Eric, just to follow up on this:
$ load "C:/jmol-dev/workspace/Jmol/bobtest/2bxa"
TRANSPORT PROTEIN 26-JUL-05 2BXA
HUMAN SERUM ALBUMIN COMPLEXED WITH 3-CARBOXY-4-METHYL-5-
PROPYL-2-FURANPROPANOIC ACID (CMPF)
$ print {*}.temperature%1
68.6
$ select *
8,664 atoms selected
$ color temperature
$ select color = "white"
306 atoms selected
$ print {selected}.temperature.min
81.81
$ print {selected}.temperature.max
86.15
$ print {*}.temperature.min
16.45
$ print {*}.temperature.max
151.5
$ print (151.5 + 16.45)/2
83.975
So I think you can see there that white is right in the middle between the
two extremes.
Note that you could certainly use white for the average. You would just have
to figure out what range you wanted and then color those atoms white.
Bob
On Mon, Jun 27, 2011 at 6:29 PM, Robert Hanson <[email protected]> wrote:
> it's just a straight scale from on end to the other. No weighting.
>
>
> On Sun, Jun 26, 2011 at 11:01 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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>
>
>
> --
> 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
>
--
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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