Hard to know for sure - I often set occ to 0.0, then redo refinement and
maps, only to find they have reappeared in the density at a low level.. In
the end all our models are defective - LYS and ARg and GLU etc often have
alternate conformations which we cant model at low resolution, and the
temperature factor gives an indication that that is so..
But remember - any atom with B = 60 is going to be more spread out than one
with B = 20, and you need to drop the contour level when you assess the
high B factor structure..
Eleanor
On Mar 1 2012, Tim Gruene wrote:
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>Dear Ros,
>
>yes, the lack of electron density is most likely the cause the these red
>bars (unless you set the map level rather high, but at the default
>chosen by coot that should be fine).
>
>yes - if you don't see electron density you don't have experimental
>evidence of the atom positions, so it is best to delete them.
>
>Tim
>
>On 03/01/2012 03:26 PM, Uma Ratu wrote:
>> Hello,
>>
>> I run my model in Coot to do "Temp Fact Variance Analysis".
>> There are red bars from the B-factor Variance graphy.
>> I click each red bar to exam the residues in Coot. Many of these residues
>> do not have the electronic density on their side chains, especially Lys
>> residues.
>>
>> Here is my questions:
>>
>> 1. The lack of electronic density is the cause of these red-bars?
>> 2. How do I fix them? delete the side chains?
>>
>> The diffraction data is 2A, and data completness is 98.8%.
>>
>> Thank you for comments
>>
>> Ros
>>
>
>- --
>- --
>Dr Tim Gruene
>Institut fuer anorganische Chemie
>Tammannstr. 4
>D-37077 Goettingen
>
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--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
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