James,
Thank you for your help.
I appreciate the very thorough explanation. I have never heard of noise
although I have produced a 'kicked' map in phenix and refined the
structure using those maps..though I guess this is different. I will try
it. Thanks.
-Yarrow
Formally, the best way to
Formally, the best way to compare B factors in two structures with
different average B is to add a constant to all the B factors in the
low-B structure until the average B factor is the same in both
structures. Then you can compare apples to apples as it were. The
extra B being added is
You only entertain addition+subtraction--why not use
multiplication/division to normalize the b-factors?
JPK
On Mon, Mar 4, 2013 at 2:04 PM, James Holton jmhol...@lbl.gov wrote:
Formally, the best way to compare B factors in two structures with
different average B is to add a constant to all
Yep, I agree calculate the average B per structure and divide each B by this
value, then multiply it by any value that is reasonable so you can visualize
color differences :-)
Jürgen
On Mar 4, 2013, at 2:16 PM, Jacob Keller wrote:
You only entertain addition+subtraction--why not use
Good point; I've tested this (n=1) in the past with a high-resolution
dataset (synchrotron data) and low-resolution dataset (in-house) of
crystals of the same protein grown in the same drop. Same space group,
same unit cell. B-factors for the low-resolution dataset were higher.
After dividing
No, you can only add and subtract B values because that is
mathematically equivalent to multiplication in reciprocal space (which
is equivalent to convolution in real space):
exp(-B1*s^2) * exp(-B2*s^2) = exp(-(B1+B2)*s^2)
Multiplying and dividing B values is mathematically equivalent to
Seriously?
I believe this specific forum has become quicksand rather than a useful tool.
Normalization based simply on ratios of one struct to the other should allow
normalization. Correct?, or have I just simply lost my mind here?
J
John Fisher, M.D./PhD
St. Jude Children's Research Hospital
Perhaps I was a bit gruff, but what I was trying to do was throw out a
voice of caution. In crystallography, it is very tempting to
normalize everything by setting the mean to zero and the RMS
deviation to one, but this is a linear transformation, and linear
transformations only work when the
Hello,
Does anyone know a good method to compare B-factors between structures? I
would like to compare mutants to a wild-type structure.
For example, structure2 has a higher B-factor for residue X but how can I
show that this is significant if the average B-factor is also higher?
Thank you for
Hello,
Does anyone know a good method to compare B-factors between structures? I
would like to compare mutants to a wild-type structure.
For example, structure2 has a higher B-factor for residue X but how can I
show that this is significant if the average B-factor is also higher?
Thank you for
Why not normalize each to its average b-factor? And...maybe they are not
significantly different in the first place?
JPK
On Mon, Feb 25, 2013 at 3:08 PM, Yarrow Madrona amadr...@uci.edu wrote:
Hello,
Does anyone know a good method to compare B-factors between structures? I
would like to
Thanks Nat,
I was planning on plotting B-factors vs. residue anyway, so maybe this
will save me time. I will take a look.
-Yarrow
Not a CCP4 solution, but the structure comparison program in the
Phenix GUI will plot B-factors for different structures of the same
protein. (I am happy to make
Thank you Manfred,
To be honest I have tried to understand the Pearson linear CC since
reading the nature crystallography methods paper by Karplus and
diederichs, but I am having trouble. I do not clearly understand what it
represents. Do you know any good resources that could help me out?
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How to compare B-factors between structures?
Thanks Nat,
I was planning on plotting B-factors vs. residue anyway, so maybe this will
save me time. I will take a look.
-Yarrow
Not a CCP4 solution, but the structure comparison program
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