WHAT IF can at several places apply symmetry. Examples are: crystal
contact analysis, graphical reproduction of multiple cells, cell
content analysis, etc. Some options in WHAT IF work differently if the
flag USESYM has been enabled, e.g. FBRT, GRAACC, SETACC, CONTAC, and
the HB2 module. The specific symmetry options can be accessed from
the SYMTRY menu. The options in this menu will be described in this
chapter.
The options available can be partitioned in two groups: there are
options that just perform a complete operation, and a number of
expert/low-level commands. The latter group of commands is only
available when the MORE option in the SYMTRY menu has been activated.
In general a symmetry transformation consists of a transformation
matrix in combination with a translation vector. Symmetry
transformations describing crystallographic symmetry are most often
described in terms of the fractional (cell) coordinates. Other
transformations, e.g. non crystallographic symmetry giving approximate
relations between different subunits of the protein, are most often
described in an orthogonal coordinate system. WHAT IF can use symmetry
transformations that are given in both different forms. Internally,
all matrices are stored in WHAT IF as matrices operating on orthogonal
coordinates.
Whenever WHAT IF reads a PDB file, a consistency check on the crystal
information is performed. Also the symmetry matrices that are
explicitly given in the PDB file on MTRIX cards are read and
stored. HOWEVER: most of the options in the symmetry menu start by
erasing all symmetry matrices, and retrieve the symmetry matrices
associated with the space group. Since WHAT IF knows all space groups
that proteins can use (and a number of synonymous ones), this is only
a problem if there is non-crystallographic symmetry. There is
currently no good way of handling that automatically.
A general remark: all of the options starting "GRA" or "SOU" in the
SYMTRY menu are higher level routines which call the lower level
SYM*** and/or CEL*** commands (mostly hidden behind MORE). If you use
any of these high-level commands, the transformations that are needed
are automatically deduced from the space group, and any
transformations that were loaded before will be deleted first. If
"MORE" has been activated, matrices will only be deleted after asking
your permission to do so.
WHAT IF reads the SYMTR and MTRIX cards (representing
crystallographic- and non-crystallographic symmetry, respectively)
from an MCF or PDB-file if they are present. Furthermore the other
information needed to apply symmetry transformations is also extracted
from the CRYST1 and SCALE cards.
You might need input transformations not present in the coordinate
file, or might choose not to use transformations that are given in the
coordinate file. You have several ways to manipulate the "active"
transformations. BUT: remember that a lot of the higher-level routines
(SOU*** and GRA***) replace all matrices in memory by the spacegroup
matrices before doing their jobs.
SYMINI (SYM INItialize) deletes all active transformations. The unit
transformation is automatically entered.
The command SYMSPG (SYM SPace Group) causes WHAT IF to add all the
matrices implied by the current space group. To change the current
space group, see SYMISG. Only the space groups without inversion and
mirror symmetry are known to WHAT IF. See SYMISG for information on
how to enter a space group symbol.
The command SYMINP (SYM INPut) allows you to repeatedly enter
transformations from the keyboard, in the form of a matrix and a
vector. WHAT IF will first ask whether you want to input in orthogonal
coordinates or in fractional (cell) coordinates. After that, you will
repeatedly be prompted for the 12 values needed for the
transformation. After the transformation has been entered, WHAT IF
performs some basic consistency checks, and warns you if the matrix
may be incorrect. Since "0" is a valid input as a matrix value,
quitting this option can only be done by just typing return at the
prompt for the value of "M(1,1)".
This option is only available via "MORE" in the symmetry menu.
The SYMIIT (SYM Input International Tables) command allows you to
enter any International Tables transformation (e.g. "-X,Y+1/2,Z" for
space group P21). Transformations with a determinant other than +1
will be rejected.
This option is only available via "MORE" in the symmetry menu.
The SYMDEL (SYM DELete) command asks for the numbers of the
transformations that you wish to delete. See SYMSHO to find out about
the symmetry transformation numbers. Please note: transformations are
renumbered as soon as SYMDEL exits!
The SYMRDU (SYM Remove DUplicates) command deletes all duplicate
copies from the array of active transformations.
This is a low-level option that is only available via "MORE" in the symmetry menu.
The SYMPIC (SYM Put In Cell) command shifts all the active
transformations over integral cell translations, to make sure that the
centers of all the transformed molecules are in the unit cell. Usually
SYMSPG needs to be executed first. SYMPIC does not shift the unit
transformation.
This is a low-level option that is only available via "MORE" in the symmetry menu.
The SYMNEA (SYM NEAr) command replicates/shifts/deletes active
matrices, such that the matrices that remain all generate molecules
that "touch" the central molecule. Shifts over integral numbers of
unit cells are performed to make sure all "Touching" molecules will be
found. The touching-test is done using SYMDNT, see this option for a
descripion. The tolerance parameter used can be changed by SYMPAR.
This is a low-level option that is only available via "MORE" in the symmetry menu.
The SYMDNT (SYM Delete Non-Touching) command deletes active matrices
which generate molecules that do not touch the untransformed
molecule. "Touching" is defined as "having two atoms, one in the first
and one in the second molecule, for which the interatomic distance is
smaller than the sum of the Vanderwaals radii plus a tolerance
value". The tolerance value is 0.25 Angstrom by default, and can be
changed by SYMPAR.
This is a low-level option that is only available via "MORE" in the symmetry menu.
If you choose SYMRES (SYM REStore), reading matrices from a file, you
will be prompted for the name of the file. The format of the file
should be "12F8.0", one transformation per line, formatted. The order
of the elements has to be:
m11,m12,m13,m21,m22,m23,m31,m32,m33,t1,t2,t3.
In general, the unit transformation is not needed.
If you choose SYMSAV (SYM SAVe), writing transformations to a file,
you will be prompted for the name of the file. If the file already
exists, you will be prompted to confirm its deletion. All active
matrices will be written to the file, formatted according to
"(9F8.5,3F8.3)", one transformation per line. The order of the
elements will be:
m11,m12,m13,m21,m22,m23,m31,m32,m33,t1,t2,t3.
A few different checks exist to verify the sanity of the
currently available symmetry transformations
If your symmetry matrices are supposed to form a closed group, you
can check that
with the SYMCGP (SYM Check GrouP) option. WHAT IF will then first
remove all duplicate active matrices, and after that run Randy Read's
CHECKSYM algorithm to see if all of the remaining matrices form a
closed group. Translations of an integral number of unit cells are
ignored in this procedure.
This (expert) option is only available when "MORE" has been executed
in the symmetry menu.
The command SYMSHO (SYM SHOw) causes WHAT IF to display all presently
active transformations. First WHAT IF will ask you whether you want to
see them as operating on orthogonal coordinates or on fractional
coordinates. For each transformation WHAT IF attempts to classify it,
for rotations giving the direction of the axis and the multiplicity. A
warning will be shown for strange transformations.
The command SYMPNI (SYM Print Non Integral) Prints a warning message
for all active transformations that either not represent a rotation, or
represent a non-integral rotation.
This (expert) option is only available when "MORE" has been executed
in the symmetry menu.
Normally there is no need to generate symmetry related atoms in the
soup. Doing this can cost enormeous amounts of memory and disk space.
Furthermore for large proteins with many ligands adding copies to the
soup may be a very slow procedure. However, might there be a need to
do so, the commands SOUSYM, SOUSM1, SOUCEL, SOUSHL, SOUBOX, SOUSPH and
SOUSRS can be used to add different parts of symmetry related
molecules to the soup. For all of these equivalent GRA*** commands
exist that put the resulting molecules in a mol-item instead of the
soup. The last 5 of the 7 change the array of symmetry matrices in
WHAT IF's memory, so saving might be a good idea.
WARNING: It is very easy using symmetry to soup to overload WHAT IF's
SOUP array's. Not everywhere adequate checks are performed.
SOUSYM (SOUp SYMmetry) applies all active transformations except the
unit transformation to all or part of the soup, adding the symmetry
transformed results to the soup. Obviously, this option and all other
options calling it modify the soup in a way that is not reversible by
a simple command, so saving first might be a good idea.
SOUSM1 (SOUp SyMmetry 1) applies one active transformation to all or
part of the soup, adding the symmetry transformed results to the
soup.
SOUCEL (SOUp unit-CELl) finds all molecules which have their center in the
unit cell, and add these to the soup. Results can be rather strange if
the original molecule does not have its center in the unit cell.
SOUSHL (SOUp SHelL) generates all symmetry related residues "touching"
the central molecule, and adds them to the soup. For a definition of
"touching" see the command SYMDNT.
SOUBOX (SOUp BOX) generates all symmetry related residues that are in
a specified rectangular box and adds them to the soup.
SOUBOX asks for XMIN, YMIN, ZMIN and XMAX, YMAX, ZMAX of the
box. Here two opposing corners of the box should be given as two sets
of three orthogonal coordinates.
SOUSPH (SOUp SPHere) generates all symmetry related residues that are
in a specified sphere and adds them to the soup.
SOUSPH further asks for the X, Y, Z and Radius for the sphere. No
defaults are available for the orthogonal center coordinates X, Y,
Z. The radius defaults to 10 Angstrom.
SOUSRS (SOUp Sphere around ReSidue) generates all symmetry related
residues that are in a sphere with a specified radius around a
specified residue and adds them to the soup. If "MORE" has been
activated in the symmetry menu, SOUSRS will ask the user whether the
current symmetry matrices are to be used or the space group symmetry
should be loaded instead. In the latter case the routines SYMINI and
SYMSPG will be executed first.
SOUSRS further asks for the residue number and for the radius of the
sphere. The radius defaults to 10 Angstrom.
As an alternative to the generation of symmetry related residues in
the soup, it is possible to only display them in a mol item. This will
not allow you to pick the symmetrized atoms, nor will WHAT IF be able
to calculate inter-atomic distances or other values, but it allows you
to view the intermolecular contacts in a way that can be easily
reversed and it does not risk overloading the soup with molecules or
residues.
GRASYM (GRAph SYMmetry) applies all active transformations except the
unit transformation to all or part of the soup, adding the symmetry
transformed results to a mol-item.
GRASM1 (GRAph SyMmetry 1) applies one active transformation to all or
part of the soup, adding the symmetry transformed results to a
mol-item.
See SYMGCA if you want a CA display only
GRACEL (GRAph unit-CELl) will make a graphics object containing all
symmetry related molecules that have their center in the unit cell.
Results can be rather strange if
the original molecule does not have its center in the unit cell.
See SYMGCA if you want a CA display only
GRASHL (GRAph SHelL) generates all symmetry related residues
"touching" the central molecule, and shows them as a mol item. For a
definition of "touching" see the command SYMDNT.
This option can be
(mis)used to find a dimer transformation: assuming that the dimer-contact
is much tighter than any other symmetry contact, you can easily locate the
transformation number of the dimer transformation in the screenoutput of this
option.
See SYMGCA if you want a CA display only.
GRABOX (GRAph BOX) generates all symmetry related residues that are in
a specified rectangular box and displays them in a mol-item.
GRABOX further asks for XMIN, YMIN, ZMIN and XMAX, YMAX, ZMAX of the
box. Here two opposing corners of the box should be given as two sets
of three orthogonal coordinates.
See SYMGCA if you want a CA display only
GRASPH (GRAph SPHere) generates all symmetry related residues that are
in a specified sphere and adds shows them as a mol item.
GRASPH further asks for the X, Y, Z and Radius for the sphere. No
defaults are available for the orthogonal center coordinates X, Y,
Z. The radius defaults to 10 Angstrom.
See SYMGCA if you want a CA display only
GRASRS (GRAph Sphere around ReSidue) generates all symmetry related
residues that are in a sphere with a specified radius around a
specified residue and adds them to the soup.
GRASRS further asks for the residue number and for the radius of the
sphere. The radius defaults to 10 Angstrom.
See SYMGCA if you want a CA display only
When reading an MCF or a PDB file, WHAT IF reads and remembers the
cell dimensions, and performs some sanity checks. It is possible to
review or change the active cell dimensions using CELSHO and CELINP.
You can see the CELL dimensions, the corresponding transformation
orthogonal-to-cell-coordinates, and the current space group on the
screen by using the command CELSHO (CELl SHOw).
If you want to set or change the cell dimensions, you can use the
command CELINP (CELl INPut). You will then be prompted for all six
cell dimensions a, b, c, alpha, beta, gamma. No defaults exist for the
axis lengths; angles default to 90 degrees.
This is an expert option that is only available when MORE has been
activated from the symmetry menu.
Normally WHAT IF will read the space group symbol from the MCF or PDB
file. If you want to change the active space group you can do so using
the SYMISG (SYM Input Space Group) command. SYMISG will ask you for a
properly spaced standard Hermann-Mauguin symbol (eg. "P 21 21 21") of
the space group. A warning will be given if WHAT IF detects an
inconsistency.
This is an expert option that is only available when MORE has been
activated from the symmetry menu.
The LCKSYM (LoCK SYMmetry) command toggles a flag in WHAT IF that can
lock the symmetry transformations in memory. If the symmetry matrices
are locked, all options that can potentially delete symmetry
transformations are disabled.
This is an expert option that is only available when MORE has been
activated from the symmetry menu.
The tolerance used to see if two atoms "Touch" (See SYMDNT) can be set
using SYMPAR (SYM PARameters). Default value is 0.25 Angstrom.
This value is used by the SOUSHL and GRASHL commands. It corresponds
to the value used by CONTAC and a large number of other WHAT IF options.
Sometimes a PDB file contains symmetry equivalent molecules. In those
cases the SYM*** routines may find overlapping molecules. Using the
SYMDSM option (SYM Delete Symmetric Molecules) all molecules that can
be regenreated using the current active symmetry transformations will
be deleted from the soup.
This (expert) option is only available when "MORE" has been executed
in the symmetry menu.
The command USESYM toggles an internal flag in WHAT IF that tells
options that can use symmetry to do so. Options currently affected are
(please don't assume this list is up to date): ACCESS, HB2RED, CONTAC,
TABBMP
The SYMANA (SYMmetry ANAlyze) command checks whether any residues in
the protein bump with neighboring molecules in the crystal, and if so,
prints a summary of the intermolecular contacts found. A "very severe"
bump is reported if any atom-pair from two amino-acids have an
interatomic distance less than SUM(VanDerWaals)-2.0 Angstrom. A "less
severe" bump is reported if any atom pair from two amino-acids have an
interatomic distance less than SUM(VanDerWaals)-1.0 Angstrom. In the
current version it is not possible to change these two parameters.
From the ANACON menu, using the CONTAC option it is also possible
to check for contacts between symmetry related molecules.
This (expert) option is only available when "MORE" has been executed
in the symmetry menu.
The SYMAMB (SYMmetry AMBiguous) command calls SYMANA for the two cells
as obtained from the CRYST1 card and the SCALE cards. If there is a
significant difference in the bumping pattern, a choice is made
between the two.
The CELAPP (CELl APPly) command applies an earlier found INPUT TO
CONVENTIONAL transformation on the unit cell. No attempt is made to
validate the new unit cell. The SPACE GROUP is most probably invalid
after this transformation. See CELNEW for a way to check if there is
previously undetected symmetry between different molecules.
This (expert) option is only available when "MORE" has been executed
in the symmetry menu.
The CELNEW (CELl NEW) command looks for pairs of polymeric molecules
(DNA or PROTEIN) that can be superimposed by transformations that can
be symmetry transformations in the conventional cell. This procedure
can be used to check for crystallographic symmetry that would be
introduced by the input->conventional cell transformation as given by
WHAT IF upon reading a molecule. See CELAPP for a procedure to actually
perform the transformation of the unit cell.
This (expert) option is only available when "MORE" has been executed
in the symmetry menu.
SYMGCA (SYM Generate C-Alpha) toggles the flag that controls
generation of mol items to either display full AA's or CA only.
This only holds for the GRA*** options in the SYMTRY menu!!!
An internal option to check the symmetry information in a list
of PDB files.
An internal option to check the symmetry information in a list of
PDB files.
Not all commands are immediately active in the ACCESS menu. By typing
MORE, more commands will be activated.