the “Wilson
B-factor” of the calculated intensities and compare this to the observed Wilson
B-factor.
My 2 cts, Herman
Von: CCP4 bulletin board Im Auftrag von Edward Berry
Gesendet: Mittwoch, 8. April 2020 03:52
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Average B factors with TLS
Apologies for my previous email appearing to put words in Dale's mouth- I'm
using my school's
webmail and it apparently doesn't indicate the quoted text.
The following is what I added:
I think it is not just that the distribution is asymmetric and limited to
positive numbers-
it is due to
>>> Dale Tronrud 04/07/20 12:37 PM >>>
This topic has been discussing on the BB many times and a little
searching should give you some long-winded answers (some written by me).
The short version. If you refine a model with a common B factor for
all atoms, or keep a very narrow distribu
On Tuesday, 7 April 2020 05:16:58 PDT Nicholas Keep wrote:
> I am at the point of depositing a low resolution (3.15 A) structure
> refined with REFMAC. The average B factors were 31 before I added the
> TLS contribution as required for deposition which raised them to 157-
> this is flagged as a
This topic has been discussing on the BB many times and a little
searching should give you some long-winded answers (some written by me).
The short version. If you refine a model with a common B factor for
all atoms, or keep a very narrow distribution of B's, you will end up
with an average
Hi - I think it has to be the high ones - TLS "B" values are only relative
to the overall TLS set.
what happens to the B values if you do refinement without TLS?
Eleanor
On Tue, 7 Apr 2020 at 13:17, Nicholas Keep
wrote:
> I am at the point of depositing a low resolution (3.15 A) structure
> r
I am at the point of depositing a low resolution (3.15 A) structure
refined with REFMAC. The average B factors were 31 before I added the
TLS contribution as required for deposition which raised them to 157-
this is flagged as a problem with the deposition, although this did not
stop submssion
This is quite straightforward in any package with a reasonable scripting
interface. In ChimeraX, for example:
-load your model
-make your selection
(https://www.rbvi.ucsf.edu/chimerax/docs/user/selection.html)
-open the shell (Tools/General/Shell), and in it, type:
from chimerax.core.atomic i
Easy with GUI2
Import coordinates and select the part you want
Under validation and analysis
Choose analysis Bs etc and you will get your answer
BAVERAGE will give you Bs for main chain & side chain for each monomer but
there is no selection option - you would have to do that in some other way
Dear all,
Sorry for naive CCP4 question, is there a simple way to calculate average
B-factors (side chain, backbone, all)
for only part of a model, such as a domain, loop, etc…
Thanks,
Amir
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