PIG extracts atom data from the input archive bdf
and/or the peaks data from the
pekbdf or the sites
from a
BUNYIP
.bunfile. At the
conclusion of a PIG session the results of the site
manipulations are stored in the
lratom:
record
of the output archive bdf and these may be used directly
for subsequent calculations. A list of
atom lines is also output
to the file
add. Note that atom
labels are truncated to eight characters in PIG. PIG may be
used to display both the molecule and cell. Sites may be
rotated, deleted, added, relabelled and retyped. Bond
distances, angles and torsion angles may be displayed. The
orientation of the the displayed sites is stored on the
output archive bdf for use by programs such as
ORTEP
. The saved orientation matrix is in
lrgraf:
of the output bdf and will be used by ORTEP as
the default plot orientation, unless
npig
is entered (on the
ORTEP line).
The molecular view can be rotated by
LEFT-mouse-click-drag-release events. The magnification can
be altered by MIDDLE-mouse-click-drag-release events (based
on up/down translations) (NOTE that the MIDDLE mouse button
is emulated by simultaneous LEFT and RIGHT mouse buttons on
two button mice). The molecule can be translated by
RIGHT-mouse-click-drag-release events.
PIG can be used as a WYSIWYG (what you see is what
you get) interface to
POVRAYfor
raytraced 3D images or ORTEP for traditional 2D thermal
ellipsoid plots. Provided that a
bdfis written at exit
(containing the molecular view orientation), every site
visible on screen at the time of exit will be displayed in
the subsequent ORTEP/PREVUE. In addition, if labels are
switched on, then the ORTEP will be labelled, and if the
current view is a unit cell, then ORTEP plots the unit cell
outline. Up to 15
ORTEP control lines may be
specified in
PIG, (prefaced with
ORTCTL ) and these are
substituted for or added to the resultant ORTEP control
file commands.
PIG can be used to generate a molecular information
file for conversion of XTAL molecular data for use in other
programs that do not yet read Crystallographic Information
Files (CIFs). Two formats are provided. The Protein Data
Bank (
.pdb ) format, containing
space group, cell parameters, symmetry independent sites in
cartesian cordinates, anisotropic temperature factors and
bond connections. The second format is the Minnesota
Supercomputer Centre XMOL
.xyz file which contains
the cartesian coordinates and atom types of all atoms on
screen at PIG exit time (analogous to ORTEP exit mode). The
.xyz file maybe useful as a
means of generating symmetry related atom sites for use in
other software packages such as
RASMOL. If the
.xyz file is relabelled as
a
.spf file it can also be
used by
PLATON (Ton Spek
1980).
More recently any H atoms built in PIG, iether
automatically or manually (with the exception of
free sites
or peak assignments) add constraint linkage
information to the archive file. This permits the
recalculation of H atoms when invoking the CRILSQ riding
model refinement. However, the H atom linkage and labelling
is dependent on parent atom coordination. Any attempts to
relabel parent atoms or H atoms after building will render
the output linkage incorrect. In the event that a
riding model refinement is subsequently
attempted, it will be necessary for users to iether edit
the
.add file manually and
include it as part of an ADDATM run, or rerun ADDATM in
update mode and overwrite existing linkage lines on the
archive with their own versions as described in
ADDATM
.
The display is controlled at two levels. (1) Input
control lines are used to define the starting parameters
for the atom and peak sites to be used, the atom radii, the
display colours, the type of display (molecule or cell) and
so on. These values are applied prior to displaying the
sites. (2) Control is via the interactive cursor and the
menu buttons.
The user is guided by the instructions provided
in the message panel.
Rotation control is provided by 6 buttons in the
lower RH corner. The box immediately to the left of this
enables the user to switch from course (90
) to fine (adjustable via up down arrows)
rotations. These controls are in addition to using the
left mouse button.
Zoom and translation control is provided by 6
buttons in the upper RH corner, or alternatively by
middle and right mouse button click-drag events.
A toggle switch to display or not display the site
labels.
Selectively hide or display interatomic bond lines.
In this mode bonds may be hidden or displayed by clicking
on selected labels. The actual change to the display
status of the line bond is not effected until the pig
icon is clicked (top right hand corner). Note that site
markers are NOT hidden with this command, only the
connecting bonds (see also the
HIDE atoms panel).
Clicking the cursor on this panel places PIG in
type-atoms mode. In this mode the user must first select
which atom type by clicking on one of the atom type boxes
displayed in the upper right hand area of the display.
Then click on each of the sites (to be specific, on each
site
label ) that is to be changed to the
selected atom type. The atom type of selected sites will
not be changed until the pig icon is clicked. Note that
the site
labels are
not changed on the display, only the
colours of the bonds. However, PIG
will automatically attach the new atom type code to the
atom label when it is output to the
pch file and the archive
bdf. To change the displayed site label,see the
LABL
atom command described
below.
Clicking the cursor on this panel activates the
label-atom mode. The user must click on the atom label to
be changed and then enter the new label on the keyboard.
Duplicate labels will be rejected when exiting from this
mode. When labeling is complete click on the pig's nose
to exit.
Clicking the cursor on this panel places PIG in the
hide atoms mode. In this mode the
user may select any number of sites (by clicking on the
appropriate site labels) which are to be removed from the
display. The actual removal of site markers, labels and
attached bond lines does not take place until the pig
icon is clicked.
Clicking the cursor on this panel will cause all
hidden atom sites to be returned to the display. It
reverses the
HIDE atoms effect.
Clicking the cursor on this panel places PIG in the
show distance mode. A distance will
be displayed for two selected sites (by clicking on the
appropriate site labels). These sites need not be bonded
(this may be used on a 'cell' display as well as a
'molecule' display). This mode is exited by clicking on
the PIG icon.
Clicking the cursor on this panel places PIG in the
show angle mode. An angle and two
connecting distances will be displayed for three selected
sites (by clicking on the appropriate site labels). The
second selected site is assumed to be the central atom.
These sites need not be bonded (this may be used on a
'cell' display as well as a 'molecule' display).This mode
is exited by clicking on the PIG icon.
Clicking the cursor on this panel places PIG in the
show bond distances mode. All bond
distances connected to a site will be displayed by
clicking on the site label.This mode is exited by
clicking on the PIG icon.
Clicking the cursor on this panel places PIG in the
show torsion angle mode. The torsion
angle and distances will be displayed for the four
selected sites (by clicking on the appropriate site
labels). These sites need not be bonded (this may be used
on a 'cell' display as well as a 'molecule' display).This
mode is exited by clicking on the PIG icon.
Using this mode the user can examine the fractional
coordinates of all sites currently displayed, as well as
determining the ORTEP/BONDLA symmetry and translation
operations required to generate dependent sites, and the
peak heights of peaks displayed from PEKPIK data.
Clicking the cursor on this panel causes the
currently displayed orientation to be saved in a rotation
matrix. On exiting PIG this matrix is stored in the
output archive bdf and may be used by ORTEP to produce a
plot with the same orientation. Note that doing a LS
PLANE calculation will override the save
operation.
This control activates (by default) or deactivates
the animated spin mode. With animation mode activated,
using the left mouse button to rotate the molecule via a
click-drag-release, imparts an angular momentum to the
molecule, proportional to the length and direction of the
effective drag displacement vector. To stop a freely
spinning molecule simply click and release the mouse
button without moving it. Reselect the ANIM control to
cancel this mode.
The CENTRE control permits re-centring of the
molecule, iether about the collective centre of the
current molecule, or, about a specific atom site by
selecting its label.
Red, green stereo mode. Technically this is an
anaglyph. Two images of the current
molecule are draw, one of which is rotated by 3 degrees
about the molecular centre. By wearing spectacles with
one red and one green lens, a 3 dimensional affect may be
apparent. Note that if the lens colors are reversed, a
freely rotating molecule will appear to rotate backwards,
which could be cause for confusion.
This control button is only present if (1) the
PEAKS command line was
invoked from the control file (2) a .pek file exists, or
(3) PIG was invoked with the
msol
multi-solution command. It is a two state
button, which switches on or off the display of peaks
from a
PEKPIK .pek file.
However, when peaks are switched ON, a scrollbar facility
allows the user to adjust the lower peak eight threshold
at which peaks will be displayed. This is useful if there
are many insignificant electron density peaks obscuring
the larger peaks in which you are interested. The
PEAKS button must be
reselected to confirm that the current threshold is what
the user requires.
Clicking the cursor on this panel places PIG in the
least squares plane mode. The user
must then select
at least three sites (by clicking on
the appropriate site labels) to define the least squares
plane and then click on the pig icon. This will cause the
plane to be calculated, and the atoms sites to be
displayed with the plane perpendicular to the z axis. PIG
remains in the least squares plane mode and the
perpendicular distance of any site from this plane may be
displayed by clicking on the site label. This mode is
exited by clicking on the pig icon again. Note that the
orientation of the plane is automatically stored in the
rotation matrix, for subsequent storing on the output
archive bdf.
The FRAGMENT mode has been enhanced over previous
versions of PIG. There are now four FRAGMENT choices -
select
,
deselect
site connect
and
site reject
. The additional modes were designed
primarily as tools for contolling display contents for
generating ORTEPS and the .xyz file for export to other
programs such as RASMOL.
The
select
and
deselect
modes enable all sites within a LEFT mouse
button click-drag-release event to be iether exclusively
retained or exclusively deleted from the currently
displayed molecule. The selected region is highlighted by
a rectangular border.
site connect
and
site reject
modes permit the current molecule to be
iether extended by adding all bonded sites to a specific
atom by selecting its atom label, or by deleting the
selected label from the current fragment.
It is important to note that deselecting an atom
site or group of atoms using the FRAGMENT modes is quite
different from HIDEing an atom in HIDE mode. Using the
HIDE button, hidden atoms are irretrievably lost at the
next NEW MOLE or EXIT, with potentially disastrous loss
of cell contents on the archive file. Whereas, by using
the fragment delete modes, the atom sites sites are
merely hidden from display. This is why the
FRAGMENT
mode is preferred as a means of specifying
ORTEP plots.
To return to the full molecular display click on
the
new
MOLECULE panel.
Click on this panel when new sites need to be added
to the atom display list. If new H atoms are built, on
exit they are assigned Uiso values corresponding to 1.5
or 1.25 times the Uiso value of their bonded C/N/O parent
(if present), dependent on whether it is a methyl group
or otherwise, respectively. Because of this it is more
generally useful to have refined the vibrational motion
of the heavier atoms before building H atoms.
Five additional panels will be displayed in the
message area. Clicking on one of these panels places PIG
into a particular 'build atom site' mode. For each mode
follow closely the instructions displayed in the message
area. The modes are:
-
Linear Requests a
new site which is linearly aligned with two other
sites in the structure. First select an atom type
for the new site. Then click on the two sites
aligned with the new site; the furtherest site
first and then the site to which the new site will
be bonded. The new site will automatically be
assigned a site label composed of the label of the
bonded site with the character 'a' appended.
-
Trigonal Requests a
new site which is trigonally aligned with three
other sites in the structure. First select an atom
type for the new site. Then click on the three
sites which form an apex to which the new site will
be attached; the apex site is clicked second in the
sequence. The new site will automatically be
assigned a site label composed of the label of the
bonded site with the character 'a' appended.
-
Tetrahedral Requests one, two or three
new sites which are tetrahedrally bonded with
neighbouring sites in the structure. First select
the atom type for the new site(s). If one or two
sites are sought, click on the three sites which
form an apex to which the new site(s) will be
attached; the apex site is clicked second in the
sequence. If three tetrahedrally related sites are
sought (e.g. methyl hydrogens) click on the two
sites which form the fourth member of the
tetrahedral bonding; the furtherest site first and
then the site to which the new sites will be bonded
The display will be then aligned so that the bond
of the two clicked sites will point directly at the
viewer and be surrounded by a circle. The position
of the three new sites around this bond is selected
by clicking the position of the first at a point on
this circle. All new site(s) will automatically be
assigned a site label composed of the label of the
bonded site with the characters 'a', 'b' or 'c'
appended.
-
Free site Requests
a new site which is not geometrically related, but
is bonded, to another site in the structure. First
select an atom type for the new site. Click on the
site to which the new site will be bonded. Then
click on the screen to determine the orientation
(relative x and y coordinate; z will be set at the
value of the bonded site). Note that the display
usually needs to be carefully oriented before this
mode is used. The new site will automatically be
assigned a site label composed of the label of the
bonded site with the character 'a' appended.
-
Auto H atom In this
mode PIG searches every independent C atom in its
atom array and examines its connectivity, based on
current radii values. If the C atom is underbonded
its bondlengths and angles are assessed for linear,
trigonal and tetrahedral H atom bonding. Where
there are no ambiguities, these H atoms are
automatically built and labelled according to their
parent C atoms label. No H atoms are built on
parent O atom or N atoms because the number (for N)
and orientation (for O) of such H atoms are in
general not well defined. In general, bond angles
below 116 degrees are treated as tetrahedral, and
C-C bond lengths below 1.46 Angstroms are
considered double bonds.
Use the RADII button to set the atomic radii for
bonds to be calculated in future. Formerly the radii
button was subsumed with the
new MOLE
command, but it is now accessible from the
main menu to assist with fragment extension. In
RADII mode selecting an
atom type box will display the current radius, and
reselecting that atom type enables a new value to entered
via the keyboard (closed with a return carriage).
This control is used to temporarily hide specific
atom types from view, such as hydrogen atoms in cluttered
diagrams. When invoked, selecting an atom-type panel
immediately switches the display state of all sites of
that type on or off. Select PIG to cancel this mode. Atom
types hidden in this manner are not lost and may be
redrawn later by repeating the same procedure.
Clicking this panel causes the currently displayed
sites (not the hidden sites) to be included in the
calculation of a new connected molecule and its display.
Hidden atoms (from Hide Atom) will be removed from the
site list and will not be available for output to the
archive bdf. Conditions for the connected molecule search
are set by the PRESET line and by the three panel buttons
that appear in the message area. These buttons control
the following:
-
SYM-EXT on/off - a
toggle switch to include/exclude atom sites related
by symmetry which are within the bonding distance.
This switch should be on if a molecule contains a
symmetry element but may need to switched off when
peaks are active.
-
Clusterng - A three
position switch to enable/disable the reclustering
of sites, or revert to the input site list (losing
all changes) when the molecule is redrawn. The
cluster mechanism attempts to optimally connect all
input sites to the first atom site in the input
list. For very large molecules clustering is time
consuming. If a molecule contains more than 500
atoms, clustering is automatically switched
off.
-
Cluster Packing - A
four position switch governing the treatment of
multiple disconnected clusters. The first mode (
Pack Off ) switches
off any extra packing treatment. The three
additional packing modes provide variations on the
optimal packing of secondary clusters about the
primary aggregate molecule.
Pack close attempts
to arrange clusters in order to minimize distance
between the centres of gravity of all clusters.
Pack
centre attempts to minimize the distances
between the largest cluster center of gravity and
other clusters
Pack
contact attempts to find the shortest
contact between clusters - to accentuate hydrogen
bonding for example.
Clicking the New Molecule panel a second time will
start the display process using the current display
parameters.
Clicking the cursor on this panel causes the
currently displayed sites (not the hidden sites) to be
included in the calculation of a new cell display. The
mcut option allows for
all molecules to be cut at the cell boundary of the first
unit cell, but otherwise all sites within +/-1 cell along
all three axes are calculated and added to the display
view. Hidden atoms (using
HIDE ATOM ) will be
removed from the site list and will not be available for
output to the archive bdf, or the
add file. Note that the
current display limit is 10000 atoms. If nine unit cells
result in more sites than the current limit, then PIG
will terminate with an error message.
This mode provides the user with limited control
over the creation of
compid.pov files
containing a three dimensional description of the current
display for rendering using the freely available
Persistence of Vision
Ray Tracer(TM) (Pov-Ray). XTAL is in no way
associated with POV-Ray(TM) and makes no warranties as to
that programs reliability, usefulness, or suitability for
any purpose whatsoever. Consequently no support is
offered or will be given towards installation of such
external software. That being said, POV-Ray is a very
powerful visualization tool and its use is recommended.
In addition (under unix), if the environment variable
POVEXE is set to the
location of the POV-Ray(TM) executable, POV-Ray(TM) will
be automatically invoked as a background process and the
current scene rendered, on screen and also to the file
compid.ppm.
In
POV IMG mode the user can
adjust several options by selecting the apropriate
controls in the PIG message window. When satisfied, the
user should reselect
POV IMG to create the
.pov file and render it - or choose
PIG to cancel the mode.
In addition, if labels are switched on in PIG then the
output image will be labelled, and if the unit cell is
being drawn, then it too will be rendered in the
POV-Ray(TM) image.
-
CPK model This
control sets the desired molecular representation
to either close packed overlapping spheres (
CPK ), Ball and
stick model, Rods or thermal ellipsoids.
-
400x300 This is the
smallest of five preset image dimensions. Rendering
time increases significantly with image
dimension.
-
No Octants This is
intended for ellpsoid plots where the principle
axes may not be obvious.
-
Prob 50% This sets
the default probability level for rendering thermal
ellipsoid plots.
Users should note that the ASCII text
compid.pov file generated
by XTAL includes important header information from the
xtalpov file located in
the directory specified by the
XTALHOME environment
variable. However, if a user has an alternate
xtalpov file in the
current working directory, it will be used by default. In
this way image renderings can be customised by the user,
setting different backgrounds, adjusting perspective,
scaling and atom colors. Also the xtal.pov files
generated by XTAL are sufficiently well commented that
they can be edited by users to delete selective atoms,
their labels or bonds, and redisplayed by manually
running POV-Ray(TM) from the command line.
Clicking on this panel toggles the output mode of
the archive bdf between on and off. The default mode is
on. If the mode is on, the displayed atom sites
(including the retained peak sites and labels), and the
orientation matrix of the displayed sites, will be stored
on the archive file by the program
ADDATM
. Independently of the bdf mode, a file .add is
output containing all displayed atom sites and the
display orientation.
Clicking on this panel will commence the exiting
process from PIG. First the display will be redrawn in
the currently stored orientation. If the user wishes to
sort the output atom list based on atomic number and
labels, there are three possible label SORT modes. The
user can choose one mode and continue, or ignore and
continue by reselecting the
EXIT
button. At this point the user has the
option to proceed with an
ORTEP/PREVUE
process based on the current screen
display, (assuming that a new
bdfwill be written)
or to complete the exiting process by clicking on the
EXIT
button again. An accidental
exit>
can be canceled by selecting the
PIG
icon.
When PIG is automatically invoked after CRISP, as a
structural solution viewer, (run as
PIG msol from the
command line) two additional control buttons are invoked
between the message panel and the atom-type buttons.
These buttons permit the stepping forwards and backwards
through structural solutions loaded from the
.sol file produced by
CRISP.
The three atomlist sort modes all sort sites
according to atomic number, but they differ in their label
sorting algorithms. The method to choose for sorting labels
is largely dictated by the structure and the site labelling
scheme adopted. It is inevitable that the atom sites
written to the
.add file will require
additional manual ordering for publication purposes, but
the three modes provided sould provide a helpful starting
point. The different schemes are best illustrated by way of
example.
sort left
sorts with the leftmost label character most
significant
sort right
sorts with the rightmost label character most
significant
sort numeric
sorts labels into numeric order
