note that in Jmol you can get the average B-factor using, for example:
print {:A}.temperature.average
and also get .stddev
On Mon, Jun 27, 2011 at 11:47 AM, Thomas Stout <[email protected]>wrote:
>
> Hi Eric --
>
> I can't comment on how Jmol works out the B-factor color mapping, but I did
> want to comment on the comparing of B-factors amongst structures. The
> comparison of B-factors between structures is quite tricky. You absolutely
> CANNOT directly compare B-factors from one crystal structure to another.
> They are only valid within a single experiment. While a B-factor is
> ostensibly a "thermal parameter" and often interpretted to represent some
> measure of the "mobility" of an atom within a crystal, it is actually a
> measure of the certainty of atomic location, and in practice more of a scale
> factor. Many, many unmodeled sources of experimental error will get sopped
> up into this parameter, and it must not be construed as an absolute value.
> Within a single crystal structure, it is valid to compare B-factors since
> they have all been applied based on the same set of data and errors. Thus,
> if a loop has B-factors twice that of the core of the protein, it's pretty
> safe to say that that loop is more mobile. However, even the same
> structure, determined a second time from a second data set (all atoms being
> equal) cannot have its B-factors compared directly to those of the first
> structure since it arises from a different sample (crystal), different data
> collection and different data processing events. That said, there is a
> somewhat better argument for comparing relative B-factors between
> structures, but even that must be done with caution. For example, if you
> have two structures of the same protein in complex with different ligands
> (or, even a structure of Protein A and a site-mutant of the same protein),
> then you can reliably compare relative B-factors amongst the two
> structures... a statement like "the average B-factors of the backbone of
> loop 232-240 are 1.2X the average B-factor of structure "A", while the
> average B-factors of the backbone of loop 232-240 are 2X the average
> B-factor of structure "B"" would imply that there has been some causal
> disordering of that loop between structures "A" and "B".
>
> There is some literature out there on this, but it is probably more
> in-depth than is necessary....
>
> Cheers,
> Tom
>
>
>
> On Sun, Jun 26, 2011 at 9:01 PM, Eric Martz <[email protected]>wrote:
>
>> By experimentation, I have reached the following tentative
>> conclusions regarding the way Jmol maps colors in its
>> fixedTemperature and relativeTemperature color schemes:
>>
>> http://www.proteopedia.org/wiki/index.php/Temperature_color_schemes
>>
>> That page has several examples and buttons that allow you (via hover
>> reports: touch an atom with the mouse [don't click]) to ascertain
>> what temperature value is mapped to white.
>>
>> 1. I have been unable to deduce how Jmol determines the white value
>> for the relative temperature scheme. It is neither the average nor
>> the median temperature value. Can someone enlighten me?
>>
>> 2. Are the conclusions in my first table correct?
>>
>> 3. Are these points documented somewhere?
>>
>> 4. From the examples in my second table, comparing resolution to the
>> range and average temperature values, it appears to me that
>> temperature values or B factors are absolute, rather than relative.
>> If so, these values can be meaningfully compared between experiments.
>> Are there any crystallographers reading this who care to comment?
>>
>> Thanks, -Eric
>>
>>
>>
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>
>
>
> ------------------------------------------------------------------------------
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> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
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