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Structure factor file manipulations with Xmanip
Author(s)
PurposeManipulation of reflection data and models UsageCommand line interfacexmanip can be invoked via the command line interface with instructions given in a specific definition file: phenix.xmanip params.defThe full set of definitions can be obtained by typing: phenix.xmanipwhich results in::
xmanip {
input {
unit_cell = None
space_group = None
xray_data {
file_name = None
labels = None
label_appendix = None
name = None
write_out = None
}
model {
file_name = None
}
}
parameters {
action = reindex manipulate_pdb *manipulate_miller
reindex {
standard_laws = niggli *reference_setting invert user_supplied
user_supplied_law = "h,k,l"
}
manipulate_miller {
task = get_dano get_diso lsq_scale sfcalc *custom None
output_label_root = "FMODEL"
get_dano {
input_data = None
}
get_diso {
native = None
derivative = None
use_intensities = True
use_weights = True
scale_weight = True
}
lsq_scale {
input_data_1 = None
input_data_2 = None
use_intensities = True
use_weights = True
scale_weight = True
}
sfcalc {
fobs = None
output = *2mFo-DFc mFo-DFc complex_fcalc abs_fcalc intensities
use_bulk_and_scale = *as_estimated user_upplied
bulk_and_scale_parameters {
d_min = 2
overall {
b_cart {
b_11 = 0
b_22 = 0
b_33 = 0
b_12 = 0
b_13 = 0
b_23 = 0
}
k_overall = 0.1
}
solvent {
k_sol = 0.3
b_sol = 56
}
}
}
custom{
code = print >> out, "hello world"
}
}
manipulate_pdb{
task = apply_operator *set_b
apply_operator{
operator = "x,y,z"
invert=False
concatenate_model=False
chain_id_increment=1
}
set_b{
b_iso = 30
}
}
}
output {
logfile = "xmanip.log"
hklout = "xmanip.mtz"
xyzout = "xmanip.pdb"
}
}
Detailed explanation of the scopes follow below.
Parameters and definitionsThe xmanip.input scope defines which files and which data xmanip reads in::
input {
unit_cell = None # unit cell. Specify when not in reflection or pdb files
space_group = None # space group. Specify when not in reflection or pdb files
xray_data {
file_name = None # File from which data will be read
labels = None # Labels to read in.
label_appendix = None # Label appendix: when writing out the new mtz file, this appendix will be added to the current label.
name = None # A data set name. Useful for manipulation
write_out = None # Determines if this data set will be written to the final mtz file
}
model {
file_name = None # An input pdb file
}
}
One can define as many sub-scopes of xray_data as desired (see examples).
The specific tasks of xmanip are controlled by the xmanip.parameters.action key. Possible options are:
Examples
Reindexing a data set and model ::
xmanip {
input {
xray_data {
file_name = mydata.mtz
labels = FOBS,SIGFOBS
write_out = True
}
xray_data {
file_name = mydata.mtz
labels = R_FREE_FLAG
write_out = True
}
model {
file_name = mymodel.pdb
}
}
parameters {
action = reindex
reindex {
standard_laws = *niggli
user_supplied_law = "h,k,l"
}
}
output {
logfile = "xmanip.log"
hklout = "reindex.mtz"
xyzout = "reindex.pdb"
}
}
Applying a symmetry operator to a pdb file ::
xmanip {
input {
model {
file_name = mymodel.pdb
}
}
parameters {
action = manipulate_pdb
manipulate_pdb {
task = apply_operator
apply_operator{
operator = "x+1/3,y-2/3,z+1/8"
}
}
}
output {
logfile = "xmanip.log"
xyzout = "shifted.pdb"
}
}
Printing out some useful information for an mtz file ::
xmanip {
input {
xray_data {
file_name = mydata.mtz
labels = FOBS,SIGFOBS
name = fobs
}
}
parameters {
action = custom
custom{
code = """
print >> out, "Printing d_spacings, epsilons and intensities"
#change amplitude to intensities
fobs = fobs.f_as_f_sq()
#get epsilons
epsilons = fobs.epsilons().data().as_double()
#get d spacings
d_hkl = fobs.d_spacings().data()
#print the lot to a file
output_file = open("jiffy_result.txt", 'w')
for ii, eps, dd in zip( fobs.data(), epsilons, d_hkl):
print >> output_file, ii, eps, dd
print >> out, "Done"
"""
}
}
}
Possible ProblemsLiteratureAdditional informationList of all xmanip keywords
-------------------------------------------------------------------------------
Legend: black bold - scope names
black - parameter names
red - parameter values
blue - parameter help
blue bold - scope help
Parameter values:
* means selected parameter (where multiple choices are available)
False is No
True is Yes
None means not provided, not predefined, or left up to the program
"%3d" is a Python style formatting descriptor
-------------------------------------------------------------------------------
xmanip
input
unit_cell= None Unit cell parameters
space_group= None space group
xray_data Scope defining xray data. Multiple scopes are allowed
file_name= None file name
labels= None A unique label or unique substring of a label
label_appendix= None Label appendix for output mtz file
name= None An identifier of this particular miller array
write_out= None Determines if this data is written to the output file
model A model associated with the miller arrays. Only one model can be
defined.
file_name= None A model file
parameters
action= *reindex manipulate_pdb manipulate_miller Defines which action
will be carried out.
reindex Reindexing parameters. Acts on coordinates and miller arrays.
standard_laws= niggli *reference_setting primitive_setting invert
user_supplied Choices of reindexing operators. Will be
applied on structure and miller arrays.
user_supplied_law= 'h,k,l' User supplied operator.
manipulate_miller Acts on a single miller array or a set of miller
arrays.
task= *get_dano get_diso lsq_scale sfcalc custom None Possible tasks
output_label_root= None Output label root
get_dano Get ||F+| - |F-|| from input data.
input_data= None
get_diso Get |Fder|-|Fnat|
native= None Name of native data
derivative= None Name of derivative data
use_intensities= True Scale on intensities
use_weights= True Use experimental sigmas as weights in scaling
scale_weight= True Whether or not to scale the sigmas during
scaling
lsq_scale
input_data_1= None Reference data
input_data_2= None Data to be scaled
use_intensities= True Scale on intensities
use_weights= True Use experimental sigmas as weights in scaling
scale_weight= True Whether or not to scale the sigmas during
scaling
sfcalc
fobs= None Data name of observed data
output= 2mFo-DFc mFo-DFc *complex_fcalc abs_fcalc intensities
Output coefficients
use_bulk_and_scale= *as_estimated user_upplied estimate or use
parameters given by user
bulk_and_scale_parameters Parameters used in the structure factor
calculation. Ignored if experimental
data is given
d_min= 2.0 resolution of the data to be calculated.
overall Bulk solvent and scaling parameters
k_overall= 0.1 Overall scalar
b_cart Anisotropic B values
b_11= 0
b_22= 0
b_33= 0
b_12= 0
b_13= 0
b_23= 0
solvent Solvent parameters
k_sol= 0.3 Solvent scale
b_sol= 56.0 Solvent B
custom A custom script that uses miller_array data names as variables.
code= None A piece of python code
show_instructions= True Some instructions
manipulate_pdb Manipulate elements of a pdb file
task= set_b apply_operator *None How to manipulate a pdb file
set_b
b_iso= 30 new B value for all atoms
apply_operator
standard_operators= *user_supplied_operator
user_supplied_cartesian_rotation_matrix
Possible operators
user_supplied_operator= "x,y,z" Actualy operator in x,y,z notation
invert= False Invert operator given above before applying on
coordinates
concatenate_model= False Determines if new chain is concatenated
to old model
chain_id_increment= 1 Cain id increment
user_supplied_cartesian_rotation_matrix Rotation,translation
matrix in cartesian frame
r= None Rotational part of operator
t= None Translational part of operator
output Output files
logfile= xmanip.log Logfile
hklout= xmanip.mtz Ouptut miller indices and data
xyzout= xmanip.pdb output PDB file
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