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SuperposeCrystals(1) Manual Page

Name

SuperposeCrystals - Determine the RMSD for crystal polymorphs using the Progressive Alignment of Crystals (PAC) algorithm.

Synopsis

SuperposeCrystals [-hrVw] [--ca] [--gc] [--ih] [--in] [--lm] [--mw] [--sm] [--st] [--ac=<excludeAtoms>] [--ac1=<excludeAtomsA>] [--ac2=<excludeAtomsB>] [--ht=-1.0] [--if=5.0] [-l=1] [--mt=0. _ 0015_] [--na=20] [--pc=0] [--ps=-1.0] [--save=-1.0] [--sc=0] [--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 is the same for both crystals.

--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).

--ca, --carbonAlphas

Consider only alpha carbons for proteins.

--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

AUs in 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).

--save=-1.0

Save structures less than or equal to this cutoff.

--sc, --saveClusters=0

Save files for the superposed crystals (1=PDB, 2=XYZ).

--sm, --saveMachineLearning

Final structures for each comparison will be written out with RMSD in a CSV.

--st, --strict

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.

--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).

Arguments

files…​

Atomic coordinate file(s) to compare in XYZ format.