-> Table of Contents
Moloc: Molecular Modelling on UNIX Workstations: 17 X-ray and NMR Utility [xnr]
X-ray and NMR Utility [xnr]
A collection of utilities, useful for structure evaluation
in connection with structure determination by X-ray or NMR
methods.
g: geometry display (see
Geometry Section)
t: display temperature factors
If temperature factors for the atoms of a structure are
given, they can be displayed here in a color coded form.
Upon picking a structure, its bonds are colored accord
ing to the average temperature factors of the adjacent
atoms. The representation switches automatically to the
half-bond representation. Scale: yellow > 32, red > 24,
pink > 16, blue > 8, else white.
a: anisotropic R-factor ellipsoids
If anisotropic R-factor data are available (.shx files)
the corresponding anisotropy ellipsoids can be dis
played. Upon choosing this option the corresponding
entry has to be picked. In the set menu the atoms have
to be determined for which an anisotropy display is
needed.If no atom is given, the whole entry will be
treated. There are three different display modes among
which a choice is taken by selecting the dot variable
with the slider that appears next. A negative value
leads to ORTEP-type ellipsoid representations. The
quality of the ellipses increases with decreasing
value. Positive values below 20 give simple distorted
icosahedra, higher values below 40 give a representa
tion by surfaces containing 60 triangles each, while
still higher values induce a representation with dotted
surfaces with roughly as many dots per ellipsoid as
indicated by the chosen number.
After matching several structures of identical topology
and producing an average structure (match utility) this
average contains data analogous to anisotropic R-fac
tors. The corresponding ellipsoids indicate the spread
in the original structures.
e: generate crystal environment
If crystal parameters are known for a structure, an
additional entry can be generated which contains copies
of the entry positioned in equivalent crystal posi
tions. Whether a copy appears or not is decided on dis
tance criteria with the original structure. Two types
of checks may be chosen: An exact one which compares all
possible atom pairs and takes a copy if one of the dis
tances falls within the specified threshold. This check
may be rather time consuming, if the structure contains
many atoms. The simpler version works out a gross cri
terion for the distances between centroids. It works
fast but may produce copies that lie outside the exact
criterion. In a first step possible copies are gathered
with the rough criterion. Then the user is dropped into
the set menu with an entry that contains the original
structure and isolated atoms at the location of the
centroids of the gathered copies. Final copies of the
original structure are only taken if the corresponding
centroids have been selected in the set menu. If exact
checking has been specified it is performed at this
point.
i: generate immediate crystal environment
Atoms of the environment are only kept if they are
within the specified distance of an atom of the origi
nal. For polymer entries, a monomer is kept as a whole
if any one of its atoms satisfies the specification.
For non-polymeric entries this option may lead to
strange fragments of the copied original.
j: generate equivalent positions
This option does not generate a new entry. Rather, the
information on neighboring equivalent positions is
gathered and used to display those by transforming the
bond drawing of the original. The displayed equivalent
positions are updated immediately. Only newly added
further residues lack the information about the equiva
lents. To have them displayed, this option has to be
repeated.
c: generate cell
Upon picking a structure, a display of the unit cell is
generated. If no information is available a default
cell is assumed and displayed. Then a menu is entered
that allows to interactively change cell dimensions and
angles. The default cell can also be produced. These
manipulations destroy the original information!
d: NOE violation display
Violations of distance constraints on a structure can
be displayed here.
m: matching, generate symmetry related entry
To generate a symmetry related entry make a duplicate
and use the match utility to read in the desired trans
formation and to move the duplicate.
h: H-bond pattern search
Find a likely H-bond pattern when several conformations
of the same structure are given.
z: get SS bridge pattern
Find a likely SS-bridge pattern when several conforma
tions of the same peptide structure are given, which
contains several cysteine residues.
r: color residue-wise sets on proteins
A menu is entered suited for coloring of sets of identi
cal protein structures, a case that occurs in NMR
structure solution.
o: generate threshold sets (occ., T-fact.)
Upon picking a structure the user is asked whether the
threshold is to be applied to the T-factor field
(default: occupation field). Then, a slider is pre
sented by which the user can set the threshold between
the minimum and the maximum values encountered in the
structure. The resulting set is characterized in the
dialog window.
n: NOESY peak assignment
Assignment of a NOESY spectra of an entry.
Violation of distance constraints can be examined here.
First a file has to be read in with a list of constraints.
Currently the DIANA format is supported. The violations are
indicated by dashed lines of a color indicative of the amount
of violation. The color code is given on the menu bar. The
threshold value can be adjusted by the user. Depending on its
value different things will be displayed.
r: read a NOE-file
The distance specification file is expected to corre
spond to the picked structure. The file is assumed to be
written in DIANA format.
t: set distance threshold
The value of the threshold can be changed here. If a
positive value is chosen too long distances are under
stood to be violations. For negative values too short
distances are considered to be violations. However, if
the absolute value is below 0.01 all distance con
straints are displayed in white
p: print violations
For each violation displayed a line is printed
f: forge structure (see
Forge)
d: photo-sized display (see
Display)
h: PostScript file (see
Display)
An encapsulated PostScript file of the current view is
written. It is suited to be sent to a PostScript
printer.
H-bond Pattern Search [hbpt]
For a set of molecules of identical topology a list of
possible patterns of hydrogen bonds is calculated. After
specification of the participant donor-acceptors (donac),
weights for all possible donor-acceptor pairs of are
calculated. A weight is determined by the energy of the
corresponding H-bond within the MAB force field. If only a
fraction of all donac's is specified one has to be aware of
the fact that H-bonds to non-specified donac's may exist. As
a consequence the true number of donor or acceptor counts
attributable to a donac may be lower than assumed in the
evaluation!
d: define entries to participate
A selector with the structures in memory is presented,
from which the ones are chosen, that participate in the
evaluation.
a: specify donor-acceptor atoms
A representative entry is displayed on which a set of
atoms must be defined. From these atoms, the ones capa
ble of building H-bonds are selected for the pattern
evaluation.
f: set flags
The width of the H-bond function, i.e. the range of
attraction can be influenced by the user in discrete
steps. A value of zero corresponds to the standard
function. This may influence the final pattern
obtained. Furthermore, a choice between an approximate
and an exact pattern evaluation is provided, the latter
being rather time consuming in the case of complex pat
terns.
c: calculate patterns
The program prints a list of possible individual H
bonds, sorted by energy. Then a sorted list of patterns
is presented.
For a set of proteins of identical topology a list of
possible patterns of disulfide bridges is calculated. In a
first step weights for all possible pairs of cysteines are
calculated. The weight is determined by the distance of the
corresponding beta carbons or sulfurs. It is highest for the
ideal distance. The width of the weight function determines
the weights for other distances. Several parameters that
determine the details of the evaluation can be set by the
user.
d: define entries to participate
A selector with the structures in memory is presented,
from which the ones are chosen, that participate in the
evaluation. After the choice a list of cysteines is
presented to identify the bonds later on.
f: set flags
Three flags can be set to modify the evaluation proce
dure: The first determines whether the weight for an
individual bridge stays at a constant high value for
small distances or whether it decreases in a bell-
shaped form. The second determines whether the combined
weight for several bridges is taken to be the product or
the sum of the individual weights. The third determines
whether the distance between the two S-gamma atoms or
between the two C-beta atoms is taken for the evalua
tion of the individual bridge weight.
w: set parameters for weight function
Three parameters for the weight function for individual
S-S bonds are set. The first is the distance at which
the function assumes its maximum value of one. The sec
ond determines the standard deviation, i.e. the charac
teristic distance over which the weight decays with
increasing (or decreasing) distance. The third is a
threshold, which determines the minimal value an indi
vidual weight has to assume for participation in the
pattern evaluation.
c: calculate patterns
The program prints a list of possible individual S-S
bonds, sorted by weights. Then a sorted list of pat
terns is presented. One must be aware that for many cys
teines and a low threshold, the pattern evaluation may
be very time consuming!
This utility allows to display sets of all-atom protein
structures selectively by specifying which residues should
appear in which color and which portions of the backbone
should be displayed. The backbones are drawn in the color of
the entries, while the residues can be assigned to color-
specific sets. Alternatively, the specified residues can be
made to assume the entry color. As a first step a structure
has to be picked, whereupon the associated Calf structure is
generated. It becomes visible whenever the user chooses to
specify a color-specific or the backbone set. When leaving
the menu all specified sets are lost.
b: color of backbone
This switch determines whether the specified residues
should be drawn in the color of their own backbone or in
the color that was assigned to the set, which specifies
them.
e: define set of entries to be colored
A selector of structures in memory is presented, to
specify the structures to which the coloring should be
applied.
s: define or modify color sets
Upon choosing this option the user is presented with a
color choice, and consecutively dropped into the set
menu with the originally generated Calf structure.
Here, all the residues are specified that should appear
in the specified color.
b: define backbone set
Again the set menu is entered with the Calf structure.
The defined set determines which parts of the backbone
are displayed
c: color residues
All specified proteins will be colored according to the
predefined sets for colors and backbone.
r: reset colors
All entries are reset to their entry color. The speci
fied sets are kept.
-> Table of Contents