: [ccp4bb] Lower b-factors with increasing T
I guess the big question is what is the question that you’re trying to address
from those numbers? I’d be nervous about making conclusions about trends in B
factors from just 1 data set per temperature. As you probably know, the B
factors will reflect
Cool, typed a long reply but only about 1/3 of it is still relevant and is
given below.
The crystal would have to be capillary mounted for these data collections or
the humidity controlled somehow. Only 253 K would be a good one to use.
Pre-cryo, this used to give good data at SRS! Interested i
Hi all,
This is my first JISC post so I am still working on how to navigate this. I
have to say I feel like there is a much better way to have a forum on
structural biology... I could imagine a discord server where we can post
individual questions, have live chats, etc. I'd be happy to set th
Hmmm - very puzzling..
One expects the for the atoms to more or less match the Wilson B for
the data sets..
There are some mini bugs which can mislead you.
Is your average a mean or an RMS value? RMS ones can be hugely inflated if
you have a few crazily high Bs and the refinement programs can out
Hi Graeme
good to know that I haven’t forgotten everything.
Rgarding the data collection - I don’t think the OP mentioned how many crystals
were used in the data collection (unless, of course, I’ve been reading even
less carefully than normal…).
Harry
> On 8 Sep 2022, at 10:29, Winter, Graeme
Hi Harry,
You’re not wrong - “conventional wisdom” these days is pointing to CC of about
0.3 but I suspect that the difference is pretty modest in general
However, in the case, the difference could have an impact as the higher
resolution reflections may have something to say about the overall B
hi folks
I’ve been away from data processing for a while, but am I alone in thinking
that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of useful data? I
seem to remember that AutoProc and xia2.multiplex use a default of >= 0.3.
Harry
> On 7 Sep 2022, at 19:46, Matt McLeod wrote:
>
>
ard on behalf of Phoebe
A. Rice
*Sent:* Thursday, September 8, 2022 10:48 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Lower b-factors with increasing T
I guess the big question is what is the question that you’re trying to
address from those numbers? I’d be nervous about making conclusi
Hi Matt,
You mention that you process with DIALS - one thing I would recommend is
scaling all the data together then merging each temperature point separately -
I could do with preparing a HOWTO on this [1] - this would then mean that they
are being scaled to be as similar as possible before yo
temperature (which I also
> > think is a little strange and I don't have an explanation).
> > cheers, tom
> > --
> > *From:* CCP4 bulletin board on behalf of Phoebe
> > A. Rice
> > *Sent:* Thursday, September 8, 2022 10:48 AM
>
ent:* Thursday, September 8, 2022 10:48 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Lower b-factors with increasing T
>
>
> I guess the big question is what is the question that you’re trying to
> address from those numbers? I’d be nervous about making conclusions abo
of Matt McLeod
Date: Wednesday, September 7, 2022 at 1:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Lower b-factors with increasing T
Hi everyone,
I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K
(2.2A) and I am curious as to the details in determining B-factors.
: Wednesday, September 7, 2022 at 1:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Lower b-factors with increasing T
Hi everyone,
I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K
(2.2A) and I am curious as to the details in determining B-factors.
I have treated
On Wed, Sep 7, 2022 at 11:57 AM Matt McLeod wrote:
> Hi everyone,
>
> I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A),
> 313K (2.2A) and I am curious as to the details in determining B-factors.
>
In the larger physical universe those temperatures are not very far apart.
I
In addition, I computed the wilson B.s
253 - 41
273 - 35.4
293 - 36.5
313 - 0.19
Looks like there is definitely an issue with the data scaling. Still looking
for suggestions as to what to tweak.
Matt
To unsubscribe from
Hi everyone,
I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), 313K
(2.2A) and I am curious as to the details in determining B-factors.
I have treated these datasets more-or-less identically for comparison's sake.
I used DIALS to index, integrate, and scale the data. I sc
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