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
