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Overview of all scripts

The complete list of all scripts bundled with Biskit


The biskit scripts are sorted into four sub-folders of biskit/scripts. Each script has a help screen which is shown if the script is called without parameters or (especially in scripts/Mod) with the -help option. This page simply collects the help screen of each script.


General purpose scripts

Convenience and management

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    Update old python pickles. Unpickle some python objects and pickle them back
    to the same filename.  Disable strict class checking if necessary -- this
    allows to load classes that have meanwhile changed their base
    Usage:  file1 file2 ..

    Re-create LocalPath in PDBModel or Complex from the original
    file name (and the current environment variables).
    Usage: -i |file1 file2 ..|

    kill all processes containing a given phrase on all hosts
    Syntax: -n |part_of_name| [-a -f
               -h |host1 host2 host3 ..| -e |host4 host5 ..|]
               -n ... search phrase
               -a ... kill all without asking
               -f ... don't ask anything at all
               -h ... only look on these hosts  (default: all)
               -e ... exclude one or more hosts from killing

    xload: show osxview for several machines.
    Syntax:     xload |machine_file|
                machine_file ... text file with one machine name per line

    remove files from disk and cvs
    Syntax: cvsrm file1 file2 file3...
    Changes still need to be committed (cvs ci).

    delete all /tmp/pvm* files on all hosts
  • bispy:

    script to start the python interpreter with standard Biskit imports

    replace_wildcard_import -i |src_file| -m |module_name|
                           [-as |import_as| -e |exclude_method1 ..| ]
    example: replace_wildcard_import -i -m Numeric -as N -e Complex
             will replace all calls to any Numeric method (except Complex) by N.|method|

    Fix the import of Numeric.array_constructor in pickled Biskit modules
    Many Biskit pickles have e.g. array_constructor dumped as

    prints the current test root

    Restart a distributed calculation.
    Syntax: -i |rst_file| [-a]
             i  .. restart file containing result of TrackingJobMaster.getRst()
             a  .. add hosts to PVM

Structure sampling

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    Prepare the restart of a broken Amber MD run. Current *crd etc. are
    moved to oldName_TIMEps.* and the nstlim option in the input file
    is set to the number of steps remaining to the end of the MD. -f |folder| [ -t0 |time_offset| -tot |nstlim_total|
                    -rst |rst_file|
                    -inp |inp_file| -e |exclude_files_from_renaming| ]
       tot   - needed for 2nd restart, total number of MD steps (w/o restart)
       t0    - starting time in ps of this MD

    Convert single amber crd into Trajectory object -i sim.crd -o traj_0.dat -r ref.pdb [-b -wat -hyd -rnres -code PDBC ]
         -r     ref.pdb - must have identical atom content as sim.crd
         -b     traj has box info (3 additional coordinates per frame)
         -wat   delete WAT, Cl-, Na+ residues (after parsing)
         -hyd   delete all hydrogens (after parsing)
         -rnres rename amber residues HIE/HID/HIP, CYX to HIS and CYS
         -code  PDB code of molecule (otherwise first 4 letters of ref file name)

    Concatenate 2 amber crd/vel files. -i sim1.crd sim2.crd -o sim_merged.crd -n n_atoms [-b
                   -p |int_precission| -rst |last_sim1.rst last_sim2.rst| ]
      -n     number of atoms (obligatory)
      -b     traj has box info (3 additional coordinates)
      -p     when looking for overlapping block, round coord. to p positions
      -rst   try repairing last frame of sim1, sim2 from given restart file(s)

    Prepare ensemble MD with amber - requires template_pme_ensemble folder
    Syntax: -parm |parm_file| -crd |crd_file| -out |result_folder|
                                 -pdb |0_pdb_file|
                               [ -nb_nodes   |n_nodes_per_host|
                                 -template   |template_folder|
                                 -nodes_eq   |2 hosts for minimiz.|
                                 -nodes_prod |10 hosts for prod.|
                                 -n_members  |10|
                                 -rseed      |int_random_seed|
                                 -dt         |production_time_step|
                                 -n_steps    |production_step_number|
                                 -ntwx       |production_coordinate_writing_interval|
                                 -ntwv       |production_velocities_writing_interval|
                                 -place_holder1 |value| -place_holder2 |value| ..]
    The script prepares a new folder |out| with all the input and start files
    to run multiple copies of an Amber MD. All input/start files/folders are
    copied from a template folder. Template files and folders ending in 'xx'
    are recreated |n_members| times. Strings ala '%(place_holder)s' in any
    template file in any template folder are replaced by the value of
    self.|place_holder| which can be given at the command line. If
    self.place_holder contains a list of values, each item is only used once
    (e.g. nodes_prod or nodes_eq ).
    Requirements: -$AMBERHOME must be set
                  -LAM environment must be set up in .cshrc or .zshenv or etc.
                  -start_eq must be run from first host in nodes_eq.dat !

    Create amber topology and coordinate files from a PDB.
    Syntax: -i |PDBfile| [-o |out.parm| ...any of options below ]
        OR: -i |PDBfile| -mirror [-o |out.parm| ]
    Result: out.parm, out.crd, out.pdb, (and leap.log in current folder)
    Special option -mirror: create a parm for exact atom content of input PDB
                          (no S-S bonds formed, atoms missing from residues..)
                          This parm can be used for ptraj but not for simulations!
            ocrd      - str, target file for crd (coordinates) [|f_out_base|.crd]
            opdb      - str, target file for pdb               [|f_out_base|.pdb]
            hetatm    - keep hetero atoms                                             [don't]
            cap       - put ACE and NME capping residue on chain breaks   [don't]
            capN      - int int, indices of chains that should get ACE cap     []
            capC      - int int, indices of chains that should get NME cap     []
            box       - float, minimal distance of solute from box edge    [10.0]
            fmod      - str str, list of files with amber parameter modifications
                        (to be loaded into leap with loadAmberParams)              []
            fprep     - str str, list of files with amber residue definitions
                        (to be loaded into leap with loadAmberPrep)                []
            leap_template - str, path to template file for leap input [use default]
            leaprc        - str, path to parameter file for leap [use default]
            leap_out      - str, target file for leap.log [default: discard]
            leap_in       - str, target file for script [default: discard]
            leap_pdb      - str, target file for cleaned input pdb      [discard]
            leap_bin      - str, path to tleap binary [use default]
            norun         - do not run leap, only prepare files
            debug         - keep all temporary files
            more -key value pairs for place holders in  leap input template
    - The protonation state of histidines is decided from the H-atoms that are found
      (HD, HE, or both). After that all H are removed to be added again by leap.
    - Cleaning tries to convert non-standard residues to the closest standard one.
    - Cleaning removes non-standard atoms (and atoms following them) from standard residues.
    - Cleaning keeps the largest / first of multiple occupancies
    - Ends of chains are assumed if the residue numbering jumps backward, if there
      is a TER record or chain ID or segid change, or if there is a chain break.
    - A chain break is assumed if there is an untypical gap in the chain of back-
      bone atoms (see PDBModel.chainBreaks() ).
    - The index of the first chain is 0.
    - Original waters are deleted.
    - As usual, options can also be put into a file and loaded with the -x option

    Extract PDB files from Xplor PCR trajectories.
    Syntax: pcr_crd2pdb -i |pcrFolder| -t |psfFolder| -o |outFolder|
                        [ -n_iter |n_iterations| -skip |stepping| -z ]
         -z       gzip crd files
         -skip    MD-step intervall for PDBs (500 = 1/ps)
         -n_iter  number of iterations per ensemble member (50 = 50ps)

    Reduce all-atom trajectory to trajectory with only one backbone and
    up to 2 side chain atoms per residue.
    The new atoms are the centers of mass of several atoms and carry the
    weight of the pooled atoms in an atom profile called 'mass'. -i traj.dat [-o traj_reduced.dat -amber -red |red_traj.dat|]
         i     - pickled Trajectory object (all atoms)
         o     - alternative output file name (default: 'reduced_' + input.dat)
         red   - pickled reduced traj, just update ref model in given traj.
         amber - rename amber HIE/HIP/HID, CYX -> HIS, CYS; unwrap atom names

    Start single Xplor PCR job on remote host.
    Syntax: runPCR -t |psfFolder| -h |host|
                  [-f |Force| -r |resultFolder| -n |nice| -i |inpFolder| ]
            -f     force constant for PCR restraint
            -r     base folder for result (sub-folder will be created)
            -t     folder with topology (psf, pdb)
            -n     nice value
            -h     host computer (accessible via ssh)
            -i     folder with all input files, must contain restart_h2o.inp'
            -parm  folder with param19.* files
    A MD folder called pcr_<PDBCode> is created. The force constant is
    written to a file 'oldenergy' in this folder. The topology folder is
    copied to the new md folder and renamed to the PDB code
    (which is taken from the first 4 letters of the psf file name).
    The job is started via ssh on the remote host.
    A summary of all used parameters is written to runReport.out.
    NOTE: The pdb/psf file has to be 4 characters long and start with
          a number (the segId has to conform to the same format).
    By using python -i .. a python shell remains open and
    the job can be killed with the command r.kill()

    This script is used only for the test_multidock example and is
    used to remove frames from the test trajectory to speed up
    subsequent test steps. With he default setting of step=5 this
    will result in a 100 frame trajectory. -i traj.dat [-step |int|]
          i     - pickled Trajectory object
          step  - int, 1..keep all frames, 2..skip first and every second, ..

    Pool several trajectory objects to one ensemble trajectory.
    Each sub-trajectory is considered as traj of one ensemble member.
    This script is ignoring any profiles of the given trajectories and
    re-assigns new frame names ( the Trajectory.concat() method is not
    used to allow handling of larger trajectories ) -i |in_traj1 in_traj2 ..| -o |out_traj|
                    [-s |start_frame(incl.)| -e |end_frame(excl.)| -step |step|
                     -ref |ref_pdb_or_model| -pdb |PDBCode| -prot ]
        s,e,step - start, end position and stepping for each of the input traject.
        ref      - PDB or pickled PDBModel with reference coordinates, by default,
                   the reference frame of the first trajectory is taken
        pdb      - PDB code to be stored in trajectory
        prot     - delete all non-protein atoms (not by default)

    Add file names of frames to trajectory -i |in_traj.| -o |out_traj.| -f |file1 file2 file..|
    Add/replace file names of frames to existing (pickled) Trajectory.
  • Calculate global and side chain fluctuation per atom
                  for a trajectory.
    Syntax:     trajFluct -i trajectory_file [-o result_trajectory]
    Options:   -i     pickled trajectory
               -o     file name for pickled result Trajectory

    Convert one normal Trajectory into EnsembleTraj. The input trajectory must
    have frame names that allow sorting by time and ensemble member (see for details). -i |in_traj| -n |n_members| -o |out_traj| -pdb |PDBCode| ]
        o        - out file name        (default: replace input file)
        n        - number of ensemble members to expect (default: 10)
        pdb      - PDB code to be stored in trajectory

Biskit Setup

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    setup the biskit environment
  • Setup the host list neded for Biskit distributed calculations.
    Usage: Run this script once and let it create the empty host list in  ~/.biskit/hosts.dat.
           Add your avaliable hosts to the list. There are three different sections
           to which you can choose to add a host:
               - own_hosts:    omputers reserved for own use, highest priority
               - shared_hosts: computers shared with others, medium priority
               - others_hosts: computers mainly used by others, lowest priority
           Add your hosts to the corresponding 'dual' or 'single' cpu option.
           Separat the different hosts with a blank space. If you whish to
           temporarily exclude a host from being used, add it to the 'exclude' option
           Optional settings (noce and ram):
           The nice settings can be changed for a specific computer (default values
           are 0 for 'own' and 'shared' and 17 for 'others'). To add nice value
           add the host(s) and the nice value separated by a colon (:) to the
           'option' 'nice'. Separate multiple hosts with a blank space.
           Example:  computer2:8
           In the same way avaliablbe RAM in GB can be added. The default values
           here are 0.5 for a single cpu machine and 1.0 GB for a dual cpu machine.
    Syntax:  setup_hosts  -i |list, input file| -w |str, out file|
         -i  |filename| read variable names from this file
         -w  |filename| write variables to this file, if the file already exists
               it will be updated,
         -d  |Yes| accept default values for -i and -w

Structure manipulation

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    Syntax: -i |file1| [-o |outfile| -psf |psf_file| -wat -amber
                          -pdb |PDBCode| ]
    Result: self-sufficient pickled PDBModel or PCRModel, with itself as source
        -i      input PDB or pickled PDBModel
        -psf    psf file name -> will generate PCRModel instead
        -o      output file name (default: pdbfile.model)
        -wat    skip water residues (WAT TIP3 WWW H2O) and Cl-, Na+
        -amber  rename CYX -> CYS, HID/HIE/HIP -> HIS
        -pdb    pdb code to be stored in model.pdbCode
  • - a script that collects the average (of 500 structures)
                     molecular surface (MS) and solvent accessible surface
                     (AS) for all 20 amino acids in a GLY-XXX-GLY tripeptide.
    Syntax: -i |template.pdb| -r |path|
                              [ -l |str| -mask |resmask|]
    Options: -i     file, pdb tripeptide template file
             -r     path, calculation root folder (many directories with be
                       created in this folder)
             -l     str, label for the three result dictionaries
             -mask  residue mask to delete padding residues (i.e GLY)
    Result:  4 dictionaries AS, AS_sd, MS and MS_sd, written to root folder

    castPdbs: Convert two similar PDBs in two PDBs with equal atom content.
    PDBs must not have any HETATOMs. TIP3 residues are removed.
    Syntax: -i1 |pdb1| -i2 |pdb2| -o1 |outFile1| -o2 |outFile2|
                        [ -c1 |0 1 ..| -c2 |2 3 ..| ]
    i1, i2   file names of PDBs to be compared
    o1, o2   file names for result pdbs
    c1, c2   chain numbers (starting 0) to take from i1 and i2 (default: all)

    Syntax: -s sourceModel -i otherModels
                      [-so sourceOut -o othersPrefix -dic old_model_dic ]
    Add conservation, accessibility profiles and foldX energies to a reference
    model and models linking to this reference.
    1) if sourceOut is given: Remove waters from source, put conservation score
       into profiles, saveAs sourceOut
    2) update each of |otherModels| from their respective source, make |sourceOut|
       their new source, remove atoms (shouldn't be changed from |sourceOut|) and
       pickle them down to same file name plus |othersPrefix| if given.
    3) update old model dic if given
    Example 1:
   -s ../../rec_wet/1B39.pdb -so ../../rec_wet/dry.model \
            -i *.model -dic 1B39_model.dic
            -> create source and update model.dic
    Example 2:
   -s ../../rec_wet/dry.model \
            -i *.model -dic 1B39_model.dic
            -> source already there, update model.dic

    Count number of SS bonds in protein.
    Syntax: |input1.pdb| |input_2.pdb| ..

    Convert a pickled PDBModel into a PDB file.
    Syntax: -i |infile| -o |outfile| [ -wat -ter 0|1|2 -codeprefix ]
        -i      one or more pickled PDBModel(s)
        -o      output file name (default: infile.pdb ) (ignored if >1 input file)
        -wat    skip water residues (WAT TIP3 WWW H2O) and Cl-, Na+
        -ter 0  don't write any TER statements
        -ter 1  try restoring original TER statements
        -ter 2  put TER between all detected chains
        -codeprefix  add model's pdbCode entry as prefix to out file name

    Syntax: -i |file1 file2 ..| [-h |host| -c |chunk| -a -w
                           -o |other_outFolder| -wat -s]
        pvm must be running on the local machine!
    Result: pickled PDBModel object for each pdb file with same file name
            but ending in '.model'
        -h    number of hosts to be used
        -a    first add hosts to pvm
        -c    chunk size, number of pdb's passed to each node at once
        -w    display a xterm window for each node
        -o    destination folder (default: same where pdb file comes from)
        -wat  skip water residues (WAT TIP3 WWW H2O)
        -amber  rename CYX -> CYS, HID/HIE/HIP -> HIS, unwrap atom names
              (this creates models with the same atom/res names as pdbs created
               with ambpdb -p top.parm -aatm -bres < some.crd > some.pdb )
        -s    sort atoms alphabetically within residues

    Extract AA sequence from PDB.
    Syntax |pdb_file|
  • Collect many coordinate frames ( pdb or pickled PDBModel ) of one
                 molecule. Write Trajectory object. Waters are removed.
    Syntax:    pdb2traj -i pdb1 pdb2 ..  [ -e -r |ref_structure| -o |out_file| -f -wat -c ]
        OR:    pdb2traj -d folder/with/pdbs/or/models [ -r ... ]
    Options:   -i     input pdb files or pickled PDBModel objects
               -d     folder containing input pdb or pickled PDBModel files
               -e     create EnsembleTraj, input files must be ordered first
                      by time then by member; x_30_10.pdb sorts before x_100_09.pdb
               -r     reference structure with PDB records (incl. waters),
                      if not given, the first file from -i is used
               -wat   delete TIP3, HOH, Cl-, Na+ from ref and all frames
               -o     file name for resulting pickled Trajectory object
               -f     fit to reference (dry reference if given)
               -c     analyze atom content of all files seperately before casting
                      them to reference. Default: only analyze first file in -i.
    Note about reference structure: The atom order and content of the files given
    with -i is adapted to the order/content of the reference PDB but NOT
    vice-versa. Snapshots can hence have additional atoms (which are removed) but
    they must have, at least, all the atoms that are in the reference.

    The xplor input file will be assembled from 3 template files. The template
    files should be independent of the particular PDB and should instead contain
    place holders which pdb2xplor will replace by actual file names, numbers, etc.
    Place holders look like that:
         %(segment_pdb)s  .. means, insert value of variable segment_id as string
    All the variables of the Xplor class (see Xplor.__init__()) can be adressed
    this way. The available variables are listed in the log file. Some variables,
    like segment_pdb, amber_patch, segment_id will only have meaningfull values in
    a segment template.
    pdb2xplor combines the templates as follows:
    one header_template
    + (one segment template per segment)
    + disulfide patches (generated without template)
    + one tail template
    the most relevant variables are:
    for header:   project_root .. root folder of cvs project
    for segment:  segment_id   .. segid of currently processed segment
                  segment_pdb  .. file name of segment pdb (generated)
                  amber_patch  .. terminal patches for amber ff (generated)
    for tail:     pdbcode      .. first 4 letters of input pdb file name
                  outname      .. suggested file name for output pdb and psf
                                  (with absolute path but w/o '.pdb' or '.psf')
                  path         .. output path (specified with option -o)
    For hackers:
    All command line options are also available as variables (e.g. i, o, t).
    Even more, you can invent any command line option (e.g. -temperature 298)
    which will then be available as variable. Taken the example you could
    add a place holder %(temperature)i to your template file which would be
    translated to 298 (or whatever you specify).
    For hackers++:
    With option -x you can specify a file containing variable - value pairs ala:
    temperature    298   # the temperature in K
    steps 100            !! minimization steps
    Give one pair per line, only the first 2 words are parsed.


protein-protein docking scripts -- back to Content


    pcr2hex  pool many pdb's into one seperated by MODEL/ENDMDL to be used by hex.
    Syntax:  pcr2hex -psf |in.psf| -pdb |in1.pdb| |in2.pdb| ... [-s |modelFolder| ]
             -psf     psf file name
             -pdb     list of pdb file names
             -nos     don't pickle each PDB as pickled w/o waters to this folder
    Result:  -pdb file, pdbCode_hex.pdb (first 4 characters of the first pdb file
              are taken as pdbCode)
             -model dictionary, pdbCode_models.dic
             -modelFolder/in1.model, in2.model, unless -nos has been given
  • -i -o
                           -mo out_folder_for_changed_models
                           -rdic correct_rec.dic -ldic correct_lig_models.dic

    contacter: Take ComplexList, calculate contactMatrix and other stuff
               for all complexes on several nodes. Pickle ComplexList to a file.
               The result values are put into the info dict of each complex.
    Syntax:        contacter [-i |complex_lst| -o |file_complex_lst|
                          -c |chunk_value| -ref |ref_complex| -v |complex_version|
                          -a -h |n_hosts| -u
                          -f |name| -s | -n |min_nice| -all -e |host1 host2..|]
    Options:   -i     pickeled list of Complex objects (file name)
               -o     file name for pickled complex dictionary
               -c     chunk size (number of complexes passed to each node)
               -a     add hosts to pvm
               -h     number of nodes to use (default: all available)
               -e     exclude hosts
               -ref   pickled reference Complex for fraction of native Contacts
               -w     show xterm for each node (default: off)
               -u     only fill empty info fields, or missing keys from -f
               -f     force calculation on sub-set of measures, current measures:
                         'fnrc_4.5', 'fnac_10', 'fnac_4.5',
                         'fnarc_9', 'fnarc_10', 'c_ratom_9', 'c_ratom_10',
                         'eProsa', 'ePairScore', 'foldX',
                         'cons_ent', 'cons_max', 'cons_abs'
                         'rms_if', 'rms_if_bb', 'xplorEnergy'
               -v     work on a previous version of each complex, only valid if
                      input is ComplexEvolvingList (e.g. status before and after
                      refinement). 0..use oldest version, -1..use latest version
               -n     renice calc to, at least, this nice value
               -s     splits complex list into sublists of this size, dumps temporary
                      contacted lists, collects result (can be resumed)
               -all   allow more than 512 solutions per model pair (keep all)

    hex2complex:    Parse output file from hex docking run, create dictionary of
                    Complex(es), and pickle it to a file.
                    Creates a plot of the cluster distribution (using hex rmsd).
                    rec, lig  - receptor and ligang model dictionary
                    hex       - output file from hex
                    o         - name of resulting complex list
                    p         - create biggles plot of rmsd vs. solution
                    mac       - force rec and lig 'model 1' to be used for all
    Syntax:    hex2complex -rec |models_rec| -lig |models_lig| -hex |hex.out|
                           -o |output name| -p |create plot|
    Example:    hex2complex -rec 1BZY_models.dic -lig 2AKZ_models.dic
                            -hex 1BZY_2AKZ_hex.out -o -p

    hexInput    Create a macro file for hex.
    Syntax      hexInput -r |rec pdb| -l |lig pdb|
                         [-c |com pdb| -rm |rec model| -lm |lig model|]
                  r, l   - pdb file in hex format (single or multi model)
                  rm, lm - model number to use,
                           if not given perform multi model docking
                  c      - a reference complex pdb file (for rmsd output)
                  sol    - number of solutions to save
    Result      Hex macro file

    hexResults   Get info about docking results from one or more complexGroup files.
    Syntax       hexResult -cg || [ -p |plot name| -o |file name| ]
    Result       Plot and report file

    Check info dict of ComplexList for missing values.
    Syntax: ||

    Seperately dock several receptor models against several ligand models. -rdic |rec_model.dic| -ldic |lig_model.dic|
                [-rpdb |rec_hex.pdb| -lpdb |lig_hex.pdb| -com |refcomplex_hex.pdb|
                 -out |outfolder| -e |excludeHost1 excludeHost2..| mac |1 or 0|
                 -rid |A A ..| -lid |B| -soln |int|]
             rdic, ldic  .. dict with PCRModels indexed by 1 .. n (rec, lig)
             rpdb, lpdb  .. HEX-formatted PDB with same models (rec, lig)
             com         .. HEX-formatted PDB with reference complex
             out .. folder for results (created), may contain %s for date
             e   .. dont use these hosts
             mac .. 1|0 force the use of macro docking, if not given, the size
                    of the receptor will decide if macro docking is used.
             rid,lid .. force these chain IDs into HEX PDB file of rec / lig
             soln    .. number of solutions to keep from each docking
  •  - create a reference Complex (without waters)
    Syntax:  -c |complex pdb|
                             -r |chain index| -l |chain index|
                             -o |output name|
    Options:   -c     complex pdb file or pickled PDBModel object
               -r     receptor chain list (e.g. 0 1 )
               -l     ligand      ~       (e.g. 2 )
               -o     output file
               -lo,lr ligand, receptor model output file

    Reduce macro docked complex list (rec * lib * 5120)
    to a normal complex list (rec * lig * 512)
       i - complexList to be reduced
       o - name of reduced list

    selectModels: Select non-redundant frames from a trajectory dump them and put
                  them into a PDB file for HEX docking.
    Syntax:  selectModels -i |traj.dat| -o |out_folder| [ -psf |psf_file|
                          -dic |out_model_dic|
                          -n |number| -ref
                          -co |TrajCluster.out| -a |atom1 atom2 atom..|
                          -s |startFrame| -e |endFrame| -step |frameSkip|
                          -id |chaiID]
                          -conv |convergence_diff| ]
             i    - pickled Trajectory object
             dic  - alternative name for model.dic
             psf  - create PCRModels with psf file info
             ref  - add trajectory's reference model to dictionary and pdb if
                      a reference pdb file is given this will be used insted
             id   - set ligand and receptor chainID
             a    - atoms to use for clustering,
                    default: C and roughly every second side chain heavy atom
             conv - float, convergence criterium [1e-11]
    Result:  - n pickled PDBModels '|PDBCode|_|frame|.model' in out_folder
             - pickled TrajCluster if requested
             - |PDBCode|_model.dic with these n PDBModels indexed from 1 to n


homology modeling scripts -- back to Content


    Syntax: [ -o |outFolder| -log |logFile| -h |host_computer| ]
        -o       output folder for results      (default: .)
        -log     log file                       (default: STDOUT)
        -h       host computer for calculation  (default: local computer)
                 -> must be accessible w/o password via ssh, check!
        -? or help .. this help screen

    Built multiple alignment for each project given directory (parallelised).
    If run from within a standardized modeling/validation folder structure,
    i.e from the project root where the folders templates, sequences, and
    validation reside all options will be set by the script.
    Syntax: -d |list of folders| -h |hosts|
                             [-pdb |pdbFolder| -ft |fastaTemplates|
                              -fs |fastaSequences| -fta |fastaTarget|
                              -fe |ferror|]
    Note:  pvm must be running on the local machine!
        -d    [str], list of project directory (full path)
        -h    int, number of hosts to be used
        -a    first add hosts to pvm
        -pdb  str, pdbFolder for the pdb *.alpha
        -ft   str, path to 'templates.fasta'
        -fs   str, path to 'nr.fasta'
        -fta  str, path to 'target.fasta'
        -fe   str, path to the error file for the AlignerMaster

    Syntax: -d |main project folder| [-s |1||0] ]
    Result: Performing model analysis for each main project folder given.
            Outputs a folder 'analyse' containing:
            * analyse/global_results.out
              various data about the model, see file header.
            * analyse/local_results.out:
              residue rmsd profile to taget and mean rmsd to tagret
            * modeller/final.pdb:
            the 'best' model with the mean residue rmsd in the B-factor column
            -d          [str], list of project directory
            -s          show the structure final.pdb im PyMol

    Syntax: -d |list of folders|
                         [ -modlist |model_list| -ref |reference|]
    Result: Performing various benchmark tasks for each folder given.
            A folder validation/benchmark containing:
            * validation/????/benchmark/Fitted_??.pdb:
            Benchmark model iteratively superimposed on its known structure.
            * validation/????/benchmark/rmsd_aa.out:
            All-atom rmsd of the benchamark modela. (1) without iterative fitting,
            (2) with iterative fitting and (3) the percentage of atoms that has
            been removed during the iterative fitting.
            * validation/????/benchmark/rmsd_ca.out:
            same as above, but only for C-alpha atoms
            * validation/????/benchmark/rmsd_res_??:
            gives the C-alpha rmsd for each residue.
            * validation/????/benchmark/PDBModels.list:
            pickled PYTHON list of PDBModels. Each model contains
            the benchmark information in the atom and residue profiles:
            'rmsd_aa', 'rmsd_ca', 'rmsd_res'. See PDBModel.profile()!
        -d          [str], list of project validation directories
        -modlist    str, the path to the 'PDBModels.list' from the
                      project directory
        -ref        str, the path to the 'reference.pdb' from
                      the project directory (known structure)

    Syntax: [-o |output_folder| -i |chainIndex| -log |logFile|
    input: templates/nr/*.pdb
    output: templates/t_coffee/*.alpha    (input for Alignar)
            templates/modeller/*.pdb      (input for Modeller)
        -o       output folder for results      (default: .)
        -i       chain index file for templates
                     (default: '/templates/nr/chain_index.txt')
        -log     log file                       (default: STDOUT)

    Build model using Modeller.
    Syntax: [ -o |outFolder| -log |logFile| -h |host_computer| ]
        -o       output folder for results      (default: .)
        -log     log file                       (default: STDOUT)
        -h       host computer for calculation  (default: local computer)
                 -> must be accessible w/o password via ssh, check!
        -s       show structures on Pymol superimposed on average
        -? or help .. this help screen
    input: templates/modeller/*.pdb
    output: modeller/modeller.log
            /*.B9999000??   <- models

    Syntax: -d |list of folders| -h |host|
                           [-fta |fastaTarget| -pir |f_pir|
                           -tf |template_folder| -sm |starting_model|
                           -em |ending_model| -fe |ferror|]
        pvm must be running on the local machine!
    Result: Parallel modelling for each project directory given
            -d    [str], project directories  (default: ./validation/*)
            -h    int, number of hosts to be used  (default: 10)
            -fta  str, path to find 'target.fasta'
            -pir  str, alignment filename
            -tf   str, directories for input atom files
            -sm   int, index of the first model
            -em   int, index of the last model
            -fe   str, filename to output errors from the Slave

    Biskit.Mod example script that models a structure from a fasta
    formated sequence file in 4 steps:
    1) Searches for homologe sequences and clusters the found
       sequences to a representative set using NCBI-Tools.
    2) Searches for temptale structures for the homology modeling.
       Similar structures are removed by clustering.
    3) Build a combined sequence/structure alignment using T-Coffee.
    4) Build models using Modeller.
    Syntax: -q |query file| -o |outputFolder|
                                [-h |host| -log  -view ]
       -q     file; fasta formated sequence file to model
       -o     folder; directory in which all project files will be
       -h     host name; the quite cpu consuming stasks of aligning
                and modeling can be sent to a remote host that also
                has access to the output directory
       -log   write stdOut messages to log file (~project/modelling.log)
       -view  show the superimposed models in PyMol
    HINT: If you want to inspect the alignment used for modeling:

    another modelling example

    Syntax: [-q |target.fasta| -o |outFolder| -log |logFile|
                   -db |database| -limit |max_clusters| -e |e-value-cutoff|
                   -aln |n_alignments| -psi |psi-blast rounds|
                   -... additional options for blastall (see ]
    Result: folder 'sequences' with files:
            - blast.out - result from blast search (all alignments)
            - cluster_blast.out - blast alignments of cluster sequences
            - cluster_result.out - clustering output
            - all.fasta - all found sequences in fasta format
            - nr.fasta - clustered sequences in fasta format
        -q       fasta file with query sequence (default: ./target.fasta)
        -o       output folder for results      (default: .)
        -log     log file                       (default: STDOUT)
        -db      sequence data base
        -limit   Largest number of clusters allowed
        -e       E-value cutoff for sequence search
        -aln     number of alignments to be returned
        -simcut  similarity threshold for blastclust (score < 3 or % identity)
        -simlen  length threshold for clustering
        -ncpu    number of CPUs for clustering
        -psi     int, use PSI Blast with specified number of iterations

    Syntax: [-q |target.fasta| -o |outFolder| -log |logFile|
                   -db |database| -e |e-value-cutoff|  -limit |max_clusters|
                   -aln |n_alignments| -psi
                   -... additional options for blastall (see ]
        -q       fasta file with query sequence (default: ./target.fasta)
        -o       output folder for results      (default: .)
        -log     log file                       (default: STDOUT)
        -db      sequence data base
        -limit   Largest number of clusters allowed
        -e       E-value cutoff for sequence search
        -aln     number of alignments to be returned
        -simcut  similarity threshold for blastclust (score < 3 or % identity)
        -simlen  length threshold for clustering
        -ncpu    number of CPUs for clustering
        -psi     use PSI Blast instead, experimental!!

    Setup the cross-validation folder for one or several projects
    Syntax: [ -o |project folder(s)| ]
        -o          .. one or several project folders (default: current)
        -? or -help .. this help screen


scripts for analysis and visualisation of results -- back to Content

  • -i |com_folder1 com_folder2 com_folder3..|
    com_folder must contain com_wet/dry_com.model,
                            analysis_500-5.opt for -cl and -cr option
    E.g: -i c11 c12 c13 > result.txt 2> log.txt

    no documentation

    CAD (contact area difference) calculation by icmbrowser.
    The calculation is performed only for residues that are in contact
    in the reference complex.
        cl  - complexList, has to contain info dictionary data for key
        ref - reference complex

    Run many AmberEntropist calculations on many nodes. The Master has
    a standard set of 13 protocols to run on rec, lig, and com
    trajectories, as well as on every single member trajectory - in
    total 113.  It accepts one variable parameter, e.g. s(tart). Each
    protocol is then run for all values of the variable parameter.
    The script puts many temporary trajectories into the folder with the
    input trajectories -- consider creating a new folder for each trajectory!
    Syntax: -rec |rec.traj| -lig |lig.traj| -com |com.traj|
                             -out |out.dat| [ -cr |rec_chains| -zfilter |cutoff|
                             -s |from| -e |to| -ss |from| -se |to|
                             -thin |fraction| -step |offset|
                             -var |option| -vrange |v1 v2..| -jack
                             -exrec |members| -exlig |members| -excom |members|
                             -hosts |name1 name2..| -clean  -single ]
        rec    - str, free rec trajectory
        lig    - str, free lig trajectory
        com    - str, complex trajectory
        out    - str, file name for pickled result
        cr     - [int], chains of receptor in complex trajectory [n_chains rec]
        var    - str, name of variable option [ s ]
        vrange - [any], set of values used for variable option
                 OR 'start:stop:step' i.e string convertable to arange() input
        jack   - set up leave-one-trajectory-out jackknife test [don't]
                 (replaces var with 'ex1' and vrange with range(1,n_members+1))
        zfilter- float, kick out outlyer trajectories using z-score threshold
        exrec  - [int], exclude certain members of receptor ensemble    [[]]
        exlig  - [int], exclude certain members of ligand  ensemble     [[]]
        excom  - [int], exclude certain members of complex ensemble     [[]]
        clean  - remove pickled ref models and member trajectories [0]
        hosts  - [str], nodes to be used [all known]
        h      - int, number of nodes to be used from all known [all]
        single - run only one job on multi-processor nodes [0]
        mem    - float, run only on machines with more than |mem| GB RAM [0]
        debug  - don't delete output files [0]
        ... parameters for AmberEntropist -- can also be given as -var
        cast    - equalize free and bound atom content [1]
        s,e     - int, start and stop frame                 [0, to end]
        ss, se  - int, start and stop frame of single member trajectories
                  (only works with EnsembleTraj; overrides s,e)
        atoms   - [ str ], names of atoms to consider       [all]
        heavy   - delete all hydrogens                      [don't]
        step    - int, frame offset                         [no offset]
        thin    - float, use randomly distributed fraction of frames [all]
                  (similar to step but sometimes better)
        all     - only calculate with all members, no single member values
        ex      - [int] exclude same members from rec, lig and com
        ex_n    - int, exclude last n members  OR...                 [0]
        ex3     - int, exclude |ex3|rd tripple of trajectories       [0]
                  (0 excludes nothing, 1 excludes [0,1,2] )
        ex1     - int, exclude ex1-th member remaining after applying ex [None]
                  (0 excludes nothing, 1 excludes [0] )
        ... parameters for AmberCrdEntropist, Executor, Master
        f_template - str, alternative ptraj input template  [default]
        verbose    - print progress messages to log     [log != STDOUT]
        w          - show x-windows   [no]
        a          - 0|1, add hosts to PVM [1]
  • Plot interface rmsd (heavy and/or backbone) vs.
                               fraction native atom/residue contacts at
                               different cutoffs.
      creates up to 4 plots: rms_if_vs_cont.eps
    Syntax:             -i
                    -o  str, output directory
                    -v  [str], list of keys to plot
                    -if     1||0 create plot of key vs. interface rmsd
                    -if_bb  1||0 create plot of key vs. interface backbone rmsd
    Abbreviations: fnac  - Fraction of Native Atom Contacts
                   fnrc  - Fraction of Native Residue Contacts
                   fnarc - fnac with Reduced atom models

    Calculate change in access. and molecular surface upon binding.
    Syntax: -r |rec_model| -l |lig_model| -c |com_model|

    Analyze ensemble MD.
    Syntax: -i traj.dat [ -z |outlier-z-score| -step |offset|
                           -o |out.eps| -title |plot_title| ]

    Syntax:  a_foldX   -c || -o |out_folder| -ref |ref.complex|

    load model dictionary and report
      * average pairwise rmsd
      * average rmsd to free structure (assumed to be model 1)
      * average rmsd to bound structure
     model 1 is not included in the calculations

    a_multiDock  Visualize multidock results
    Note: interface rms values are for contact atoms not contact residues.
    Syntax       a_multiDock -cl ||
                 cl - complexList, has to contain info dictionary data for key
                 r  - hex receptor pdbs (i.e rec/*_hex.pdb)
                 l  - hex ligand pdbs (i.e lig/*_hex.pdb)
                 ref - reference complex
                 key - info dictionary key to plot (high values are considered good)
                 inv - 1||0 inverse data associated with key (i.e. for rmds plots)
                 maxContour - scale contour circles to fit at most x solutions
                 additional_profile - add to profile plot (rec_model lig_model)
    Result       5 plots, info txt file, dumped data

    a_multiDock  Visualize multidock results
    Syntax       a_multiDock -cl ||
                 cl         - complexList, has to contain info dictionary data for key
                 inv        - 1||0 inverse data associated with key (i.e. for rmds plots)
                 maxContour - scale contour circles to fit at most x solutions
  • -i .. -ref ref.complex
                           -nat [ -t ]
                           [ -nout summary_output_file
                             -rout random_output_file ]
    Get confidence of native scores from several scores to random reference.
    Prints table 3 of multidock paper, i.e. fnac, score, rms, ..
    of free vs. free docking, the docking with highest fnac, and the docking
    with highest score - FOR EACH complex list. The ref.complex is used to
    calculate the interface rmsd to the bound.
    Calculates averages and confidence of highest score, rms..
    The 'real' table 3 line for the native is appended to a separate file.
    t   .. print table header
    nout .. append line with native fnac, scores,.. and confidence to this file
    rout .. append lines with random fnac, scores,.. to this file [STDOUT]

    Analyze the result of
    Syntax: -i |result.dic| [-eps |file| -tall -tsd -t
                                                 -prefix |str|]
      -i      dictionary from
      -eps    output plot with entropies for all values of variable parameter
      -tall   print table with all entropy values
      -tsd    print single line with entropy values and standard dev
      -t      print header row of table
      -prefix prefix for tables (e.g. a01)

    Collect, calculate and save to disc (both as text files and pickled
    dictionaries) various data about a complex list. This script is written
    to collect data from multidocking runs and assums that the first
    ligand and receptor model is the free xray structure.
    Syntax: -cl ||
                             -ref |ref.complex| [-key |str| -inv [int|]
          cl  - complexList, has to contain info dictionary data for key
          ref - reference complex
          key - info dictionary key to plot (high values are considered good)
          inv - 1||0 inverse data associated with key (i.e. for rmds plots)
    Output:   An output directory 'model_vs_rmsd' is created and various text
              files and corresponding dictionaries are written to it.

    Create figure for multidock paper with the change in docking performance
    plotted against the change in rms_to_bound (both relative to the free-free
    k .. key to be plotted (rms_to_bound, rmsCA_to_bound, ..)
    o .. file name of output eps
    i .. one or many complexists with
  • [ -i -ref ref.complex -t ]
    Creates one line of table 3 of multidock paper, i.e. fnac, score, rms, ..
    of free vs. free docking, the docking with highest fnac, and the docking
    with highest score.
    t .. print table header

    Analyze entropy of a single or one rec and one lig trajectory with ptraj.
    Syntax: -i |traj1.dat+traj2.dat| [ -o |result.dic|
                          -ref |ref_structure| -cast -chains |chain_indices|
                          -border |chain| -split -shift -shuffle
                          -s |startFrame| -e |endFrame| -step |frameOffset|
                          -ss |member_startFrame| -se |member_endFrame|
                          -ex_n |exclude_n_members|
                          -ex1 |ex_from_traj1| -ex2 |ex_from_traj2|
                          -ex3 |exclude_member_tripple|
                          -atoms |CA CB ..| -heavy
                          -nice |level|
                          -parm |parm_file| -crd |crd_file| -f_out |ptraj_out|
                          -f_template |ptraj_template|
                          -log |log_file| -debug -verbose ]
        i          1 trajectory or 2 trajectories connected by '+'
        o          file name for pickled result dictionary
        s          skip first |s| frames (of complete trajectory)
        e          skip frames after |e| (of complete trajectory)
        ss         skip first |ss| frames of each member trajectory
        se         skip frames after |se| of each member trajectory
        atoms      considered atoms (default: all)
        heavy      remove hydrogens (default: don't)
        ref        pickled PDBModel, Complex, or Trajectory
        cast       equalize atom content of traj and ref         [no]
        chains     list of integer chain indices e.g -chains 0 1 [all]
        border     1st chain of 2nd molecule for -split, -shift, -shuffle
        split      split complex trajectory and fit rec and lig separately
                   (requires -border with first lig chain)       [no]
        shuffle    shuffle the order of rec vs. lig frames
        thin       use randomly distributed fraction of frames, e.g. 0.2 [all]
        step       frame offset, use every step frame, e.g. 5            [all]
        ex1        exclude these members from 1st trajectory, e.g. 3 6
        ex2        exclude these members from 2nd trajectory (if given)
        ex_n       exclude first n members                       [0]
        ex3        exclude |ex3|rd tripple of members, e.g. 2 excludes 3,4,5
                   (0 excludes nothing)                          [0]
        f_template alternative ptraj input template [default template]
        f_out      target name for ptraj output file        [discard]
        nice       nice level                                     [0]
        log        file for program log                       [STOUT]
        debug      keep all temporary files
        verbose    print extended progress messages to log    [log != STDOUT]

    Syntax: a_trajQuality -i |traj_1 traj_2 .. traj_n| [-a -h |n_hosts| -w]
        pvm must be running on the local machine!
    Result: eps with quality plots in folder of traj files
        -h    number of hosts to be used
        -a    first add hosts to pvm
        -w    display a xterm window for each node
  • -r |rec_model| -l |lig_model| [ -o |out_file| -n |number|
                        -traj |traj_out_name| -ro |rec_out| -lo |lig_out|
                        -debug copy_inp_file ]
    to create valid PCRModels for rec and lig use (in rec_wet/, lig_wet/)
   -i ????.pdb -psf ????.psf -o xplor.model
    The waters in the PSF are deleted. They can be in the model but don't have to.
         r     pickled PCRModel, receptor (psf file has to be valid)
         l     pickled PCRModel, ligand   (psf file has to be valid)
         ro    file name for rec copy (centered and no waters)
         lo    file name for lig copy (centered and no waters)
         o     file name for result ComplexList
         n     number of random complexes to generate
         traj  file name for optional amber crd and pdb (for visualisation)
         debug keep Xplor input file and don't delete temporary files

    select set of non-redundant, non-native random complexes -cl |complex_list|
          ref .. pickled native complex
          h   .. number of hosts
          co  .. folder name for result complexes
          o   .. base name for other result files
          a   .. add hosts to PVM before starting