aanma.pdbs. bio3d 2.3-0

Usage

"aanma"(pdbs, fit = TRUE, full = FALSE, subspace = NULL, rm.gaps = TRUE, ligand = FALSE, outpath = NULL, gc.first = TRUE, ncore = NULL, ...)

Arguments

pdbs: an ‘pdbs’ object as obtained from read.all.
fit: logical, if TRUE C-alpha coordinate based superposition is performed prior to normal mode calculations.
full: logical, if TRUE return the complete, full structure, ‘nma’ objects.
subspace: number of eigenvectors to store for further analysis.
rm.gaps: logical, if TRUE obtain the hessian matrices for only atoms in the aligned positions (non-gap positions in all aligned structures). Thus, gap positions are removed from output.
ligand: logical, if TRUE ligand molecules are also included in the calculation.
outpath: character string specifing the output directory to which the PDB structures should be written.
gc.first: logical, if TRUE will call gc() first before mode calculation for each structure. This is to avoid memory overload when ncore > 1.
ncore: number of CPU cores used to do the calculation.
...: additional arguments to aanma.

Value

fluctuations: a numeric matrix containing aligned atomic fluctuations with one row per input structure.
rmsip: a numeric matrix of pair wise RMSIP values (only the ten lowest frequency modes are included in the calculation).
U.subspace: a three-dimensional array with aligned eigenvectors (corresponding to the subspace defined by the first N non-trivial eigenvectors (‘U’) of the ‘nma’ object).
L: numeric matrix containing the raw eigenvalues with one row per input structure.
full.nma: a list with a nma object for each input structure (available only when full=TRUE).

Description

Perform normal mode analysis (NMA) on an ensemble of aligned protein structures using all-atom elastic network model (aaENM).

Details

This function builds elastic network model (ENM) using all heavy atoms and performs subsequent normal mode analysis (NMA) on a set of aligned protein structures obtained with function read.all. The main purpose is to automate ensemble normal mode analysis using all-atom ENMs.

By default, the effective Hessian for all C-alpha atoms is calculated based on the Hessian built from all heavy atoms (including ligand atoms if ligand=TRUE). Returned values include aligned mode vectors and (when full=TRUE) a list containing the full ‘nma’ objects one per each structure. When ‘rm.gaps=TRUE’ the unaligned atoms are ommited from output. With default arguments ‘rmsip’ provides RMSIP values for all pairwise structures.

When outmodes is provided and is not ‘calpha’ (e.g. ‘noh’. See aanma for more details), the function simply returns a list of ‘nma’ objects, one per each structure, and no aligned mode vector is returned. In this case, the arguments full, subspace, and rm.gaps are ignored. This is equivalent to a wrapper function repeatedly calling aanma.

Examples


  # Needs MUSCLE installed - testing excluded

    ## Fetch PDB files and split to chain A only PDB files
    ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
    files <- get.pdb(ids, split = TRUE, path = tempdir())


  |======================================================================| 100%

    
    ## Sequence Alignement
    aln <- pdbaln(files, outfile = tempfile())

Reading PDB files:
/tmp/RtmpTDihxb/split_chain/1a70_A.pdb
/tmp/RtmpTDihxb/split_chain/1czp_A.pdb
/tmp/RtmpTDihxb/split_chain/1frd_A.pdb
/tmp/RtmpTDihxb/split_chain/1fxi_A.pdb
/tmp/RtmpTDihxb/split_chain/1iue_A.pdb
/tmp/RtmpTDihxb/split_chain/1pfd_A.pdb
.   PDB has ALT records, taking A only, rm.alt=TRUE
.....

Extracting sequences

pdb/seq: 1   name: /tmp/RtmpTDihxb/split_chain/1a70_A.pdb 
pdb/seq: 2   name: /tmp/RtmpTDihxb/split_chain/1czp_A.pdb 
   PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 3   name: /tmp/RtmpTDihxb/split_chain/1frd_A.pdb 
pdb/seq: 4   name: /tmp/RtmpTDihxb/split_chain/1fxi_A.pdb 
pdb/seq: 5   name: /tmp/RtmpTDihxb/split_chain/1iue_A.pdb 
pdb/seq: 6   name: /tmp/RtmpTDihxb/split_chain/1pfd_A.pdb 

    
    ## Read all pdb coordinates
    pdbs <- read.all(aln)

    ## Normal mode analysis on aligned data
    modes <- aanma(pdbs, rm.gaps=TRUE)

Fitting pdb structuresdone

Details of Scheduled Calculation:
  ... 6 input structures 
  ... storing 282 eigenvectors for each structure 
  ... dimension of x$U.subspace: ( 288x282x6 )
  ... coordinate superposition prior to NM calculation 
  ... aligned eigenvectors (gap containing positions removed)  
  ... estimated memory usage of final 'eNMA' object: 3.7 Mb 


    
    ## Plot fluctuation data
    plot(modes, pdbs=pdbs)

Extracting SSE from pdbs$sse attribute
    
    ## Cluster on Fluctuation similariy
    sip <- sip(modes)


    hc <- hclust(dist(sip))
    col <- cutree(hc, k=3)
    
    ## Plot fluctuation data
    plot(modes, pdbs=pdbs, col=col)

Extracting SSE from pdbs$sse attribute

    
    ## RMSIP is pre-calculated
    heatmap(1-modes$rmsip)


    
    ## Bhattacharyya coefficient
    bc <- bhattacharyya(modes)

Calculating covariance matrices
Calculating pairwise bhattacharyya coefs

    heatmap(1-bc)

Author

Xin-Qiu Yao & Lars Skjaerven

Ensemble Normal Mode Analysis with All-Atom ENM