Dear Liu,
If you are really confident in your MR solution some good tools to refine low
resolution structures are LORESTR pipeline and iSOLDE software.
Best.
Michel.
> Le 21 nov. 2023 à 13:03, Yahui Liu a écrit :
>
>
> Dear all,
> I got a protein crystal dataset of 4.3 A and would like to
Not sure if it's been mentioned that NCS can help a lot at that resolution. We
did some mutants derived from a 2 Angstrom native structure at about that
resolution with 4-fold NCS and the maps were quite convincing, well, I thought
anyway. That was in the days of RESTRAIN which, I think, had an
Also forget to observe side chains at 4A! At this resolution is crucial
to critically assess the position of each amino acid in your model,
taking into account factors such as hinges in your structure,
hydrophobic and hydrophilic regions, and the types of contacts between
secondary structure
Hello,
At low resolutions, model bias becomes a significant issue, capable of
yielding inaccurate MR solutions even with favorable figures of merit.
In my experience, it is always necessary to validate MR solutions at low
resolution. One effective approach involves systematically omitting
Q0. Echoing Randy - how accurate is your starting model - Xray structure at
resolution 1.5A or high quality EM or NMR??
Q1. Are the solutions the same? There is a CCP4 tool in ccp4i2 - Match my
model which will check this taking into account symmetry and origin shifts.
On Tue, 21 Nov 2023 at
Hi,
Whether or not you’ll get anything useful from a 4.3 A MR solution depends on
your question — maybe you’re interested in something large-scale like complex
formation or domain movement, in which case it could tell you something.
In any case, it’s important to have a good starting model.
.AC.UK>
Assunto: Re: [ccp4bb] low resolution data refinement
On 21/11/2023 12:02, Yahui Liu wrote:
>
> Dear all,
> I got a protein crystal dataset of 4.3 A and would like to some the
> structure with MR.
> Now I am suffering with the refinement.
Just for the record, then inten
On 21/11/2023 12:02, Yahui Liu wrote:
Dear all,
I got a protein crystal dataset of 4.3 A and would like to some the
structure with MR.
Now I am suffering with the refinement.
Just for the record, then intention of refinement is not to make you suffer.
Paul.
Sorry - the simplest answer - is get higher resolution data!
But there are some improvements possible.
How clear is your MR solution.
What is the similarity between model and your sequence?
Etc.
On Tue, 21 Nov 2023 at 12:03, Yahui Liu wrote:
> Dear all,
> I got a protein crystal dataset of 4.3
Dear all,
I got a protein crystal dataset of 4.3 A and would like to some the
structure with MR.
Now I am suffering with the refinement. I used both Refmac and Phenix.
Someone could give me a hand or any suggestions?
All the best
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