which retain
> data and = 2 as the nominal resolution of the dataset. If you have
> the HKL2000 scaling log, you should be able to retrieve this information. I
> frankly wish we’d just deposit all data in the PDB rather than truncate
> based on some criterion or another.
>
>
>
> Best,
> -Original Message-
> From: CCP4 bulletin board On Behalf Of Matt McLeod
> Sent: Wednesday, April 17, 2024 3:04 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Rescale merged data?
>
> Hi all,
>
> I am looking at a old students data and it looks like they didn'
Hi all,
I am looking at a old students data and it looks like they didn't properly cut
off the data during scaling. All of the files I have appear to be the merged
.sca (or mtz after converting with scalepacktomtz) - is there a way to
retruncate the data after merging or do I have to
Hi all,
Has any heard of or has ideas on how to view a sample after being plunged in
liquid nitrogen but while still under LN2?
Thanks!
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Hi all,
Im wondering about occupancy refinements - both what's going on under the hood
and what are best practices.
In the example I have, there is a ligand found in two distinct, partially
overlapping sites that can be modeled is some confidence, but likely there are
very low occupancy
nformation unless there was some
> feature in an earlier map to suggest it existed?
> Good luck Eleanor
>
>
> On Wed, 6 Sept 2023 at 03:18, Pavel Afonine wrote:
>
>> Hi Matt,
>> I believe figure 3 here:
>> https://www.nature.com/articles/s41467-018-06957-w
>> is rele
Hi all,
I am trying to get some insight in the accuracy/precision of occupancy
refinements. I have done some 2-state occupancy refinements and have observed
the refinement achieving ~0.25-0.3 occupancy for the minor population. This
population, when observing the electron density maps, had
Hi all,
I have a lot of large datasets that I want to screen to determine if there are
one or two lattices in the diffraction. I was wondering if there was a simple
and quick way to do so.
Currently, I am processing with DIALS and getting to the indexing where the
percent indexed indicates
Hi all,
I have been refining a structure and somehow along the way the residue numbers
have completely shifted. For instance, the first section of residues are
shifted by say 8 numbers, then there is a gap from where the resnumbers go from
121, 151, 152, 153...and so on. Its quite the mess.
Hey everyone,
Thanks for all the suggestions there are a few different things I can try now.
The data is very aniosotropic (STARANISO might help) in regards to how the
crystal diffracts and I think changing the bin size will help specifically with
PAIREF (its an warning so it completes the
Hi all,
I am having a bit of trouble with PAIREF. I am trying to determine the
resolution cutoff of a dataset which has a high Rwork (0.223)/free (0.275)value
for the resolution (2.24A). I have truncated this data further to 2.4A and the
R values get better but the electron density maps do
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
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
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
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