Biological Units Construction
Construct biological assemblies/units based on a 'pdb' object.
biounit(pdb, biomat = NULL, multi = FALSE, ncore = NULL)
pdb |
an object of class |
biomat |
a list object as returned by |
multi |
logical, if TRUE the biological unit is returned as a
'multi-model' |
ncore |
number of CPU cores used to do the calculation. By default
( |
A valid structural/simulation study should be performed on the biological unit of a protein system. For example, the alpha2-beta2 tetramer form of hemoglobin. However, canonical PDB files usually contain the asymmetric unit of the crystal cell, which can be:
One biological unit
A portion of a biological unit
Multiple biological units
The function performs symmetry operations to the coordinates based on the
transformation matrices stored in a 'pdb' object returned by
read.pdb, and returns biological units stored as a list of
pdb objects.
a list of pdb objects with each representing an individual
biological unit.
Xin-Qiu Yao
# PDB server connection required - testing excluded
pdb <- read.pdb("2dn1")
biounit <- biounit(pdb)
pdb
biounit
## Not run:
biounit <- biounit(read.pdb("2bfu"), multi=TRUE)
write.pdb(biounit[[1]], file="biounit.pdb")
# open the pdb file in VMD to have a look on the biological unit
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.