On 04/01/2021 14:38, Silvia Napolitano wrote:
Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of 23KDa. The protein is
generally quite "loopy" and I think I am mid-way refinement.
At the moment I am struggling, among other things, with an extremely high
B-factor
I take it that you mean "extremely high average B-factor" - to which I
ask "is it though?" - and then I would ask "what of it?"
The B-factor distribution is something that is more worthy of your
attention. If you are using Coot then you can use
b_factor_distribution_graph(imol)
to see it. High (and low in the general case (but probably not for you))
outliers are of particular interest. Masmaliyeva, Babaib, Murshudov
(2020) Acta Cryst D for more on that.
and I'm not sure how to lower it.
Do you have any suggestions on how I can proceed to obtain a lower average
B-factor?
Is the calculation of the average B-factor occupancy weighted? If not,
you can use Coot to generate some waters that will bring down the
average B-factor.
First, using scripting
set_default_temperature_factor_for_new_atoms(1.5)
Then use the difference map peaks dialog and set the threshold to 1.5,
scroll to the bottom of the list. Now work your way up the list (using
",") adding waters as you go. Make a note of the start and end residue
numbers.
When you've added enough (you will probably need to add quite a few to
bring the average B-factor to less than 74.3) then use
set_occupancy_residue_range() so that the occupancy of the new waters in
the given residue range is 0.01.
(TFPIC, natch)
Paul.
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
