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Morphing a model with morph_model
Author(s)
Purposemorph_model is a procedure for distorting a model to match an electron density map. It is suited for a case where a poor but unbiased map is available and a model that is generally locally similar to the target structure but where longer-range distances are not conserved. This is often the case in homologous structures. Summary of the procedure used in morph_modelThe basic idea in morph_model is to apply a smoothly-varying offset to the template structure so as to make it match the map as closely as possible. In this way information about the local structure of the template is retained while allowing longer-range changes in structure. Morphing is carried out in 3 steps:
After morphing, the morphed model is refined. This process is then repeated morph_cycles (typically 6) times. Maps for morph_modelNormally you should specify that morph-model use a prime-and-switch map (map_type=prime_and_switch), as that is usually the most effective map for morphing. You can however choose instead to use a 2mFo-DFc map, a density-modified map, or an omit map. The prime-and-switch map is a map calculated in the same way as a density-modified map, except that once the initial model-based map is calculated (priming), the model information is no longer used (switching). This map is typically quite unbiased by the model. Standard run of morph_modelRunning morph_model is easy. If you have a template (coords1.pdb) and a data file fobs.mtz with FP SIGFP and FreeR_flag, you can type: phenix.morph_model data=coords1.mtz model=coords1.pdband morph_model will run automatically. Supplying a map for morph_modelIf you have your own map you want to use in morph_model, you can type: phenix.morph_model data=coords1.mtz \ model=coords1.pdb map_coeffs=my_map_coeffs.mtzand morph_model will start off with your map coefficients instead of calculating a new map. If you specify update_map=True (default) then new maps will be calculated on each subsequent cycle. If you specify update_map=False then your map will be used throughout. Getting a default parameters file for morph_modelUsually you will want to edit a parameters file so that you can specify more details of the run. You can get a default parameters file with: phenix.morph_modeland then just edit the file morph_model_params.dat. Possible ProblemsSpecific limitations and problemsLiteratureAdditional informationList of all morph_model keywords
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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
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morph_model
input_files
data= None Data file with experimental data ( FP SIGFP or I SIGI ).
data_labels= None Optional labels for experimental data Normally these
would be something like I,SIGI or F,SIGF
space_group= None Optional space group specification
free_r_data= None Optional data file with free_r flags. By default this
is the same file as used for experimental data.
free_r_labels= None Optional labels for free_r flags. Normally these
would be something like FreeR_flags or R_free_flags
hl_data= None Optional data file with hl coeffs. By default this is the
same file as used for experimental data.
hl_labels= None Optional labels for hl flags. Normally these would be
something like HLA,HLB,HLC,HLD
labin= None Optional Labin line for file with data. This is present for
backward compatibility only. Normally use data_labels instead.
Only allowed if the data file contains myFP mySIGF and
myFreeR_flag: LABIN FP=myFP SIGFP=mySIGFP FreeR_flag=myFreeR_flag
model= None Input PDB file with coordinates to be refined and morphed.
map_coeffs= None Data file (mtz format) with map coeffs ( FP PHIB FOM or
FWT PHWT) for use in morphing. Normally use None. If set,
then these map coefficients will be used instead of an omit
map.
labin_map_coeffs= None Labin line for map coeffs file Something like
FP=FP PHIB=PHIM FOM=FOMM Normally use None; used by
morph_model in iteration
output_files
log= morph_model.log Output log file
morphed_model= morphed_model.pdb Output morphed model
params_out= morph_model_params.eff Parameters file to rerun morph_model
directories
temp_dir= "" Optional temporary work directory
workdir= "" Optional work directory. Base path for all work
output_dir= "" Output directory where files are to be written
top_output_dir= None Output directory for entire set of runs
gui_output_dir= None Base directory for PHENIX GUI. Ignored if running
the command-line version.
crystal_info
resolution= 0. high-resolution limit for map calculation
solvent_fraction= None Optional solvent fractoin
chain_type= *PROTEIN DNA RNA Chain type (for identifying main-chain and
side-chain atoms)
correct_aniso= False Remove anisotropy from data
final_b= None Overall B of aniso-corrected data. If None, then minimum
of the diagonal of anisotropic B values is used
morphing
number_of_cycles= 6 Number of cycles of morphing
rad_morph= 6 Radius for morphing
rad_morph_final= None Optional final radius for morphing. If set,
rad_morph will be changed from initial value to final
value over the cycles of morphing
map_type= simple_omit refine_omit 2fofc density_modified
*prime_and_switch Map type to use in morphing. Ignored if
map_coeffs is set
use_ncs_in_ps= False Use NCS (if available) in prime-and-switch maps
update_map= True Create new map for morphing at each cycle. Ignored if
map_coeffs is set
refinement
refinement_params= None Input parameters file for phenix.refine
skip_clash_guard= True Skip clash guard check in refinement
correct_special_position_tolerance= None Adjust tolerance for special
position check. If 0., then check
for clashes near special positions
is not carried out. This sometimes
allows phenix.refine to continue
even if an atom is near a special
position. If 1., then checks within
1 A of special positions. If None,
then uses phenix.refine default. (1)
reference_restraints= False Restrain angles to starting model. This may
be useful at lower resolution.
use_hl= None You can choose to use HL coefficients in refinement If
None, hl coeffs will be used if available
control
verbose= False Verbose output
debug= False Debugging output
raise_sorry= False Raise sorry if problems
dry_run= False Just read in and check parameter names
nproc= 1 Number of processors to use
group_run_command= "sh " Not currently enabled. Command to use to run
multiple jobs This may be sh if you are using a
single machine (where you might set background=True)
or something like 'qsub' or 'qsub -q all.q@theta' on
a cluster (where you should leave background=False)
queue_commands= None Not currently enabled. You can add any commands
that need to be run for your queueing system. For
example on a PBS system you might say:
queue_commands='#PBS -N morph_model'
queue_commands='#PBS -j oe' queue_commands='#PBS -l
walltime=03:00:00' queue_commands='#PBS -l
nodes=1:ppn=1'
condor= None Not currently enabled. Specifies if the group_run_command
is submitting a job to a condor cluster. Set by default to True
if group_run_command=condor_submit, otherwise False. For condor
job submission morph_model uses a customized script with condor
commands. Also uses one_subprocess_level=True
one_subprocess_level= None Specifies that a subprocess cannot submit a
job
single_run_command= "sh " Command to use to run single jobs Normally
this is sh
background= None Run in background. If None, automatically set to True
if nproc is greater than one and group_run_command is sh
ignore_errors_in_subprocess= True Generally use
ignore_errors_in_subprocess=True to ignore
errors in sub-processes. This allows you to
continue even if a few jobs crash. If all
jobs in a group crash, the process will
stop. NOTE: if a job hangs or never
runs...this will not be detected and you
will have to either put a file with the
name FINISHED in the directory where the
job was to run (e.g,
MORPH_MODEL_3/FINISHED) or stop the whole
job by putting a file with the name
STOPWIZARD in the main run directory (e.g.,
MORPH_MODEL_3/STOPWIZARD)
check_run_command= False Try out run command to make sure it works Use
False if your queue may not be available at the
beginning of your run. Use True if you want to check
things out
max_wait_time= 100 Maximum time (sec) to wait for a file to be written
(Useful for queues or nfs-mounted systems)
wait_between_submit_time= 1.0 You can specify the length of time
(seconds) to wait between each job that is
submitted when running sub-processes. This can
be helpful on NFS-mounted systems when running
with multiple processors to avoid file
conflicts. The symptom of too short a
wait_between_submit_time is File exists:....
wizard_directory_number= None Directory number for MORPH_MODEL_xx.
Normally None except if called from GUI
n_dir_max= 100000 Maximum number of directories to create (must be as
big as nproc or nstruct/chunk)
write_run_directory_to_file= None The working directory name is written
to this file
job_title= None Job title in PHENIX GUI, not used on command line
non_user_params
print_citations= True Print citation information at end of run
is_sub_process= False identifies if this is a sub-process or top-level
job
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