation [6] Ortep Style thermal ellipsoid Graphics. [7] Solid `Extruded Ellipse' Representation (MIDAS & Ribbons) [A4] Rendering -------------- [1] Zaphod (Stereo) Mode Transformation [2] Red-Green Stereo line drawings [3] Improved Quality Cylinder Rendering [4] Shadow Casting from Cylinders (IA & Quadric). [5] Back Clipping/Slabbing Plane [6] Shadow Casting from (Ribbon/Surface) Polygons [A5] Misc. ---------- [1] Rewrite Manual and develop tutorial introduction. [2] RESIZE command to set resolution even in non-iteractive mode. [3] Increased support for MolScript & PDBregion expressions. [4] BSD `socket'-based Inter-process Communication (OML & Flex). [5] Optimise select expressions of the form "(atomno=%d) or (atomno=%d)" [B] Machine & OS Dependent ========================== [B1] UNIX & X11 Window System ----------------------------- [1] FileOpen and FileSave Dialog Boxes [2] X Windows Resource Database (XDefaults) [3] Graphics Tablet and Spaceball Input [4] X11's SGIFullScreenStereo Extension [5] Colour 85x67 Icon for 4Dwm on SGI Machines! [B2] MS-DOS & MS Windows 3.1 ---------------------------- [1] MS Windows WINDOWS.INI File Processing [2] DDE Transfer of Valuators [3] Develop 32/24bit graphics version of RasWin [B3] Apple Macintosh & PowerMac -------------------------------- [1] Select and Copy text from the command line. [2] Simple AppleEvents to ExecuteCommands. [3] Advanced AppleEvents to Transfer Data. [4] Initialisation [Preference?] File. [B4] VAX/AXP VMS ---------------- [1] Improved filename parsing and expansion! [2] Spawn process to uncompress files. [B5] Other Systems ------------------ [1] Acorn Archimedes (ARM) version for UK schools. [2] Commodore Amiga version (???).