Hi Dialing,
if you know some python you can use PyMOL.
# get C-alpha b-factors as list
from pymol import cmd, stored
stored.bfactors = []
cmd.iterate('name CA', 'stored.bfactors.append((b,resv))')
# min/max b-factors with residue number
print min(stored.bfactors)
print max(stored.bfactors)
# data for plotting
x = [resv for (b,resv) in stored.bfactors]
y = [b for (b,resv) in stored.bfactors]
# plot to a pdf file with matplotlib
from matplotlib.pyplot import figure
from matplotlib.backends.backend_pdf import PdfPages
fig = figure()
sub = fig.add_subplot(111)
sub.plot(x, y)
pp = PdfPages('bfactors.pdf')
fig.savefig(pp, format='pdf')
pp.close()
Hope that helps.
Cheers,
Thomas
On 02/22/2012 05:04 AM, Dialing Pretty wrote:
Dear All,
Will you please tell me a server of software which can draw a curve for
the B factor of the atoms in a protein PDB file from the first residue
to the residue?Or a server or software by which we can easily order the
B factors of the atoms in the PDB file according to the B factor in
decrease or in increase? Or to get the residues with the highest B
factor and the lowest B factor?
Cheers,
Dialing
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
