Terminal_ID
 
terminal_id <mol res atom> <object>
 
Identify an atom by typing on the terminal. This command is normally used in macros.The program prompts for the atom and then the object name.
Tor_general
 
tor_general <Id 2 connected atoms>
 
This command allows one to change torsion angles by identifying two atoms that define the angles to be changed. The identified atoms must be connected and there cannot be a ring between them. One angle requres 4 connected atoms, 2 angles needs 5 etc. A maximum of 8 angles can change.
Tor_residue
 
tor_residue <id an atom> or <mol res atom>
 
This allows one to make dihedral rotations around bonds between pairs of atoms. All of the torsional angles associated with the identified residue can be changed via the dials. The number of dials activated depends on how many angles are defined for the particular residue. Therefore, dial_previous or dial_next may have to be used. Use Yes/No to accept or reject the result.If you do not have dials, remember you can use the keyboard arrow keys.
The program need to know what angles are associated with the residue and how they are defined. This torsional information is kept in the sterochemistry library. Here is a relevant portion of the library for a Serine residue:
 
residue SER
..
TORSION PHI C- N CA C CB C O OG
TORSION PSI* N CA C O O
TORSION CHI1 N CA CB OG OG
..
In this residue there are 3 torsion angles (PHI, PSI* and CHI1) defined. The first four atom names describe how each angle is defined, the remaining names specify which atoms are affected by the angle. The CHI1 angle is, therefore, defined by looking along the CA-CB bond and measuring the angle subtended by the lines N-CA and CB-OG. Only ther OG atom moves when this angle is changed.
Note that atoms from last and next residues can be included, and they will have '-' and '+' signs in their names.
If the list of atoms is too long, you can go into the next line by typing a back-slash character \. Begin the next line with at least 6 spaces for tidiness's sake.
IF YOU DO NOT FOLLOW THE STANDARD ATOMIC NAMING CONVENTION, OR IF YOU HAVE EXTRA ATOMS (E.G. HYDROGENS) IN YOUR RESIDUES, YOU MUST MAKE A NEW VERSION OF THE LIBRARY.
The program reports atoms that are defined in the torsion database but not present in the residue. If an atom is in the residue but not defined as a moving atom, it will never move.
Trig_refresh
 
trig_refresh
 
Continuously refresh the trig object. If a marked atom is moving, the trigonometric information is updated. The command can be switched off with Clear_flag or Trig_reset commands.

Trace_fill_Ca (superceded)


trace_fill_ca <non-pruned> <pruned>

Both skeletons must exist. The first one must not be pruned, while the second skeleton is the pruned version of the first.. For those atoms in the pruned skeleton that are too far apart for a pair of connected Ca atoms, extra atoms are filled in between them at the correct separation. The filled in atoms will follow the connections of the input skeleton and the 'new' atoms will be exisitng atoms from that skeleton.
 
O > tr_set newav pav
O > tr_fil
Aub> cnxlnk errcod flagged
Aub> cnxlnk errcod flagged
 
In the above example, some circular connections are flagged. If you have carried out these examples on the P2 averaged map, centred on the FA C1 atom, you now have an almost perfectly traced structure.
Trace_prune (superceded)

trace_prune

This command takes an existing skeleton and modifes its connectivity so that only bones atoms with branch points (i.e. with at lest 3 bonds) can be seen. This means that if the connection between two branch point bones consisted of a number of short bonds, they are replaced by just one bond between the two atoms. The pruning action greatly simplifies the skeleton and often allows the user to recognise structural features. If the density lacks branching features, the prined skeleton will have very long connections, and some long connections in the original skeleton may be missing.
The command is intended as a step towards building a skeleton which ends up closely resembling a Ca trace.
 
O > tra_set
Aub> Use a skeleton to make a first pass at Ca trace.
Aub> Which start skeleton ? newav
Aub> Which new skeleton ? pav
O > tr_prune
 
A new skeleton called PAV will get made and connections are only between branch points on the original input skeleton NEWAV
Trace_setup (superceded)

trace_setup <unmodified_skeleton> <modified_skeleton>

This command defines the two skeletons used in the filter operations. One skeleton will be the input to the filter, the other is an output or a modification of an existing skeleton.
 
O > tr_set
Aub> Use a skeleton to make a first pass at Ca trace.
Aub> Which start skeleton ? av
Aub> Which new skeleton ? newav
Trace_sphere (superceded)
 
trace_sphere <radius>
 
This command makes a new skeleton containing points that are within a defined radius of the screen centre. It does not take into account crystal symmetry (use the Skeleton command fr that)
 
O > skel
Qm> What map? [AV]:
Qm> All map [Y]/N?
Qm> Base level [1.25]: 2.
Qm> Skeleton name [SKL]: av
O > tr_set
Aub> Use a skeleton to make a first pass at Ca trace.
Aub> Which start skeleton ? av
Aub> Which new skeleton ? newav
O > tr_sph
Aub> Centre : 46.71 63.83 35.87
Aub> Radius [30.0] :
Trig_reset
 
trig_reset
 
Reset and delete the object containing trigonometric information.

Undo_write (080219)

Undo_write <mol>

This command allows the user to write out a backup of the ODB associated with a named molecule. The information is written into the user’s file-system in the directory defined by the OTMP environment variable. Five levels of undo are admissible, and the names of the most recently written file depends on the level of undo’s. The user can backup and restore model data as part of this multi-level undo system. At the moment, only the QDS commands implicitly make use of this system. The user, however, is free to activate a pair of commands to force backups (Undo_write) and restores (Undo_read). I plan to retrofit other commands that could make good use of this system.

O > Undo_write
New> Undo system, write data of molecule [] : m1


Undo_read (080219)

Undo_read <mol>

This command allows the user to read a backup of the ODB associated with a named molecule. The information is read from the user’s file-system in the directory defined by the OTMP environment variable. Five levels of undo are admissible, and the name of the file depends on the level of undo’s. The user can backup and restore model data as part of this multi-level undo system. At the moment, only the QDS commands implicitly make use of this system. The user, however, is free to activate a pair of commands to force backups (Undo_write) and restores (Undo_read). I plan to retrofit other commands that could make good use of this system.

O > Undo_read
New> Undo system, read data of molecule [] : m1
New> A binary file
New> Database compressed....
New> There were 51 ODBs in the file.
New> No deeper levels of undo

The final line of output indicates that there are no further levels of undo's assoicated with the Undo system
Visible_object (050805)

visible_object <object> <state>

This command controls the visibility of objects. The object prompt accepts wild cards.

O > vis
New> Change visibility state of 3D object.
New> What object? [*]m17*
New> Visibility state (on/off): [off]
O > vis sc* on
 O > vis sc* off

Wait_ID
 
Ignore any command until an ID is made. This command is used exclusively in macros. The ID must be made by picking an atom.

Water Overview (080213)

The water commands in O allow a user to easily build new water molecules and organize those that have already been built. In the building process, O makes use of a new 3D profile method that casts the selection process in units of the average carbonyl oxygen density. This profile (calculated with Water_profile) should be calculated for the particular molecule getting built. It is resolution dependent. Once calculated, waters can be added if they satisfy size, shape, contact criteria (Water_add). The integarted number of elctrons associated with each molecule can be evaluated for inspection with O's graphing system (Water_electrons). If the user wants total control of which waters are to be added, a fully interactive option (Water_peaks) is available.

It is expected that the user is making use of O's master-menu system so that the molecule with new waters gets refined, maps updated etc within O. The graphing system can be used to inspect B-factors or integrated electrons. This is usually best done with sorted data (generated with Water_sort) to decide which solvents should be removed.

Water_tidy allows the user to associate waters with the closest chain.

Water_add (080213)

This command adds water molecules to the end of an existing molecule. This option requires a 3D solvent profile and a |Fo|-|Fc| difference map. The user selects the cut-off in units of average carbonyl oxygens. These units are dependent on the project, and especially on the resolution.

O evaluates various criteria before choosing a new solvent, rejecting those with close contacts, weak and distorted peaks. The new waters are added at the end of the user's molecule, and are given a name starting with 'Z'.

O > Water_add
New> Average OX peak height..... 0.92
New> Average OX integerated peak 3.11
New> Average OX resolution...... 1.80
New> Define the molecule around which to pick waters [M1 ]:
New> What map (should be a difference Fourier!)? []: f11
New> Map used is F11
New> What fraction of an average carbonyl oxygen [0.5]:
New> Peak picking limits
New> Peak height........ 0.46
New> Integerated peak... 1.56
New> 41 deleted because of contacts.
New> 67 deleted because of height.
New> 35 deleted because not discrete.
New> 416 peaks are kept.
New> Database compressed.
New> Peaks are residues Z1 to Z416
New> SEGIDs will be checked and updated

If this command is run again, new solvents will have names starting at Z417.


Water_electr(ons) (080213)

This command evaluates the number of electrons associated with each solvet molecule. This entails calcualting a chop-Fourier around each solvent, building up a 3D profile and then integrating it. If it does not exist a new residue property called <mol>_residue_electrons is generated. The scores are normalized so that that the average carbonyl oxygen profile has 8 electrons.

O > Water_electr
New> Average OX peak height..... 0.92
New> Average OX integrated peak 3.11
New> Average OX resolution...... 1.80
New> From a sea of waters, evaluate the integrated density
New> Molecule, start, end for the sea [M1 Z1 Z591]:
New> What hkl project? [NATI]:
New> Resolution [ 1.80]:
New> Integrating electron density
New> Peak height in F11 ........ 0.92
New> Integerated peak in F11 ... 3.11
New> Peak profile 0.00 0.00 0.00 0.29 0.71 0.92 0.71 0.30 0.00 0.00 0.00
New> Peaks are normalized to profile oxygen
New> Integrated electron counts have been updated.

The results can be viewed in O's Graphing system. In the following structure, 1ogm, the 'solvent with the highest electron count is almost certainly not a water:


Water_peak (041222)

This command is designed to find water molecules that are close to a reference molecule that is being refined. However, instead of taking a simple peak-picking approach it evaluates the shape of the density when generating a set of suggestions. The command takes as input a difference Fourier (it should be of type |Fo|-|Fc| but this is NOT checked) and creates a new molecule of potential waters in the O database called ‘UFO’. It uses the current level of the FastMap to evaluate what blobs of density are present and close to the reference molecule. The algorithm searches out connected density and associates just one solvent atom with each blob. These ‘solvents’ could, therefore, be places where there are errors in the structure being refined. If the density level in the FastMap slider is too low, each blob may contain more than one real water molecule. Each UFO atom will be the symmetry copy that is  closest to an atom in the reference molecule. The user moves to the next atom in UFO by specifying Continue_Yes, or Continue_No to stop. At each position, the user is able to evaluate contacts to the reference molecule, the shape of the density etc. and then to decide what is to be done using other O commands. In particular, the Rebuild/Insert pull-down can be used to insert extra solvents, ions etc.
The UFO atom is placed at the centre of mass of the blob, and the volume, radius and sphericity is shown. The volume is measured as the number of voxels containing the blob, the radius is in Å units measured around the centre of mass of the blob, and the sphericity is an indication of how spherical (value of ~1.0) or distorted (>5.) the blob is shaped.
The user can elect to start evaluating the UFO somewhere other than the first atom.
 
O > wa_peak
 New> What map (should be a difference Fourier!)? [F11]:
 New> Map used is F11
 New> Level used   0.15360
 New> Define the molecule around which to pick waters [A     ]:
 New> Number of blobs    525
 New> Number of blobs reduced to    115
 New> Number of blobs further reduced to    111
 New> O molecule UFO created
 New> Start resdidue in the UFO of new so-called waters [1]:
 New> Peak number: 1 Volume 41.0 voxels, Radius 1.2 Ang., Sphericity 6.8
 Mol>  Database compressed.
 Mol> Created connectivity Db for UFO
co_yes
 New> Peak number: 2 Volume 39.0 voxels, Radius 1.6 Ang., Sphericity 10.0
co_yes
 New> Peak number: 3 Volume 27.0 voxels, Radius 1.3 Ang., Sphericity 10.0
co_yes
 New> Peak number: 4 Volume 24.0 voxels, Radius 1.6 Ang., Sphericity 10.0
co_yes
 New> Peak number: 5 Volume 23.0 voxels, Radius 0.9 Ang., Sphericity 6.3
co_no
 New> End water picking

Water_prof(ile) (080213)

This command generates a 3D density profile for use with the water picking commands in O. Waters are added by the Water_add command in units of the density of the average carbonyl oxygen atom. Fifty random carbonyl oxygens are selected from the specified molecule, their contributions are chopped from the calculated structure factors, a |Fo|-|Fc| map is calculated, and the average 3D profile is calculated over a 0.5 Å grid. This option requires that structure factors have been calculated for the molecule of interest.

O evaluates averages for the integrated number of electrons associated with the carbonyl oxygen densities and their peak heights.

O > water_profile
New> What molecule? []: m1
New> What hkl project? [NATI]:
New> Resolution [ 1.80]:
New> Grid points along cell axes [ 180 204 84]:
New> Multi-scale R-factor = 0.2713
New> Min, max, RMS ...... -0.72782 1.82281 0.14163
New> Integrated electron density 3.11409
New> Peak electron density ...... 0.91744

The results are resolution dependent and are stored in the user's ODB as entry .ox_real of length 1333 units. The first entry in this vector is the resolution, the second is the integrated number of electrons, followed by the 11x11x11 3D profile.


Water_sort (080212)
 
water_sort <mol start end> <property> <sort_order>
 
This command tidies up the water molecules in a structure, sorting them by atomic or residue property in increasing or decreasing order. All associated residue or atomic properties are shifted according to the sort. The following example sorts on B-factor so that the solvents with lowest Bs appear first in the order.

Qm> water_sort
Qm> From a sea of waters, tidy them up to be
Qm> ordered by a property
Qm> Molecule, start, end for the sea [1OGM C1 C540]:
Qm> Sort on property [atom_b] 1OGM_
Qm> This is an ODB of type real.
Qm> Sort in ascending order ([Y]/N) ?
 
In the above, solvent C1 will now have the lowest B-factor and C540 will have the highest. One can then use O's Graphing options to see the results:



The next example sorts on the number of electrons associated with each solvent atom (previously calculated with Water_electr) and is made in descending order so that the solvents with 'strongest' integrated density appear first in the list.

Qm> water_sort
Qm> From a sea of waters, tidy them up to be
Qm> ordered by a property
Qm> Molecule, start, end for the sea [1OGM C1 C540]:
Qm> Sort on property [atom_b] 1OGM_residue_electrons
Qm> This is an ODB of type real.
Qm> Sort in ascending order ([Y]/N) ? n
 
By executing the above instructions, solvent C1 will now have the highest electron density and C540 will have the lowest. Again, one can then use O's Graphing options to see the results:




Water_sort replaces Water_bsort after and including O version 12.

Water_tidy
Often in structures containing multiple chains, the water molecules are all grouped together in the PDB file, but spread all over space. This command is meant to clean things up by reordering the position of the waters in the molecule so that those that are associated with a particular chain are grouped together in the O molecule (and hence in an eventual PDB file). If the protein chains have segment or chain identifiers, these will be used to rename the waters. If none of the chains have an identifier, the repositioned water will have names starting with Z.
It is assumed that the waters are adjacent entries in the starting molecule, and that within the zone containing them, there is only water. During the re-ordering process, only the coordinates, temperature factors and occupancies are swapped, and residue centre-of-gravity values updated. Any other residue and atom properties associated with the start waters will need to be updated by the user.
O > wat_tidy
O > From a sea of waters, tidy them up to be
O > associated with particular chains
O > Molecule, start, end for the sea: m2 z1 z471
O > Molecule, start, end for the chain (<CR> to stop):a2 a301
O > Assume molecule: M2
O > Molecule, start, end for the chain (<CR> to stop):b2 b301
O > Assume molecule: M2
O > Molecule, start, end for the chain (<CR> to stop):
O > Each water will have the chain ID in its name
O > Waters close to chain ID: A
O > From residue A401
O > To residue A658
O > Waters close to chain ID: B
O > From residue B401
O > To residue B612
 
Window_open
window_open name x y
Opens one of the moveable pull-down menus and places it in the 3D window. The coordinates have values -1.2 > X < 1.2, -1.0 > Y <1.0
Any 'moveable' window can be opened, but the following pull-downs may be worth positioning by placing a series of window_open commands in the on_startup macro
 object_display  pulldown of objects that are presently displayed. Clicking on a pane deletes the object
 density_1(2,3,4,5)  the 5 density slider windows
 object_menu  pull-down to turn object on/off
 user_menu  pull-down of the User's menu of commands and macros
 dial_menu  pseudo dial pull-down
Write_formatted

Write_formatted <param> <[file]> <[format]>

Writes out a datablock file as an O database source file. The command prompts for a data block name, a file name, and a format specification, in standard FORTRAN syntax, for example '(10i5)'. For example:
 
write .lsq_rt_a_to_b junk.tmp (3f10.4)
 
Wild cards are permitted in the specification of data block names. In this way one can write out the entire database in ASCII format, for porting to another computer. There must not be any spaces in the format specification.
YASSPA
 
yasspa <molecule> <template> <cut-off distance>
 
An option to define the secondary structure of a protein, given a set of Ca coordinates.
The template molecule MUST reside in the users database. It is normally supplied in the data directory as an O type file. Current templates are alpha.o and beta.o corresponding to a-helices and b-strands. These coordinates are the central members of a cluster analysis (Jones, unpublished) using a 0.5Å cutoff (the default value to YASSPA). To define a-helices use this 0.5Å cut-off. For b-strands use 0.8Å (this is because b-strands show more deviation from the central cluster). If it does not exist, The option creates a residue property <molecule>_residue_2ry_struc. The following example colours a molecule depending on secondary structure:
 
mol a
yasspa a alpha 0.5
yasspa a beta 0.8
pain_prop res_2ry = ' ' yellow
pain_prop res_2ry = alpha red
pain_prop res_2ry = beta green
ca ; end
 
YASSPA must be run before Sketch_auto can be used.
Yes
 
Set the Yes flag on, the No flag off. This command is a 'utility' command, and is being used by several other commands. When input from this command, or its friend, No is required, a prompt is shown in the message area of the display. For example:
Zone
 
zone <res1 res2>
 
Add a zone of residues to an object. The connectivity between residues will be that defined in the current connectivity file (see the Connect_file command below). A blank input specifies all residues in the molecule. Entering just one residue name, specifies only that residue.