Here we give a brief overview of the necessary steps to run the program but we strongly encourage to follow the tutorials. The user guide is partitioned in three levels of usage:
For flexible fitting a single atomic structure into a EM density map enter the following command at the prompt.
imodfit <pdb> <map> <resolution> <cutoff>
where:
| pdb | PDB initial model (required). |
| map | Target EM map file (required). Situs and CCP4 formats are accepted; but extensions ".sit" and ".cpp4" are mandatory. |
| resolution | Resolution (required). Our resolution criterion follows EMAN package procedures (e.g. PDB2MRC tool) |
| Cutoff | EM map threshold (required). All density levels below this value will not be considered. |
iMODFIT outputs the following files:
- imodfit_fitted.pdb --> fitted atomic structure
- imodfit_score.txt --> score file to check for convergence
- imodfit.log--> used command log
The more common options to customize your fitting are:
| −h | Displays usage information and exits |
| −i <int> | Maximum number of iterations (default=10000). |
| −m | Coarse-Grained model: 0=CA, 1=3BB2R, 2=Full-Atom, 3=NCAC(experimental) (default=2). |
| −x | Considers first CHI dihedral angle (default=disabled). |
| −t | Outputs a Multi-PDB trajectory movie (<basename_movie>.pdb) |
| −n <int/float> | Used modes range, either number [1,N] <integer>, or ratio [0,1) <float> (default=0.2). |
| −e <int/float> | Excited modes range, either number [1,nevs] <integer>, or ratio [0,1) <float> (default=0.02) |
| −F | Enables full-atom output models. |
| −o <string> | Output files basename (default=imodfit). |
| −P <int> | Pairwise interaction potential: (default=0) 0=inverse exponential (= k/(1+(x/x0)^p), if x < c, else k=0) 1=cutoff (= k, if x < c, else k=0) 2=Topology & Secondary Structure (--func is mandatory) By default an extra torsional potential will be added. |
| −f <string> | ASCII file defining the ICs to be fixed with the format: Protein: "index phi chi psi" NAcid: "index alpha beta gamma chi epsilon zeta" Inter-chain: "index IC" Where IC-name= 0(fixed) or 1(mobile) A demo file can be generated using iMODE with the --save_fixfile option. |
| −r <float> | Randomly fixed ratio of Dihedral Coords. Example: 0.7 = 70% of dihedrals will be randomly fixed. (Rotational/Translational coords. always mobile) |
| −S | All dihedral coordinates belonging to residues matching the indicated SS identifieres will be fixed. Ex: "HE" will fix the dihedrals corresponding to alpha-helices and beta-sheets. |
Only for real expert users!
--ss <string>
Secondary Structure ASCII file with 2 cols.: <index> <char>
Where <index> is the corresponding residue index (1,2,...), and <char>
is the single character SS identifier. By default SS will be computed
internally (H=helix, E=strand, C=coil).
--func <string>
ASCII file defining the force constant functions to be applied
according to Topology and/or Secondary Structure. The 5 cols. format
is: <SS> <n> <k> <x0> <pow>
Where <SS> is the two character pairwise interaction identifier, <n>
is the topology, and <k>,<x0>,<pow> are the corresponding inverse
exponential function parameters. If --ss is not specified, only the XX
pairwise interaction identifier will be considered. If <n> is 0, any
previously not-matched topology will be matched.
--k0_c <float>
Inverse Exponential's distance cutoff (default=10A)
--k0_k <float>
Inverse Exponential's stiffness constant (default=1.0)
--k0_x0 <float>
Inverse Exponential's inflexion point (default=3.8A)
--k0_p <float>
Inverse Exponential's power term (default=6)
--k1_c <float>
Distance cutoff method distance cutoff (default=10A)
--k1_k <float>
Distance cutoff method stiffness constant (default=1.0)
--k2_c <float>
Non-bonding distance cutoff applied to --ss_func (default=10A)
--pdb_ref <string>
Reference PDB file (test only)
--morepdbs
Enable initial (basename_model.pdb) pdb model output
(default=disabled)
--nomass
Disables mass weighting (default=disabled)
--notors
Disables extra torsional potential (default=disabled)
--nowrmsd
Disables Gaussian Weighted RMSD (default=disabled)
--cutoff2 <float>
Density cutoff of simulated map (default = 0.001)
--filter <int>
Select filtration method: 1-Fourier, 2-Kernel (By default the fastest
will be selected)
--6Dref <int>
Number of iterations between local 6D pose refinement (default=200)
--6Dref_delay <int>
Number of iterations before first local 6D pose refinement
(default=disabled)
--6Dref_chain
Independent local 6D pose refinement for each single chain.
--6Dref_trans <float>
Maximum translational increment (Angstroms) for pose refinement.
(default=2)
--6Dref_rot <float>
Maximum rotational increment (degrees) for pose refinement
(default=1)
--prob <string>
Normal Mode Selection Probabitity. --nex modes will be selected and
merged from --nevs subset according to the following probabilities
(p): (default=var)
plain: equiprobability (--min_prob will be ignored)
var: proportional to the mode variance, p(i)= 1/eigenvalue(i)
line: lineally decreasing probability, p(i)= 1-i/nevs
--rediag <double>
RMSD ratio to trigger diagonalization.
(last_diag_RMSD-current_RMSD)/first_RMSD > rediag (default=0.05)
--delta_save <float>
RMSD increment from previous saved frame to trigger frame saving.
(default=0.5)
--wrmsd <float>
Sets the RMSD weighting [0:1] during model alingment (wrmsd=0, means
maximum weighting) (default=0)
--conv <double>
Convergence threshold (relative to first score) (default=1e-8)
--conv_win <int>
Window length (number of iterations) to estimate convergence.
(default=5000)
--seed <unsigned int>
Pre-define the random number generator SEED (Mersenne Twister)
(default=random-seed from /dev/urandom)
--verb <int>
Verbosity display level (0=low, 1=medium, 2=high) (default=0)
--step <double>
Initial amplitude applied to excited modes (default=10)
--step2 <double>
Final amplitude applied to excited modes (amplitude will decrease
lineally from "step" to "step2") (default=step/10)
--rand_step
Random amplitude selection between step and step2 (default=disabled)
--nex2 <int>
Final number of excited eigenvectors, either number [1,nevs]
<integer>, or ratio [0,1) <float>. Number of excited modes will change
lineally from "nevs" to "nevs2" (default=disabled)
--rand_excited
Random number of excited modes between nex and nex2
(default=disabled)
--norand_weight
Disables random excited modes weighting (default=disabled)
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
-v, --version
Displays version information and exits.