Cyana: (in the main menu)
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:
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:
July
2005:
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
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
Wit!P> set amber missing (fixed|floppy|zero)
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'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).
>> filename : append to old file (create new, if file does not exist)
>- :close curent output file
>+ : reopen and append to previous output file.
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.<atomselection> -atom [matches|fragment] <swiles>...mass ~eq 12 0.1to require the mass to be between 12-0.1 and 12+0.1.
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.
new options in set mouse command:
set mouse 2Buttons: sets up mouse map for a two button map.new variables in Confa command:
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
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 ).
Bug fix in ligance guesser:
Handling of .mol and .mol2 files:
Uses "structural alignment" to find matching pairs. Dynamic programing is used to find optimal alignment based on local geometry. Only pairs within "cutoff" (distance in A) are used in the final alignment. If cutoff is < 0, max. dist. is -cutoff*rmsd before pairlist reduction. Gerstein's structural alignment method is applied to the resulting superposition, followed by pairlist reduction using given cutoff. The better of the two alignments (lower standardized rmsd (rmsd*225/(npairs+135)) is returned as result. The atomselections targetatoms, sourceatoms) typically are sets of C-alphas.
Note: this new type of structure alignment is still under construction. The new method is intended to be used for protein structure superposition. Application to other types of structures may produce interesting and unexpected results.
It is essential that comment and message special tokens are separated by a token separator (normally white space) from the comment/message (i.e. ===>Message is treated as a single token, but ===> Message is treaded as special token, followed by a message to be sent to the message window).
Applies translation to global_object which will bring COM of atomselection to center of screen, z=hither-0.5*(hither-yon), and sets pivot of global_object to this point. The command affects only the 'displayed' coordinates. The freeze command may be used to apply the translation to the 'real' coordinates.
New screendump interface:
Files without filename extensions are dumped in Adobe
PostScript format.
New functionality in NMR module:
the new average option in
the
NMR/noes menu allows the specification of the distance averaging option
to be used on a per-noelist basis. C.f. section 18.2 of the X-Plor 3.1
manual for the definitions of the different averaging methods. The
default
method is center.
the new -summary option of
the NMR/noes/list
command may be used to produce a summary listing of NOE distance
constraints
violations. Output produced by list
-summary
consists of two lists with violations listed by constraint
(root-mean-square
violation, average violation, number of structures that violate
constraint)
and with violations listed by structure (root-mean-square violation,
average
violation, number of constraints violated by this structure).
copy -molecule source
[(-before|-after|-into) where] target
copy -atoms selection
[(-before|-after|-into) where] target
(and similarly for move). Read the Wit!P command reference for details.
Conservative users may continue to use the old command syntax for copy
and move.
Conservative users may continue to use the old command syntax for copy
and merge.
New functionality in Confa browse menu:
copy ( conformation | cluster ) name: generate new molecule(s) from current conformation or cluster.
remove: purges current conformation from internal list, sets next conformation.
write filetype filename molecule:
write molecule to file (any molecule, not just the template...).
New -atom operator in atom selections:
Example:
* -atom name cys_*/* -atom symbol C,S
(selects all atoms, restricts to atoms in cys_* residues, further
restricts
to C and S).
As of version 20000310 (March-10-2000) Wit!P looks for 'macros' (executed by <macro_name) in the directories defined by the environment variable WNP_MACPATH, e.g.
Wit!P will look for the macro load_structures
in the directories /prog/wnp/mac, .
(current
working directory), and .. (parent of current working directory), and
will
execute the first macro that it finds. If the environment variable
WNP_MACPATH
is not defined, macros are searched in the current working directory
(pre
20000310 behavior).
For "piped" macros ( <"|macro_name ..." ), the directories defined by WNP_MACPATH are searched for an executable file macro_name. If such a file is found, macro_name will be substituted by the full path-name before the command-pipe is opened. Path-name expansion limited to the first macroname.
Added new commands:
translates given object by (dx,dy,dz) in Å.
display rotate glbl_object axis angle
rotates object around 'axis' (one of X,Y,Z) by given angle.
display scale scale_factor
sets relative display scale factor.
display reset ...
to reset projection parameters (also available from main menu as 'reset ...').
display set ...
to set projection parameters
Crystal eyes stereo: