Wit!P Recently added features


November 2015:

new automatic atom name method 'alarm': may be used to generate atom names which are a combination of chemical symbol followed by sequence number for non-hydrogen atoms, and a combination of chemical symbol followed by the sequence number of the non-hydrogen atom to which they are attached. Multiple hydrogens attached to the same non-hydrogen atom receive an additional 1-letter suffix, 'A' for the first, 'B' for the second hydrogen, etc...

Cyana: (in the main menu)


February 2009:

new RPC method: wnp.loadPDB, to loadPDB from a data block.
new RPC method: wnp.dataBlock, receive data blocks from RPC client.
new options in "list" command: -atoms, -bonds, -residues.
new command option: measure monitor covalent ...
new command: delete bonds


February 2008:

Display rotate/translate now works in non-graphics mode too. Client data structure for display nodes of type DSP_GLBL now contains 4x4 rotation matrix, translation vector and pivot. If client runs without graphics, the client keeps track of  rotations, translations and pivot changes.Surface clipping.


February 2007:

Surface clipping.
Improved (Jorge Nodecal) minimizers in Minimax.
Built-in XML/RPC server in Wit!P client.


January 2007:

The session file format has changed. Files in the old format can still be read, but all new session files will be XML files. This makes it easier to browse the session files, using an XML browser. Most web-browsers should be able to read and render Wit!P session files.

The minimizers in Minimax and Piff have been replaced: in Minimax, the user may now choose between two versions conjugate gradient methods (a VA14 like Polak-Ribere written in C, and CGFAM [J. Nodecal, Northwestern University]) and a limited memory BFGS routine [J. Nodecal
Northwestern University]). The limited memory BFGS is the default method used by Minimax, with an automatic switch to the VA14 like minimizer, if the LBFGS is running out of memeory. In Piff, the VA14 implementation in C is used.


December 2006:
Read maccs macros: user defined macros may now be added to the read maccs menu, a feature which greatly enhances the browsing of multi molecule MACCS (.sdf) files. Macros may be defined through read maccs macro define, read maccs macro edit, or through the define macro maccs command in the Wit!P main menu. When defining macros through read maccs define or define macro maccs, the macro text will be read from the following lines, up to the first line that contains the tag ORCAM (MACRO, spelled backwards). The macro text is read in "raw" mode, i.e.  text that would normally have special meaning to the parser ($name, <filename, >+, >-, >filename, ==>, -->) will remain uninterpreted at the time of the macro definition. Once defined, macros may be edited through read maccs macro edit macroname. The editor defined by the $WNP_EDIT environment variable will be used to edit the macro (default: vi on Linux, UNIX, Mac OS X, and Cygwin, wordpad on Windows).

Session files
: the command write session filename (default extension .wsv) may be used to save a Wit!P session to disk. The session may be restored by read session filename. When a session is restored, the content of the current session is lost, i.e. the restore operation is not incremental. Session files contain most of the information about a session (molecular data, surfaces, graphics attributes, color map, projection, clipping, ...). Data that is currently not saved to session files include conformations and clusters from Confa, Xatom data (small molecule crystallographic data from .xcn files), library data (from .wlb files), many parameter settings (Minimax parameters, Mopac parameters,  parameters defined via set command). The debate about what should and what should not be stored in session files is still ongoing, and the exact content of session files may differ in future releases of Wit!P.


May 2006:

Confa cluster: a set of new hierarchical clustering methods have been added. The methods in this class use the following basic scheme to build the clusters:

  1. put each conformation into its own cluster,
  2. compute matrix of distances between clusters using current metric,
  3. find a pair of clusters Cp, Cq with minimal distance dpq,
  4. merge the two clusters Cp, Cq --> Cpnew,
  5. remove Cq from cluster list and compute new distances between Cpnew and all other clusters,
  6. iterate from 2., until all conformations are merged into a single cluster.
The methods differ in how they compute distances in step 4:
  1. average : dpinew = 0.5 * ( dpi + dqi ).
  2. weighted : dpinew = ( np*dpi + nq * dqi ) / ( np+nq), where np, nq are the sizes of the merged clusters.
  3. flexible : dpinew = c * ( dpi + dqi ) + ( 1 - 2*c ) * dpq , where c is a constant (0.6).
  4. single : dpinew = min ( dpi , dqi ).
  5. complete : dpinew = max ( dpi , dqi ).
  6. centroid : dpinew = ( np*dpi + nq * dqi ) / (np+nq) -  np* nq *dpq / (np+nq)2.
  7. median : dpinew = 0.5 * ( dpi + dqi ) - 0.25 * dpq .
  8. ward : dpinew = ( (ni+ np) * dpi + (ni+nq) * dqi - ni * dpq ) / (np+nq+ni).
The initial distance matrix in step 2 is computed using either root mean squared interatomic distances (rmsd) or a SEAL similarity  score ( gseal, c.f. S.K. Kearsley and G.M. Smith, An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap, Tetrahedron Computer Methodology 1990, 13, 615-633), where only the steric component of the score is used. The distance may be computed using atomic coordinates after a rigid body least-squares superposition of the two conformations being compared (fitted), or using the actual current coordinates (inplace).

Warning: the new clustering methods can be quite slow when applied to large datasets.

PDB files can now be written using the write pdb command: chain names will be truncated to the 1st character, cols 73-76 (segId), 77-78 (Element symbol) and 79-80 (formal charge) will be left blank (i.e. PDB 2.0 features are not supported). Atom names are treated as for the xpdb (X-Plor PDB) format, which may again annoy users that expect 2.0 behavior. Bonds which are not implied by the currently used internal libraries will be listed in CONECT records.

Atom selections: there are three new options in the atom selection menu:

  1. -up will expand the current selection by including all atoms that have the same parent in the molecular data tree as one of the currently selected atoms. The -up selection expander may be iterated: each additional iteration will step up an additional level in the molecular data tree.
  2. -mol will expand the current selection to include all atoms in 'molecules' that contain at least currently selected atom. For the purposes of this expansion, a 'molecule' is defined as the set of atoms that share the same display transformation matrix in the display data tree.
  3. -(sel): this token may be used to bring up an atom selection menu at places where the command parser expects a single atom name (or atom pick), e.g. in commands like bond make, join, or fuse. The -(sel) token must be followed by an atom selection which defines exactly one atom.


July 2005:

The command line parser was modified to expand environment variables ($varname, or ${varname}). Use backslash (\) to suppress the expansion (\$notavariable) and to 'quote' another backslash.

Examples:
Wit!P> set env XYZ "this is a test"
Wit!P> ==> $XYZ
this is a test
Wit!P> ==> \$XYZ
$XYZ
Wit!P> ==> \\$XYZ
\this is a test
Special variable $< : reads one line of 'interactive' input, and inserts it into current input stream.

Example: (get definition of psapassword from interactive user in a Wit!P script)
   
set env -noecho -prompt "PSA password for ${USERNAME}:" psapassword
     "$<"

The set env command has  been enhanced by adding two new options: -prompt to define a prompt string, and -noecho, which cause echoing of user input to be suppressed (useful, when reading a password, as in the example above).

New restrictor in atom selections: -atom substructure. Similar to -atom fragment, but selects only substructures which are entirely contained in the primary selection.

November 2004:

Added xray genlig command to generate ligand dictionary files for CNX and REFMAC (crystallographic refinement programs).



July 2003:

The "bad" option in the Minimax command (and the corresponding "-b" command line flag in the minimax executable) are now obsolete. The new minimizer in minimax should be able to handle very bad starting geometries automatically.

June 2003:

New set amber sloppy command: allows Amber parameter/topology files to be written even if there are missing force field parameters. New set amber missing command may be used to define how missing parameters in 'sloppy' files are treated. The 'sloppy' and 'missing' modes of Amber parameter/topology files may also be set directly in the Minimax and Amber menus.

Wit!P> set amber sloppy (always|once|never)
    always: write parmtop file even if there are missing parameters
    never: do not write files with missing parameters
    once: allow missing parameters in the next file only.

    Initially, the mode is 'sloppy never'.

Wit!P> set amber missing (fixed|floppy|zero)

    defines how missing parameters in 'sloppy' files are to be treated:

    zero: use zero force constant in parmtop file (this is the default)
    fixed: equilibrium values of -1 for bond and angle, periodicity -1 for
    dihedrals, k=500 (bond), 70 (angle), 5 (dihedral), 0 (improper)
    floppy: like fixed, but omitting dihedral term

    fixed and floppy produce non-standard files. The 'funny' equilibrium
    values and periodicity are interpreted by a new version of Minimax
    (equilibrium value equal to value in starting structure). Fixed and floppy
    sloppy parmtop files should not be used with programs other than with
    Minimax.

Note: do not use these options, if you are not sure what you are doing!

April 2003:

Build fragment has a new optiopn: mode flat|residue . If the mode is flat fragment atoms will be merged into the residue to which the fragment is joined. Initially the mode is residue, i.e. each fragment joind to the molecule under construction will start a new residue. The mode is "sticky", i.e. once set, the new mode remain in effect until it is changed by a new mode command.

 copy -flat and move -flat commands: similar to the corresponding -atoms commands, but atoms are copied into a "flat"structure, i.e. the original tree structure will be lost. NOE, Xtal info will not be copied, set memberships will not be copied. The new commands may be used to "flatten" subtrees of the molecular data structure (with side effect: some graphics attributes may be lost).

set cwd : allows navigation through menu-picking.

March 2003:

in confa: deletetion of template atoms used to lead to inconsistencies in internal datastructure ("lost template"). This problem has been fixed: coordinates of deleted atoms will be deleted from trajectory (internal data structure only, file remains untouched).

February 2003:

New output redirection feature allows to send prtGraphics text to text port as well as to user specified file:

   > filename (anywhere in command): open new file 'filename'
   >> filename : append to old file (create new, if file does not exist)
   >- :close curent output file
   >+ : reopen and append to previous output file.
Added forward/backward/loop option to Confa animate command. Mode is "sticky", i.e. once set, it will remain in effect until changed in subsequent animate command. Animate now works w/o graphics (only one forward pass, if animate mode is 'loop' in non-graphics mode).

New cluster info and cluster list commands in Confa may be used generate

Confa cluster reset now restores conformations into sequence defined by new seqnr attribute.

New atom label types: fullname (full name, including residue, chain,, molecule,...) and molecule (name of atoms grandparent node in molecullar data tree).
 

December 2002:

generated GLUT based version of sw_server. Works for IRIX, Linux, MacOS-X and Windows.

removed support for GL based graphics server.

CSD/Quest interface: added definition of geometric parameters (edit T1 parameter...). This allows llows the interface to be used for the generation of Vista input files. Added H-count atom property in edit atom menu.

October 2002:

changed definition of ARGR and ARG in all.wlb: double bond between NE and CZ (rather than CZ and NH1).

changed TAFF rules for Guanidinium groups (all three N's N.pl3)

addedd FF parameters for N.pl3 = C.cat (stretch and torsion).

made rdsyb.c (read MOL2) fault tolerant for Relibase MOL2 files (these files do not have a SUBSTRUCTURE section).


August 2002:

modified comments in X-Plor PSF files to be acceptable to NAMD.
(Note: X-Plor parameter files should not contain 'Parameter' statement  if the file is to be used in NAMD).

Added xpsf filetype to charmm menu, to allow generation of X-Plor PSF files.

Quantized MPEOE charges. New set mpeoe granularity command:

     set mpeoe granularity n

--> all MPEOE charges will be multiples of 10^-n (default:n=6)
Charges in PSF and MOL2 files will be written with 6 decimal places. This modification was made to avoid problems with roundoff when writing MPEOE charges to PSF files for CHARMm.

June 2002:

added support for X-Plor DCD (binary dynamics trajectory) files in Confa.  Changed cnf format to support fixed atoms (Mobile record).

April 2002:

added soft-harmonic positional constraints to Minimax:

    xyz  <atnr> [ x y z ] k [ T [ L ] ]

Default target position (x y z) is to current atom position, k is harmonic  force constant. For an atom at distance d from the target, the penalty  function is

    P(d) = d<T ? 0 : d<(T+L)? 0.5*k*(d-T)^2 : 0.5*k*L^2+k*(d-L)

T defaults to 0, L defaults to infinity. L<1.e-4 is treated as infinity.

February 2002:

Added Amber support to Minimax, updated interface in Wit!P.

January-2002:

Changed Minimax to use dynamically allocated non-bonded list, using malloc.

Amber support in Wit!P (write parmtop and crd files).

November-2001:

new option in modify:  modify atom sof <selection> [all] <values...>  to set site occupancy for selected atoms.

Swiles: first char '=' --> Hard, first char '?' --> Substructure, first char   '~' Soft. New convention may be used in ffrules, MPEOE atomand bond rules and
-atom [matches|fragment] selections.

 n ffrules:

     ffrule <FF> <mnem> <interp> <smiles>[,smiles]...

where <interp> = [=|~|?] defines the default interpretaion for the following smiles. In MPEOE: default interpretaion is HARD, in -atom [matches|frgament]
default interpretation is SUBSTRUCTURE.


October-2001:

Support for the CHARMm force field has been added to the standalone program minimax. The minimax interface in Wit!P has been updated to support the new features.

September-2001:

added new features to atomselection:

  <atomselection> -atom type <type>...

restricts the selection to atoms of specified FF <type>. X-Plor type wildcards may be used in type. Use \ to quote wildcards  (e.g. '*.\?' to match all atoms with type mnemonics ending with '.?'; without the \ quote, '?' would be interpreted as "any-single-character" wildcard.
  <atomselection> -atom [biso|mass|q|shift|sof|charge|ligance|seqnr] <cmpop> value...
restricts the selection to atoms with the given property equal to, less than, greater than or approximately equal to the specified value. <cmpop> is the comparison operator (-lt, -le, -eq, ~eq, -neq, ~neq, -ge, -ge). The ~ comparison operators need the specification of a 'tolerance', e.g.
mass ~eq 12 0.1
to require the mass to be between 12-0.1 and 12+0.1.
  <atomselection> -atom [matches|fragment] <swiles>...
restricts the selection to atoms which match the first atom in the fragment defined by the swiles string. In the second form (fragment) all atoms of the swiles fragment will be included in the selection. If more than one swiles follows the matches or fragment keyword, the restriction is to atoms matching any of the swiles.
  <atomselection> -pzone <dist> <atomselection>
restricts selection to atoms of the first selection that are connected via <dist> or less bonds to an atom in the seconds selection. This is similar to the -zone restrictor, except that the metric used is the minimum path length, rather than euclidean distance.




April 2001:

new options in set mouse command:

set mouse 2Buttons: sets up mouse map for a two button map.
set mouse 3Dbutton: sets up mouse map for a three button mouse.
set mouse show_map: list the current mouse map in the message window
new variables in Confa command:
angle and torsion variables may now be defined in the Confa variable add command.
new mmread option in Confa command:
The mmread option in Confa may be used to read in compressed multi conformation Macromodel files. mmread creates a new molecule for the first frame in the Macromodel file, and automatically sets up the variable part of the structure in the Macromodel file as the Confa template.
new pmoi option in measure:
measure pmoi atomselection may be used to calculate the principle moments of inertia (PMOI) of a set of atoms. The three moments are output in ascending order. The unit of PMOI is amu*Å2  ( 1 amu*Å2  =  1.66053 * 10-40 g*cm2 ).

December 2000:

Bug fix in ligance guesser:



November 2000:

Handling of .mol and .mol2 files:

Obsoleted Pluto and Ortep commands: Modifications in Build Fragment: New autopairs method (fit, measure): Comment and message tokens ---> and ===>: New display find command:
August 2000:

New screendump interface:

Menus added to -atom name and -atom symbol selections: New Surface command:
July 2000:

New functionality in NMR module:

Modifications made to copy/move commands: New syntax of merge command: Automatic deletion of empty nodes in molecular data tree:
June 2000:

New functionality in Confa browse menu:

New functionality in Confa main menu: Modification made to Confa priax command:
March 2000:

New -atom operator in atom selections:

Improved 'macro' support:
December 1999:

Added new commands:


September 1999:

Crystal eyes stereo:

Minimax: Added new option to modify atom name:
A.Widmer, NIBR/CPC/CSG-SB