Server or software for B factor analysis

From: Dialing Pretty
Date: 22 February 2012 04:04

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

----------
From: Pavel Afonine

Hi Dialing,

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?

I know one, you can do it in Excel (it is not Phenix !).

Hope this helps,

Pavel

 

----------
From: Thomas Holder

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

--
Thomas Holder

----------
From: chen c


Why not just use PROCHECK program?

在 2012年2月22日 下午6:24，Thomas Holder  写道：

--
Cheng Chen, Ph.D. Candidate

北京市海淀区清华大学生命科学馆201-212室
邮编：100084

----------
From: Gerard DVD Kleywegt


MOLEMAN2 is your friend.

Stats: http://xray.bmc.uu.se/usf/moleman2_man.html#S50

Plots: http://xray.bmc.uu.se/usf/moleman2_man.html#S57

--dvd

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?