Force Field XSuperposeCrystals(1)
Synopsis
SuperposeCrystals [-hrVw] [--as] [--ca] [--cd] [--gc] [--ih] [--in] [--lm] [--mw] [--sm] [--th] [--ws] [--ac=<excludeAtoms>] [--ac1=<excludeAtomsA>] [--ac2=<excludeAtomsB>] [--ht=-1.0] [--if=5.0] [-l=1] [--mt=0.0015] [--na=20] [--pc=0] [--ps=-1. _ 0_] [-s=-1.0] [--sc=0] [--st=0.5] [--zp=-1] [--zp1=-1] [--zp2=-1] files…
Description
Determine the RMSD for crystal polymorphs using the Progressive Alignment of Crystals (PAC) algorithm.
Options
- --ac, --alchemicalAtoms=<excludeAtoms>
- Atom indices to be excluded from both crystals (e.g. 1-24,32-65). Use if molecular identity and atom ordering are the same for both crystals (otherwise use "--ac1" and "--ac2".
- --ac1, --alchemicalAtoms1=<excludeAtomsA>
- Atom indices to be excluded in the first crystal (e.g. 1-24,32-65).
- --ac2, --alchemicalAtoms2=<excludeAtomsB>
- Atom indices to be excluded in the second crystal (e.g. 1-24,32-65).
- --as, --autoSymmetry
- Automatically generate symmetry operators.
- --ca, --carbonAlphas
- Consider only alpha carbons for proteins.
- --cd, --createDirectories
- Create subdirectories for free energy simulations.
- --gc, --gyrationComponents
- Display components for radius of gyration for final clusters.
- -h, --help
- Print command help and exit.
- --ht, --hitTolerance=-1.0
- Sum comparisons that attain a value lower than this tolerance.
- --if, --inflationFactor=5.0
- Inflation factor used to determine replicates expansion (IF * nAU in replicates).
- --ih, --includeHydrogen
- Include hydrogen atoms.
- --in, --inertia
- Display moments of inertia for final clusters.
- -l, --linkage=1
- Single (0), Average (1), or Complete (2) coordinate linkage for molecule prioritization.
- --lm, --lowMemory
- Reduce memory usage at the cost of efficiency.
- --mt, --moleculeTolerance=0.0015
- Tolerance to determine if two AUs are different.
- --mw, --massWeighted
- Use mass-weighted atomic coordinates for alignment.
- --na, --numAU=20
- Number of asymmetric units included to calculate the RMSD.
- --pc, --prioritizeCrystals=0
- Prioritize crystals based on high density (0), low density (1), or file order (2).
- --ps, --printSymOp=-1.0
- Print optimal SymOp to align input crystals (print out atom deviations above value).
- -r, --restart
- Restart from a previously written RMSD matrix (if one exists).
- -s, --save=-1.0
- Save structures less than or equal to this cutoff.
- --sc, --saveClusters=0
- Save files for the superposed crystal clusters (1=PDB, 2=XYZ).
- --sm, --saveMachineLearning
- Final structures for each comparison will be written out with RMSD in a CSV.
- --st, --symTolerance=0.5
- Add atoms to torsion based symmetries that are beneath this cutoff.
- --th, --thorough
- More intensive, less efficient version of PAC.
- -V, --version
- Print the Force Field X version and exit.
- -w, --write
- Write out the PAC RMSD matrix.
- --ws, --writeSym
- Write the created symmetry operators in the corresponding Properties/Key file.
- --zp, --zPrime=-1
- Z'' for both crystals (assumes same value).
- --zp1, --zPrime1=-1
- Z'' for crystal 1 (default will try to autodetect).
- --zp2, --zPrime2=-1
- Z'' for crystal 2 (default will try to autodetect).