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Notation: some control parameters are only visible/available if you defined
yourself at the apropriate User
Level: here we will use different colour coding for the levels
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Standard (or above),
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Advanced (or above),
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Expert.
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If it is the first time you are using BUSTER on this data, filling in
the input form will require some time and concentration. We will now
have a closer look at the ingredients of a typical calculation in
order to make you more familiar with the terminology and to describe
in more practical terms what actually happens inside the programs.
This information will be presented in the form of instructions on how
to prepare the input for BUSTER through the Graphical User Interface
BUFFET. The graphical user interface is needed in order to impose the
right hierarchical order and guide the user with on-line help (in the
form of hyperlinks). In this way, you will avoid most of the logical
inconsistencies and typing errors usually associated with free-format
ASCII file editing.
Recall the main ingredients which specify your current
"model":
- a PDB file describing the current partial structure,
for which we will use the symbol PDBFRG;
- the fractional volume (solvent content), mean electron density and
temperature factor of the solvent region.
- the (optional) definition of NCS operators in
TNT format
- if you decide to declare the presence of some missing
atoms, you need to specify their distribution and chemical
composition in one of two ways:
- with prior knowledge of the location of these missing
atoms - give the chemical composition of the
pool of missing atoms, and then use either
- a PDB file specifying the envelope for the whole molecule
(fragment + missing atoms), for which we will use the symbol PDBNUP,
or
- a CCP4 MAP file to compute the envelope for the whole
molecule (fragment + missing atoms), for which we will use the symbol
MAPNUP.
- without any knowledge about the location of these missing
atoms - just give the chemical composition of the pool of
missing atoms, and select prior based "On current
phases".
Besides these ingredients specifying the model, we have an MTZ
file containing
- observed amplitudes and their standard deviations
- (optionally) some Hendrickson-Lattman coefficients describing
experimental phase information
- an integer flag value for use in cross-validation (to distinguish
working and test set).
If you compute the envelope for the missing atoms from a map, it is
also useful to have figure-of-merit (FOM) in the MTZ file.
Note : all MTZ and PDB files used for BUSTER
need to be present in the $BDG_datafiles directory before the
input form script is called.
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The Job ID string will be used in generating a name for the
BUSTER job and a name for the subdirectory of
the logfiles directory in which all relevant
files and output will be placed.
A given crystallographic problem will need several runs of
refinement/completion, possibly some trial-and-error model updates,
etc. Our convention is to give the same name (the stem) to all
these runs, and increment an ordinal number as an extension. The stem
can be modified in the field following "JobID". For example,
if you choose MissingLoop as your job ID, your successive runs of
the MissingLoop job will be named MissingLoop.1 , MissingLoop.2
etc.
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The title (limited to one line only) is there to remind you what is
specific to the calculation you are currently undertaking. Keep in
mind that the graphical interface makes it very easy to generate many
different jobs. You will need the title to sort out which is which.
For these reasons, the first few words of the title will appear in the
popups alongside with the JobID. The title will also appear in the
LIST.html logfile, and also beside the
<jobID>.<run number>.crd field in the list of previous
runs from which new runs can be prepared through the Prepare
run button.
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A box of free-format text is provided for detailed annotations
pertaining to this job. It is recommended to make use of this feature
to document the various BUSTER jobs, as the
details may quickly fade out of memory with time.
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Select the MTZ file containing your data. Remember (see Preparing MTZ
files for BUSTER) that all the
measurement info has to be included in a multi-column MTZ file. If the
file is present in the datafiles directory,
if it is readable by the 'buster' account, and if it has the right
extension (.mtz), it will be listed in this
menu.
Compulsory columns are: structure factor
amplitudes, their sigmas and FreeR_flag. Optional columns are: Hendrickson-Lattman coefficients. The labels
present in the MTZ file can be chosen from the input form.
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These are used for accepting reflexions from the input MTZ file. Any
reflexion outside the resolution limits input at this stage will not
be used in any of the subsequent calculations.
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| MTZ Label for F |
Select the label for the column containing the
observed
F's.
Make sure that it is indeed present in the MTZ file.
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Default value: FP |
| MTZ Label for SIGF |
Select the label for the column containing the
observed
standard deviation for the F's.
Has to be present in the MTZ
file.
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Default value: SIGFP |
| MTZ Label for FreeR_flag |
Select the label for the column
containing the
integer flag to distinguish
working and free set.
Has to be present in the MTZ
file.
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Default value: FreeR_flag |
| MTZ Label for HL A |
Select the label for the column containing the
Hendrickson-Lattmann A coefficient for external phase
information (if any).
Optional
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Default value: HLA |
| MTZ Label for HL B |
Select the label for the column containing the
Hendrickson-Lattmann B coefficient for external phase
information (if any).
Optional
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Default value: HLB |
| MTZ Label for HL C |
Select the label for the column containing the
Hendrickson-Lattmann C coefficient for external phase
information (if any).
Optional
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Default value: HLC |
| MTZ Label for HL D |
Select the label for the column containing the
Hendrickson-Lattmann D coefficient for external phase
information (if any).
Optional
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Default value: HLD |
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Set the FreeR_flag of the subset of reflexions to be used as a test
set for cross validation. Only the integer values present in the
FreeR_flag column of the MTZ file are valid options. The default value
is FreeR_flag=0.
If your starting point is a structure refined with CNS, you are likely
to have set FreeR_flag=1. The sftools call
issued at the outset will perform the change of FreeR_flag in the
working MTZ file, so that the CCP4 standard FreeR_flag=0 is attributed
to your free set. Just watch out for the numbers of free-/working-set
reflexions in the LIST.html file, to confirm
that it is correct.
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This section of the input defines the structure in terms of three components:
- The partial structure, or `fragment': this
is the part of structure for which there is a PDB model and that can
be subjected to refinement with TNT;
- The missing structure: this is the part of
structure for which an atomic model does not exist yet. The scattering
from this part is modelled in BUSTER with real-space low-resolution
distributions.
- The bulk solvent.
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-
Select the PDB file specifying the partial structure which is to be
subjected to ML refinement (see Chapter 2, Task 1), or is
to be kept fixed but used as a source of phase information in a ME
completion calculation (see Chapter 2, Task 2).
This file must reside in your datafiles directory and its name must
end with .pdbfrg or simply
.pdb in order to be listed in
the scrolling menu for selection.
-
Sequence of the refined fragment in TNT format. This file can be produced
during data preparation by the script: $BDG_home/bin/buster/pirToSeq.pl. The script relies
on the presence of a perl version 5 in /bin/perl.
The script is only a preliminary attempt at easing the task of setting
up the TNT sequence file. It reads an ASCII
sequence file in pir
sequence format (pir format in a nutshell: the first line begins
with >, the second line can contain anything; the one-letter code
sequence follows, terminated by an asterisk).
The script can be executed from the unix shell:
$BDG_home/bin/buster/pirToSeq.pl <file.pir>
<file.seq> The script will ask you to specify the number
of copies of the molecule in the a.u., and the chain labels you want
to give to each molecule.
The output file file.seq is a basic TNT sequence file; you will need
to inspect it visually and possibly edit it, for example when:
- ligands (either covalently bonded to the macromolecule or not )
are present in your fragment PDB file: you will need to add a RESIDUE
card for each ligand; for covalently linked residues, you will need to
define the link as well;
- there is more than one molecule of different sequence in the a.u.,
for example heterodimers or AB complexes with A and B different: you
will need to run the script for each molecule, and paste the sequence
files together;
- you have disulphide bonds: in which case you will need to add the
SS link
to the appropriate Cysteine RESIDUE cards.
Running pirToSeq.pl with the -s flag allows you to give the starting
residue a number different from 1 - this is very useful if your PDB
and the 1-letter sequence have a different numbering, eg. if the
N-terminal residue in your PDB has sequence number -2, you go:
pirToSeq.pl -s -2 protein.pir protein.seq
Don't forget to move the protein.seq file to
the datafiles directory.
If you want to be able to add many molecules,
e.g. solvent ones, without the need for updating the sequence
file every time you add one, you can add the description of your
molecule in ASSUME
cards in the file $BDG_tntdata/assume.dat.
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- The radius in Å entered here is used to mask
around the PDB model selected as a partial structure, when this model
is to be excluded from the whole molecule mask (to obtain the missing
atoms prior distribution; see Appendix B).
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- The mean electron
density of the molecule (about 0.425
el.s/Å3 for proteins and 0.60 for nucleic
el.s/Å3 acids) given here is only used to
guess a volume for the macromolecule when the envelope for the missing
atoms is defined based on a map.
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The chemical and thermal composition of the pool of "missing
atoms" in the asymmetric unit must be input as follows: for each
type of atom, enter on one single row:
- the atomic symbol
- the number of such atoms in the asymmetric unit
- their mean B factor
- the standard deviation s(B)
of their B factor around its mean value
The mean B values should not be more than 1.5
times the average B value of the atoms in the PDB file for the partial
structure. A sensible choice for the esd's of these B factors is
usually 10% of the value of the average B itself.
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BUSTER implements four alternative techniques
to calculate the prior distribution for the missing atoms. Choose one
and only one of the following:
- Uniform prior: the missing atoms are supposed to be
uniformly distributed in all the volume not occupied by the partial structure. This is
the preferred regime in case of refinement of almost complete
structure.
- Prior based on the current phases: a first BUSTER job is run to perform scaling with a uniform
prior (as above); then a second calculation follows, with a
missing atoms envelope computed from the BUSTER electron density map just computed.
This is usally selected when a significant amount of
scattering matter is still absent from the fragment.
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- PDB-based prior: the missing atoms are distributed in an
envelope defined by the difference between two masks: one mask around
a PDB file and another one around the partial
structure( see Appendix B for
more details).
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- Map-based prior: the missing atoms envelope is computed
from an electron density read from a CCP4-format map;
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The program will run a cycle of scaling, compute phases from a model
where the missing atoms are uniformly distributed in the unit cell
(but not in the fragment regions) and base the
missing atoms envelope on the map obtained with these phases. A
crucial parameter is the fractional solvent content which is used to
assess the volume the missing atom envelope should take up.
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The program will compute a binary mask around the PDB file for the fragment, negate it to have a mask that extends
in all regions but the ones occupied by that PDB, and then blur the
resulting mask. The missing atoms are therefore assumed to be anywhere
but where the fragment is.
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Select the PDB file specifying those atoms to be used in creating a
binary mask for the region containing the whole molecule. This file
must reside in your datafiles directory, it must be readable from the
`buster' account, and its name must end with .pdbnup or simply .pdb.
The atoms in this file will typically consist of the atoms of the
partial structure where reliably known, plus some possibly unreliable
structure for the purpose of defining the region where uninterpretable
density lies.
If you specify 'None', a
uniform prior will be used; this distribution is obtained from a
uniform distribution in the whole unit cell, but excluding the volume
around the fragment atoms.
Around each of these PDB files, a mask can be drawn; the parameters to
draw the mask, and to blur it when necessary, can be selected by the
user using the selection boxes next to list of availables PDB files.
The Radius is the radius
in Å used to mask around the prior-defining PDB file; the Blurring factor defines
the temperature factor used to blur the binary mask around the same
PDB file.
For more detailed discussion of these quantities see Appendix B.
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If no PDB file is available for the part of structure that is missing,
a mask for it can be still computed based on the electron density
computed from the current phases or a user-supplied map. The technique implemented here is
based on Fermi-Dirac distributions and is described in full detail in
our Acta Cryst. D paper.
The map which is filtered to define the prior region can be selected
by the user or can be automatically generated based on the current
phases. In both cases, the parameters in this sections will be used.
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To select an external map for filtering, it must be in the CCP4
format, and covering the whole unit cell.specifying the electron
density in the whole unit cell which is to be used to calculate the
prior. The map file must reside in your datafiles directory and its name must end with
.mapnup or simply .map in order to be listed in the scrolling menu
for selection.
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The parameters to compute the mask can be selected by the user using
the selection boxes next to list of availables map files. The filter
parameters available to the user are:
- The choice between rectify/square refers to the operation
performed on the result of the high-pass filter; it need not be
changed from its default (square).
- High-pass filter
Here are the input parameters to the (optional!) high-pass filtering
stage used whan drawing the missing atoms envelope starting from an
electron density map. Both the radius and the blurring factor can be
left to the default values of zero, which amounts to base the
calculation of the prior on the local values of the electron density
rather than on its local fluctuation.
If you want an envelope based on the local fluctuation of the density,
as is the case when the low-resolution components of the map are not
to be trusted, then the high-pass filtering stage is necessary, and
the radius and Blurring factor can be changed. The Radius here is the radius of the sphere used for
the local averaging; make sure that the value is larger than the one
chosen for the low-pass filter (see below). The Blurring factor is the one of the Gaussian used for
the local averaging. Values between 50 and 100 should be appropriate.
- Low-pass filter
Here, the parameters that are used to draw the missing atoms envelope
starting from the (optionally high-pass filtered) electron density map
are entered. The Radius is the radius of the
sphere used for the local averaging; use values larger than or equal
to the resolution of the dataset in Å (e.g. for a 2.0
Å dataset, values of Radius >= 2.0 will do). The Blurring factor is the one of the Gaussian used for
the local averaging. Values between 10 and 50 should be appropriate.
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The bulk solvent contribution is specified by its
solvent fraction. The value obtained after optimisation of the solvent
contents in SHARP is a good guess. Otherwise,
it can be estimated from the CCP4 program matthews, or either of Bernhard
Rupp's or Duncan McRee's
applet servers.
An estimate of the uncertainty associated with this
solvent fraction also needs to be given.
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By default, the fragment
file is used to calculate a solvent envelope.
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BUSTER implements alternative techniques
to calculate the distribution of the bulk-solvent scattering. Choose one
and only one of the following:
- None: no contribution from the bulk
solvent to the structure factors will be
calculated.
- From a PDB: Select the PDB file
specifying those atoms to be used in creating a binary mask for the
bulk-solvent envelope. This file must reside in your datafiles
directory, it must be readable from the `buster' account, and its name
must end with .pdbnup or simply .pdb.
This file should define the whole region of
ordered atoms. It will typically consist of all ordered atoms (the
partial structure) as well as atoms in the (yet) uninterpreted
region. Therefore, it will be identical to either the PDB file used for tracing the missing atoms
prior or (if no missing atoms are
present) the fragment file.
The parameters for blurring
the solvent mask are:
- The Radius is
the radius in Å used to mask around the solvent-defining PDB
file. The binary mask around the PDB model above is then converted
into a smooth blurred distribution.
- The Blurring factor
defines the temperature factor used to blur the binary mask.
For more detailed discussion of these quantities
see Appendix B.
The blurred mask is dressed with a chemical
composition which parameters are under user's
control. Those parameters are:
- Electron density of
solvent [el.s/Å3]
This is the mean electron density for the
solvent (about 0.33 electron per cubic Ångstrom for water). In
presence of good low-resolution data, this value can be refined by
means of the scaling options below.
- Solvent temperature
factor [Å]
A mean B factor Bsolv for the
solvent atoms (typically 150 to 300 squared Ångstroms).
The blurred mask around the solvent-defining
file is than stored in the file babslv, and
the Babinet principle is used to compute the bulk solvent structure
factors.
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These check boxes activate the Maximum Likelihood refinement of
scaling parameters for the individual components of the BUSTER model. The various scale parameters are:
- For the partial
structure :
- For the missing part :
- Relative
scale parameters
A scale factor and an overall B factor will be refined for the
contribution to the structure factor from the missing atoms. When the
amount of matter declared in the chemical composition of the missing
atoms is very small, the scaling of the random atoms may be
unstable. In such cases, you may want to disable the refinement of the
relative scale parameters for the random atoms. These parameters will
adjust any initial estimates you will have made for the number and B
factors of the missing atoms; it is safer to activate this refinement
when the initial value for the number of missing atoms is in excess of
the actual number.
If the values of the relative scale factor for the random atoms are
smaller(larger) than 1 in the scaling output file, it means that
the number of missing atoms was under(over)estimated.
- Imperfection B-factor
An imperfection B factor will be refined for the contribution to the
structure factor from the missing atoms. The parameters attenuates the
structure factor from the missing atoms and increases the associated
variance (see chapter5).
You may want to turn the refinement of this parameter off when there
are very little declared missing atoms, and if the scaling is
unstable.
- For the bulk solvent :
- Relative
scale parameters
A scale factor and an overall B factor will be refined for the
contribution to the structure factor from the bulk solvent
region. This parameter will correct the input value for the solvent
electron density. It is safe to refine this parameter if you have
low-resolution data and you can trust them.
- Imperfection B-factor
An imperfection B factor will be refined for the contribution to the
structure factor from the bulk solvent. The parameters attenuates the
structure factor from the bulk solvent and increases the associated
variance (see chapter5).
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During refinement, BUSTER interacts with
TNT (Tronrud, 1997), which provides for the
stereochemical restraints, the minimiser and optionally handle
Non-Crystallographic Symmetry (NCS). Some parameters are required to
drive TNT modules, and are defined in
this last section of the input. Additional information can be found in
the TNT manual and TNT guide and in Chapter 3 of this manual
Refinement parameters are grouped in several sections: the
minimisation, the weights, the structure definition files, the
optional NCS and the databases for stereochemical restraints.
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Set the number of cycles of ML structure refinement to
<value>. Default is value=21, usually enough for a test of good
behaviour but rarely sufficient for reaching convergence.
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Set the number of cycles of
TNT short loops during ML structure
refinement to <value>. Default is value=6, usually enough for
reaching convergence.
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Up to choices are given to the user. Individual B factors can
either be
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The occupancy refinement control is implemented
as the B factor refinement described above. Turning the refinement of occupancies "on"
should not be done, as it will enforce individual refinement of every
atom in the structure, which is probably not what you want to
do ! (Moreover, this would correlate with the overall scale
factor). To refine only the occupanices of selected atoms, the user
should select "From interface" and in the additional commands to the minimiser, using CONSTANT
cards, fix all occupancies but those to be refined.
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The user can input lines to set parameters for the TNT minimiser SHIFT. The
user is referred to the relevant pages of the TNT manual. Some useful commands that can be
inserted in this window are:
- MAXSHIFT,
which trims the parameter shifts to a given value,
- RANGE, which is used to define an allowed range for
atomic parameters. Atoms outside the allowed
range of B-factors are removed from the refinement, so if you
want to keep high atoms with high B, just push to upper limit
higher.
- CONSTANT,
to fix selected atomic parameters.
- COMBINE
is used to perform rigid body refinements. In this case, the curvature
will be descarded, as TNT doesn't use them
during rigid body refinement.
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Sets the weight of the X-ray residual (here, the log-likelihood gain).
For the X-ray residual term, the default value is 3.0. Note that this
weight is not at all on the same scale as that for least-squares refinement. As a guide, a
weight of around a few units (say, 2 to 10) proves to be optimal, but
this depends a lot on resolution, on the incompleteness of the partial
structure, and on whether external phase information is available or
not. The automatic adjustment of this weight has been planned but is
not yet available. N.B. A lower value of the
X-ray weight corresponds to tighter geometrical restraints.
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NCS can be imposed as a constraint (hard NCS) or as a restraint (soft
NCS). When restrained, a weight must be applied, roughly equal to the
inverse of the square of the expected rms deviation between
NCS-related copies. These two complementary approaches of handling NCS
are not mutually exclusive: they can be used simultanously in the
refinement (for example using constraints bewteen reasonably identical
domains, but leaving more flexibility to the hinge region between
domains, thus applying only restrained NCS to this latter region).
- Soft (restrained) NCS
For soft NCS, only the part of the structure to be restrained by
NCS must be included, in the form of a TNT file bearing the extension
.ncssoft.
- Hard (constrained)
NCS
Constrained (hard) NCS files (with extension
.ncshard)
must contain the definition of the region to be constrained, but also
the definition of the NCS operators in TNT format, in in TNT
reference
frame. Note that the TNT program
ncs
will produce those operators.
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The weights for the various classes of stereochemical restraints can
also be set.,
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By default, the Engh and Huber (Engh and Huber, 1991) database,
(csdx_protgeo.dat) and the TNT database for non-bonded contacts (contact.dat) and restraints on B-factors (bcorrel.dat) are listed. Restraints for nucleic acids (nuclgeo.dat) or co-factors can be added when
needed. Ligand stereochemical restraints can be created using the
preliminary script $BDG_home/bin/buster/createTNTDict.sh.
Restraints databases can be fetched from the BDG distribution of TNT in $BDG_tntdata, or
from the user's data files $BDG_datafiles.
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You can point here to a local, customised TNT connectivity file,
containing TNT
CONNECT cards. The file defines the link type between a given pair
of residues, based on their residue type. The default
is the connect.dat file distributed with TNT.
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You can point here to a local, customised TNT
label conversion file. The file contains TNT CHANGE cards that are used to change the
type of an atom, residue, or chain to some other type. Typically, it
helps redefining the metal ion name labels. The default is the pdb_fixup.dat file distributed with TNT.
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The Maximum Entropy Completion will create details within the broad
envelope defined by the prior. It is useful to complete partial model,
and should only be used when the residual
maps on and around the partial structure are reasonably devoid of
features, i.e. the partial structure model is reasonably
good.
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The user can provide the
following parameters :
- Resolution
limits
These resolution limits are used in ME
completion in order to restrict the active use of Lagrange multipliers
to a lower resolution than that of the full dataset. It usually a good
idea not to use all the reflexions in the dataset, but to limit the
MaxEnt maps to a lower resolution (default is cutoff at 1.25*high
resolution limit of the data). The upper resolution can then be
gradually extended towards the maximum resolution of the dataset as
you grow more confident of your phases.
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- FOM Threshold
The reflexions used during Maximum Entropy completion are also
filtered according to their figure of merit:all reflexions whose FOM
is higher than the FOM threshold are included in Maximum Entropy
completion (under the condition, of course, that they fall into
allowed resolution limits).
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Here you can enter more detailed control information
as strings of the form
keyword
or
keyword=value
(no internal blank spaces in the last form!) separated by blank spaces:
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| BSSTHR=<value> |
The stopping criterion for the iterative Bayesian Score maximisation
to compute the distribution for the missing atoms is the Bayesian
Score fractional change: when this quantity falls below the threshold
the calculation stops. The default threshold value is set using this
keyword, to <value>*0.001. The default value is set
to 5, giving a threshold of 0.005 - this is a value chosen
empirically on the basis of test runs. You might want to change
the threshold if you notice that the Bayesian Score in the file unimod<shell#>.html starts decreasing at some
point: a smaller value of BSSTHR (say, 1) will carry the fitting
further. You can check at what value to set it by reading the value of
the Bayesian Score fractional change at cycle for which the Bayesian
Score reached its maximum.
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| BYPORI |
This option bypasses the automatic origin definition. It should always be present.
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| MLNORM |
This option triggers extra output from the scaling
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| NOABCD |
You might select this for instance in order to compare the results of
ML refinement with and without experimental
phase information. For a
production run, of course, you would not normally select this option.
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| NOBREF |
This keyword should be there when the refinement of individual B
factors for the atoms in the partial structure is set "on":
NOBREF will then inhibit the refinement of the overall B.
If the refinement of individual B factors in the partial structure is
switched off (e.g. when performing rigid body refinement or
refinement with low-resolution data only), then this keyword is
absent, and an overall B factor is refined and used to correct the
individual B's of the partial structure at each cycle.
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| USESIG |
This option tells BUSTER to add the sigma(Fobs) from the
MTZ file to variance computed from the error model for each
reflexion. You should normally have this keyword on, unless:
- the (Fobs,Fobs+sigma) correlation
coefficient curve shows a great loss of correlation due to noise in
the data at high resolution
- AND -
- the loss of correlation (Fcalc,Fxpct)
larger than the (Fcalc,Fobs) at high reolution.
If both these conditions are met you might profit from switching
USESIG off.
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| FILTER |
This keyword switches on debugging messages from the BUSTER code.
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| SILENT |
This keyword switches on verbose output from the CCP4 map and mtz
handling routines.
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| NOJAVA |
All plots (in PLOTMTV
format) will be linked directly, without
making use of the (JavaScript driven)
selection of Java applet versus PLOTMTV. If you get
p-roblems looking at the various plots from
within your browser it might be a good idea to
include this keyword here.
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Once all the required information has been entered, you choose to
Submit the calculation, or just
to save the contents of the form (card files); in this case, you can
submit the calculation using the Restartoption from the main control panel.
On the contrary, upon submission a hyperlink will be displayed,
leading you straight to the newly created subdirectory of your logfiles directory which will contain the output
from this BUSTER job.
The user can select a cleanup script to be run
after a successful run of BUSTER. This will
remove many output files of lesser importance. The selection of files
to be deleted can be done under user's control, from the preferences panel.
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