plot.enma. bio3d 2.3-0

Usage

"plot"(x, pdbs = NULL, xlab = NULL, ylab="Fluctuations", ...)

Arguments

x: the results of ensemble NMA obtained with nma.pdbs. Alternatively, a matrix in the similar format as enma$fluctuations can be provided.
pdbs: an object of class ‘pdbs’ in which the ‘enma’ object x was obtained from. If provided SSE data of the first structure of pdbs will drawn.
xlab: a label for the x axis.
ylab: labels for the y axes.
...: extra plotting arguments passed to plot.fluct that effect the atomic fluctuations plot only.

Description

Produces a plot of atomic fluctuations of aligned normal modes.

Details

plot.enma produces a fluctuation plot of aligned nma objects. If corresponding pdbs object is provided the plot contains SSE annotation and appropriate resiude index numbering.

Value

Called for its effect.

References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
raw.files <- get.pdb(ids, path = "raw_pdbs")

Warning message:
raw_pdbs/1a70.pdb  exists. Skipping download
Warning message:
raw_pdbs/1czp.pdb  exists. Skipping download
Warning message:
raw_pdbs/1frd.pdb  exists. Skipping download
Warning message:
raw_pdbs/1fxi.pdb  exists. Skipping download
Warning message:
raw_pdbs/1iue.pdb  exists. Skipping download
Warning message:
raw_pdbs/1pfd.pdb  exists. Skipping download
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")


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


## Sequence/structure alignement
pdbs <- pdbaln(files)

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

Extracting sequences

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


## Normal mode analysis on aligned data
modes <- nma(pdbs)


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 


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


## Plot fluctuations
plot(modes, pdbs=pdbs)

Extracting SSE from pdbs$sse attribute

## Group and spread fluctuation profiles
hc <- hclust(as.dist(1-modes$rmsip))


col <- cutree(hc, k=2)
plot(modes, pdbs=pdbs, col=col, spread=TRUE)

Extracting SSE from pdbs$sse attribute

Author

Lars Skjaerven, Barry Grant

Plot eNMA Results