Azara 2.8 changes
0. Notable changes from 30 Oct 2002 release to 07 Apr 2010 release
0.01 plot2 : fixed fitting bug
A couple of bugs in the numerical routines used to do the fitting were fixed.
0.02 plot2 : added error estimates for fitting
If 'sigmas' (giving an estimate of the data noise) in addition to 'params' is specified in the par file then an estimate of the errors in the fitting parameters is given (except in the log linear case).
0.03 plot2 : added output ticks options
In hardcopy output (PS, EPS and HPGL), ticks used to appear always on the inside of the box and always on all four borders. It is now possible to have the ticks appear on the outside and also not on all four borders.
0.04 combine : added divide function
It is now possible to divide two spectra.
0.05 project: fixed boundary bug
Data files with number of points in the non-projected dimensions not a multiple of the block size were being summed including the padded points in the last block. (In general these contain junk.)
0.06 process: added mask_pm and mask_mp
Added mask_pm and mask_mp which do what mask_ppmm does more generally, so with an arbitrary period.
0.07 contours: fixed large output bug
Fixed bug which meant that if had too many vertices (could happen with as few as 2048 vertices) in one contour then program giving incorrect output and could even crash.
0.08 process: fixed sigmas bug in par file
The (optional) sigmas in the input par file were not being copied correctly to the output par file.
0.09 plot2: fixed log linear fitting bug
With log linear fitting routine does not use points where y is negative but in those cases it was using incorrect x values.
0.10 utility: fixed Felix conversion bug
The programs mat2par and par2mat were swapping the refpt and refppm, and the latter in Felix is in Hz, not ppm, so needed to be scaled by sf.
0.11 plot1: fixed gaussian_sw bug
The option when sw was specified to be 0 was not working. This was supposed to pick up sw from the par file but if more than one par file was used in the script it was failing.
0.12 all: fixed makefile omission
Added in (MOTIF_INCLUDE_DIR) into the makefile in global for compilation.0.13 connect: added in new residues option
The residues key can now have extra arguments specifying atom names required for a match. If the last character of the name is a * then anything that matches the earlier characters is a match.
0.14 process: fixed truncate bug
The type for the length argument of truncate (used in the function truncate_file in files.c) should have been off_t, not long.
0.15 contours: added endianess options
The endianess of the output contour file can now be set in the script using either big_endian or little_endian.
0.16 new: added new utility programs
Added ucsf2azara, azara2ucsf and azara2xeasy.
0.17 process: 2D and 3D non-linear sampling
Added ability to specify 2D and 3D non-linear sampling in maxent routines, using sample2 and sample3 commands.
0.18 new: added Python module for accessing data
Added Python module in DataRows directory which allows pythonic access of blocked data files.
0.19 remove: removed some programs
Removed components, slides, viewer.
Azara help: CHANGES-2.8-0 / W. Boucher / azara@bioc.cam.ac.uk