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:
Ros,
I haven't used the Temp Fact Variance Analysis in Coot, but can guess
that the red bars indicate increased b-factor compared to the average of
your protein model?
If so, then:
*1. The lack of electronic density is the cause of these red-bars?*
Likely yes. If there is no density to support
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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
2. How do I fix them? delete the side chains?
Here we go again. Take a look at these threads
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
http://phenix-online.org/pipermail/phenixbb/2011-March/016875.html
--
Oh, suddenly throwing a giraffe into a volcano to make water is
, again for
me, is the better description of the real situation.
My 2 cents!
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Tim Gruene
Sent: Thursday, March 01, 2012 3:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Temp Fact Variance
Hi,
You could try to lower the threshold used to contour the maps for these
side-chains (middle mouse button if you have a 3 button mouse with a
wheel in the middle). Quite often such side chains have lowish electron
density that does not appear at (say) 1.0 or 1.5 sigma (in the 2mFo-DFc
Typo (my fingers type faster than my brain...)
Original Message
Subject:RE: [ccp4bb] Temp Fact Variance Analysis
Date: Thu, 1 Mar 2012 14:56:06 +
From: Oganesyan, Vaheh oganesy...@medimmune.com
To: Vellieux Frederic frederic.velli...@ibs.fr
References
Dear All:
Thank you very much for your comments.
I did not notice that this issue has been dicussed lately.
Thank you for your inputs
regards
Ros
On Thu, Mar 1, 2012 at 9:38 AM, Kelly Daughtry kddau...@bu.edu wrote:
Ros,
I haven't used the Temp Fact Variance Analysis in Coot, but can
On 01/03/12 14:26, 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,
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
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