Ribbons Release Notes

Changes from Version 3.31 to Version 3.32

Auxiliary Programs:
'pdb-ell-tri' program to fit ellipsoids to atoms now does normals right. See the image of the month...
'pov-image' GUI set to work with defaults of linux POVray.

Manual and Data:
The PDF manual is still at 3.30, the html files are still 3.31.

Changes from Version 3.30 to Version 3.31

Changes from Version 3.24 to Version 3.30

Major internal re-work to unify the Unix and Windows XP versions.
The selection of graphics objects are now done with scrolling 'ListBoxes', rather than a pull-down menu. You can now always see all of the choices, and select multiple objects for modification. Important note: the panel only shows the values of the first selected object, and thus may not reflect the state of the all the currently selected objects. All the style control panels have been rearranged to allow for the ListBox.
A new secondary structure code 'X' has been added for gaps in chains, which causes a dashed coil to be drawn. The default splitting of PDB files has been changed to split by chain ID and HETATMS. All the unusual bases of the ribosome are now recognized.
Changed default carbon color from green to white.
The 'AutoDraw' and 'Redraw' ribbons buttons have been removed from all the ribbon drawing control panels. The default is still to always redraw.

Main Program:
Added 'Crosshairs' and 'Fit to Screen' options in the View menu.
Added 'Palette Panel (alt-E)' to the Edit menu.
Polygon capping style added (still experimental).
Removed any output of Wavefront, Rayshade, or PS300 files.

Auxiliary Programs:
'entry-ribbons' has a different default and several new options.
'pdb-pro-ss' and 'pdb-nuc-ss' now add the 'X' chain break code.
'ms-input' (occasional) bug fixed.
'pdb-xxx-ring' programs now have '-k color' option.
'b-to-vet' etc, programs have new usage, with vertex fields now 1..3.
'tri-sph-tri' etc, programs have new usage, consistent with other utils.

Manual and Data:
The on-line manual is up to date, but the PDF version of the manual is a version behind.

Changes from Version 3.22 to Version 3.24

Default look has changed. Larger default graphics window, background defaults to white, slightly smaller sheets/helices and larger coils, smoother ribbons when forced to pass through C-alphas. Due to more powerful graphics matchines, set higher complexity for spheres/cylinders/dots and outlining on by default. Changed calculation for nucleic acid ribbons, where 'force through CA' option forces toward the ribose and improved 'pdb-ribo-ring'. Better lighting for POV-Ray. Added support for jpeg images. Reduced sensitivity of interactive text translation. Added 'clear' to Sequence Panel and enhanced printout for recoloring. Fixed bug of 'pdb-range-ss' utility crashing on some platforms.

Main Program:
Sequence Panel options gives better way to save custom-coloring results.
Fixed outlining of the ends of flat helices.
Fixed saving of surface outline option.

Auxiliary Programs:
'pdb-ribo-ring' now outputs bonds between sugar and base to terminal.
'pdb-range-ss' bug fixed in matching residue numbers.
'pdb-chi-ss' now handles seleno-Met residues correctly.
'pov-image' now works with linux version of pov-ray.

Manual and Data:
PDF version of the manual brought up to date.

Changes from Version 3.21 to Version 3.22

Hardly worth the bother of updating unless you use Linux, or have been having problems with the issues above.

Main Program:
Sequence Panel print option gives way to save custom-coloring results.
Sequence Panel scrolling added for very long sequences (eg, ribosomes).
Added Antialiased Lines and Round Dots for polygonal surface display.
Added explicit 'Mono' under the Stereo View menu.
To add 'SpeedDeamon' global variable to adjust motion speed per platform.

Auxiliary Programs:
'vet-rib' fixed, now outputs more information if coloring by vertex.

Manual and Data:
need to change...

Changes from Version 3.20 to Version 3.21

Hardly worth the bother of updating unless you use multiple surface options, have gotten extraneous triangles when using 'cmc-vet' or 'facets', use the 'Mock Line Drawing' option for images, get 'Buffer Overflow' messages when picking, or have long file names for your data objects.

Main Program:
More consistent error handling and diagnositic messages for file I/O. The 'ImageMockLine' variable added. Surfaces now handled correctly with this lighting model. Clipping of outlines fixed for multiple surface clipping planes, and warning added if you exceed your hardware limit. Can now give the 'Backside' of each surface different properties.

Changes to the menu:
'Transformation (Alt+6) - added under 'Edit'.
'PolyPanel' has added new widgets to control 'Backside' of surfaces.

Auxiliary Programs:
'pdb-atom-sph' and 'pdb-res-sph' now read default color file from the ~ribbons/data directory, so you can change default preferences.
'cmc-vet' added '-s #' command line smoothing option (only use 0/1). '-X' option to clobber existing output now works.
'ms' has larger default array sizes for larger structures.
'compare' and 'recompare' have better output, error checking.
'ribbons-demo' points to a new directory (see below).

Manual and Data:
'data' directory has been split. 'data' now contains only required data.
'demo' directory added, contains all display examples.

Changes from Version 3.19 to Version 3.20

Main Program:
The GeomYsize variable is no longer independent, but is fixed to 4/5 or the GeomXsize to maintain the correct scale.

Changes to the menu:
'Outlining 1' - option added for 1-pixel width outlines.
'Outline Tris' - option added to toggle outlining for surfaces.
'SidebySideDual' - option for stereo on the fancy VR box at UAB.
'AllowAutoRot' - toggle bug fixed.

Changes to the MotionPanel:
'PilotLights' fixed for flying down the ribbon. 'MotionScheme' choice widget added to the Motion Panel, options:

   widgets, cycle models, cycle+widgets, flying (see Help for description). 

'Print POV' - now has orthogonal camera in POV-ray 3.5 format.
'Print VRML' - now assumes relative directory path for sub-objects.
'Read Materials' - now more compatible with the old 16-color format.

Auxiliary Programs:
'fix-linux-map' script added to make DSN6 format work with facets.
'ribbons-data' GUI works on Macs.
'pdb-sss', utility script added to combine secondary structure, dihedral,

Manual and Data:
'Help' pages/images have gone another complete round of editing.
'Examples.model' default files have all been fixed to have a 5/4 ratio.

Changes from Version 3.18 to Version 3.19

Main Program:
The 'LZW image compression' problem saving TIFF images is fixed.
Can now change image size within a session with no problem (except on Alpha?).

Numeric keypad 3-button mouse emulation (Num Lock must be OFF):
• Left Arrow... ("4") -- Z-rotation counterclockwise (positive)
• RightArrow.. ("6") -- Z-rotation clockwise (negative)
• Up Arrow..... ("8") -- Z-translation toward you (positive)
• Down Arrow ("2") -- Z-translation away (negative)
• Page Up....... ("9") -- Z-slab increase
• Page Down.. ("3") -- Z-slab decrease

Added 'invoke ribbons-data' to Edit menu, since it is closer to an editing function (still under File also).

Force refresh of some view menu rotation/outlining options (Mac problem).

Completed separation of Graphics/non-Graphics routines in scripted actions added in version 3.18 (Mac problem).

Auxiliary Programs:
'facets' is FINALLY fixed for contouring maps.
'ribbons-data' GUI works on Macs.
'pdb-sss', utility script added to combine secondary structure, dihedral, and B-factor analysis in one easy command.
'xmapstat' to summarize a CNS/XPLOR map now is distributed as advertized.
'compare', which superposes coordinates, now extracts angle/axis from matrix.
'pdb-pro-ss' bug fix for extremely short sequence with no secondary structure.
'entry-ribbons' (rare) bug fix, added newlines in coords/ribbons files.
'tri-sph-tri' surface filter now works as advetized in the manual.
'rama-plot' and 'chis-plot' have better online instructions.
'ss-sheet-range' works on linux systems.
'pdb-geom-pdb' works again.

Changes from Version 3.16 to Version 3.18

BUG!! The *.tiff files saved in the 'ScriptedAction' below are squashed in Y! (can always re-scale to 5/4 with SGI's izoom, but... working on it).

Main Program:
New 'ScriptedAction' options to the main program:

   -V output.pov             create POV files from input and exit
   -W output.wrl             create VRML files from input and exit
   -S disulphides.cyl        create disulphide *.cyl files and exit
   -B c_beta.cyl             create ribbon-CB *.cyl files and exit
   -A base_attach.cyl        create base attachment *.cyl files and exit
   -H base_hbond.cyl         create base H-bond *.cyl files and exit
   -I image.tiff             create TIFF image file from input and exit
 

Auxiliary Programs:
'pdb-pro-ss' now outputs 'sheets' and 'runs' as default coloring options.
'luz-ps' now expects the output from CNS's 'luzzati_error.plot' output.
'entry-ribbons' no longer bombs with huge numbers of segments.
'RSR' now expects CNS/X-plor maps.
'xmapstat' prints map statistics for CNS/X-plor maps.
'facets' now reads CNS/X-plor maps by default. Additional options:

   -f  option means use old dsn6 file
   -X  option allows overwrite of existing triangle file for ribbons-data
 

General: Larger 'test' archive to better test new map options.
Adding "mandy" configure option to compile Mandrake linux version.

Changes from Version 3.15 to Version 3.16

Main Program:
'SequencePanel' added to display, pick, and color primary sequence of ribbon (Alt-1).
'outlining' now available for POV-ray, also default camera added for PC's.
MRC (wavelet) representation now in all platforms, with save/restore.
Text placement widgets now work in screen coordinates, rather than angstroms, to allow greater flexibility in interactive adjustments.
'Mock Line Drawing' now maintains a color image, rather than all black and white.
FogDepth added to LightPanel to allow much better control, thanks to fix from Albion Baucom (pitched old Ambient slider) .
Initial window size now input only as "-w X_size_in_pixels" (no Y, which is figured out automatically to maintain 5/4 aspect).
More features added to save/restore defaults, including the window size, if side by side stereo, 'backside' color of ribbons, wavelet parameters, and a "RulerOffset" for better placement of scale factor label.
'ribbon-bond' file printouts now handle intermolecular disulphides and the wavelet approximation.
Magic colors for N/O-side texturing are now 40/21 (were 4/1).
Printing no longer outputs "invisible" (color=0) ribbon residues.
Printing "Rib-as-Cyl" new menu name (vs Flatrib-cyl) to reflect action.
Cleaned up various problems with restoring all settings in reseting model's geometry, colors and lighting.
Index and Palette buffering and model reset problems solved.
Better handling of graphics possibilities on assorted platforms.
'Help' will now access our web site directly if you don't install the local ~ribbons/help files.

Auxiliary Programs: Pitched scripts/removed from the manual: first-pass error analysis tools "X-*-ss", "O-*-ss", "rsr*
Pitched old scripts: "pdbext-model, pdbext.csh, hx-dipole-cyl hx-mono-cyl, pdb-bf-bond".
Severely deprecated in manual, but still included: "ribbon-errors", to update RSN for CNS and WhatCheck.
Compiled all non-graphics on PC, added some casts and cleaned/pitched code to prevent warnings.
Fixed sele_parser.C for SOLARIS for yyerror()/yywrap() per Robert Konecny.

General: All 'makefiles' made more consistent, especially with respect to 'clean' and 'clobber'
Described 'configure' differences between 'linux' & 'mesa' better, put 'mesa' first.
Made -DMRC standard, made 'g77' the fortran compiler for Mac.

Changes from Version 3.14 to Version 3.15

Main Program:
PolyPanel now allows separate foreground/background clipping planes for surfaces.
ImagePanel variables now saved/restored from defaults files.
Better save/restore from Poly and Light Panels.
View menu now has 180 degree rotations about axes.
Update of fog parameters improved. Added 'fog' to POV output.
Allow up to 20 (was 10) chains for MRC analysis.
Fixed stupid occasional hack/bug in reading text from *.str files.

Auxiliary Programs:
'pdb-phob-sph' now recognize 1-letter nucleic acid codes.
'pdb-range-ss' warns if user doesn't enter a single character.
Add cmd line option to choose vertex field [0..2] to fill with value in surface coloring programs.

General:
Threw away all the old 'rapidApp' SGI-specific interface code, only supporting the Tcl/Tk version of 'ribbons-data'.
Made handling of temporary files by scripts consistent.
Made number of colors allowed in all programs consistent.
Fixed C++ 'assert' warnings for DEC machines.
Fixes RSR analysis on DEC machines due to map byte-swapping.

Version 3.1

Version 3.0