Version β 0.6e, 14-Jun-2004

• A section on the analysis of ribosomal RNA was added to the manual.

Version β 0.6d, 08-Jun-2004

• Notes can now be attached to models read from pdb-files. Use the notes-keyword of the aset\_read-command to make notes.
• An overview of all conformers being analysed is now displayed as a table in the html-output file.

Version β 0.6, 26-Feb-2004

• Many small fixes.

Version β 0.5, 13-Oct-2003

• ESCET can now be started by giving the name of the inp-file as the first argument. This will generate output files using filenames related to the input-file name.
• In addition to the login-information dumped to the terminal, the program now generates an output file in html-format that can be printed, cut-and-pasted etc.
• Several new entries have been added to the 'Utilities'-section of the manual.

Version β 0.3, 24-Jan-2003

• Loads of small fixes

Version β 0.2f, 27-Jun-2003

• The Bounding Box for encapsulated postscript can now be set explicitly using bx1,by1,bx2,bx1 keywords of graphics-related commands.
• Keywords xtdel1 and xtdel2 can be used to specify up to two tickmarks that will be explicitly deleted if, e.g. if tickmarks overlap on the lower or upper end of a scale.} \item{Several problems with tickmarks for multi-chain plots have been fixed
• title and frametitle are now separate concepts. frametitle is the title that will be put into the frame of a plot, title is the title that will be put on top of the actual figure. Use keywords title and frametitle to set the values. If several plots are overlayed in one figure, the titles will be overlayed as well. Setting title=" " should help in such cases. For rp_plot, the defaults are: title=" ", frametitle="something invented by the program"

Version β 0.2e, 17-Apr-2002

• Two keywords patchlen and minfraglen are now available to adjust the polishing of a solution of the rigid body search. See escet_ref.html for details.
• Diagnostics for automatic consistency checks has been improved

Version β 0.2d, 11-Apr-2002

• Some problems with automatic consistency checking of atom lists were fixed.
• The Pairwise comparison table now contains a line with the mean estimated error for the atoms that are actually compared. This allows to easily pick out the best determined atom set from a set of redundant conformers.
• STDOUT is now flushed regularly to make monitoring easier.

Version β 0.2c, 1-Mar-2002

• A warning is now given, if a pdb-file contains B-values that are smaller or equal 0.0 - such B-values would mess up the error-estimation.
• The manual is again available in pdf-format !
• The plotting if DD-matrices for multi-chain problems is still not perfect (loads of book-keeping to do ...) but at least does not hang anymore.
• The program will now give an estimate on the memory it will use. If this estimate is close to the physical RAM of your computer, try to use a mashine with more memory to avoid swapping.

Version β 0.2, 1-Feb-2002

• Rewrote documentation to reflect zillions of changes.
• Major improvements on generation of RASMOL, MOLSCRIPT, and LSQKAB-scripts.
• Substantial cleanup of the log-file.

Version β 0.1g, 5-Jun-2001

• Fixed some problems with MOLSCRIPT-output of the rigid body finder.
• Argument dd_plot=off in keyword ddm will switch off the postscript output.

Version β 0.1f, 25-May-2001

• The conformationally invariant part of a molecule can now be automatically determined using a genetic algorithm. Right now, no parameters are accessible from the interface (changing parameters still has to be done in the source ...). But using rb_find = on in the ddm-command, will run the algorithm using a reasonable set of default parameters. Setting rb_plot = on and ss_plot = on will put the information also into the plotted difference distance matrices (rigid parts are marked as dark gray, flexible as light gray). \\ The program also dumps a bunch of files to use as input to MOLSCRIPT, RASMOL, and LSQKAB. I will work hard on documenting these, promised. molscript -gl $<$ t_molscript.mol will give a pretty picture in many cases (blue for rigid, red for flexible). If it doesn't work, it will at least be a good template ...
  If more than two atom sets were selected using the setl-keyword in the ddm-command, the automatic interpretation will take all models into account automatically !
• In previous version the Cruickshank error estimate was calculated deriving some of the input numbers from the current atom set. If the calculation was done after removing some atoms or only retaining the CA's, this could give wrong results. The program now remembers the numbers from the original pdb-file and uses those as default values.} \item{The aset_egen-command now has a keyword esd_blim to select the lowest acceptable B-value.
• If secondary structure is plotted, now the data for this come from a reference set. The number of this set defaults to the first set selected, but can be changed using the setr-keyword of the ddm-command
• sele now works properly with chainid == " ".
• The aset_write-command can now write selected sets of atoms.
• The program can now hold 100 atom sets.
• Some cleanup on eps output files.
• Started a chapter on Tips & Tricks.

Version β 0.1e, 9-Jan-200

• Chorismate Mutase was included as an example into the User's Manual
• Hopefully, the use of Equation 26 or 27 from Cruickshank's paper (Cruickshank, 1999) is now somewhat clearer
• When reading coordinates from a file using the aset_read-command, atoms can now be selected directly, i.e. if you only want CA-atoms from a file called fname.pdb, use: aset_read(ifile="fname.pdb",sele=(name == "CA"))}.

Version β 0.1d, 14-Nov-2000

• A number of things concerning the refinement are now extracted from the pdb-file and passed on to the aset\_egen-command. I am not sure how to determine a sensible number of paramters to be used in Cruickshank's equation~26, so at the moment, number of parameters is set to 0 causing Cruickshank eq. 27 (the one based on Rfree) to be used.
• Fixed mistake in URL given in program startup message
• Fixed bug concerning y-ticks.

Version β 0.1c, 1-Nov-2000

• The manual was updated
• If the keyword check in the ddm-command is set to auto, the program will try to find a consistent set of atoms for the subsequent calculations all by itself. This works in many cases, but not always. If it does not work, the selection can still be done by hand using heck=loose or check=strict. I will try to make the algorithm more robust in the future, so please send me examples were the automatic selection does not work.
• Several atom sets can now be simultaneously selected by the setl-keyword of various commands. The most important application of this is for difference distance matrices: if you select a list of atom sets via the setl-keyword, all pairwise difference distances will be printed. Each matrix will be put onto a separate sheet, producing a sort of book.
• Atoms can now be selected based on their element or number in their atom set. This is very handy if you want to exclude hydrogens, see example on page, e.g. the following script will get rid of all hydrogen atoms found in a pdb-file:

    aset_read(ifile="test.pdb");
    aset_sele(sele = (element <> "H"));
    aset_write(ofile="test_without_hydrogens.pdb");
    

• A much easier mechanism for selecting stretches of residues has been implemented, e.g. selecting residues 19 to 25, 36 to 42, 45 and 56 to 58 can now be done in a statement of the form:

     sele = (resi in {19-25:36-42:45:56-58})}.
     

• Some facilities to work with multiple models from NMR spectroscopy have been included. The information about rmsd's from the NMR ensemble is translated into positional esd's using the aset_egen-command. Two models are available: esd_model=rmsd simply uses the rmsd as the coordinate uncertainty, and esd_model=rmsd2 uses the square of the rmsd as the coordinate uncertainty. In both cases, the uncertainty is multiplied by the number given via the keyword esd\_fac, to allow to put the coordinate error on some pseudo-absolute scale. This facility is useful, if you want to compare NMR-structures and X-ray structures. See under the aset_egen-command in the reference manual.
• A schematic representation of secondary structure elements can now be included into difference distance matrix plots. Helices are shown as open, sheets as filled boxes. Secondary structure can be defined using the aset_amod-command. If HELIX- and SHEET-records are found in a pdb-file, the information is used. The keyword ss_plot of the ddm-command is used to trigger plotting of the secondary structure.
• A number of small bugs have been fixed

Version β 0.1, 11-Jun-2000

• This is the very first beta-test release of ESCET. Please be patient and report all errors, problems, glitches, misunderstanding etc. p.p. to trs(at)shelx.uni-ac.gwdg.de.