allowed for some small difference in orientation of the
> monomers within the dimer.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Satvik Kumar
> *Gesendet:* Mittwoch, 20. September 2017 14:40
> *An:* CCP4
] doubt regarding MR search model
Hello,
Thanks all for your valuable suggestions. Two things that stuck me were "one
gets to know if the space group is correct only after solving the structure"
and "to try all possible space groups until one lands up with the correct
solution".
I
Hello,
Thanks all for your valuable suggestions. Two things that stuck me were "one
gets to know if the space group is correct only after solving the
structure" and "to try all possible space groups until one lands up with
the correct solution".
I ran Phaser with "all alternative space groups".
Well - you haven't said what the sequence identity between model and your
protein is, nor if you have a non-crystallographic translation.
With low homology that R factor drop is acceptable and rebuilding can fix
it, However if there is high homology you might expect better.
But this sort of
With Rs of 43/48% I don't think you can be sure that your spacegroup is right.
You should always try all the spacegroup possibilities until you get a solution
you are sure is right, i.e. that refines to Rs of around 35% or preferably even
lower.
More so in the case of screw axes, so try P222,
luck!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Satvik
Kumar
Gesendet: Dienstag, 19. September 2017 16:02
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] doubt regarding MR search model
Hello,
Thanks everyone for your explanations.
I have pasted the pointless
Hello,
Thanks everyone for your explanations.
I have pasted the pointless output to provide more information.
Best Solution: space group P 21 21 21
Laue group probability: 0.959
Systematic absence probability: 0.818
Total probability:
Dear Emily,
In this case, I was referring to the difference between 1065 obtained placing 4
copies of the monomer and 722 obtained placing 2 copies of the dimer. A
difference of over 300 is substantial when we feel that an increase of 60 is
enough to be reasonably convinced that a solution
Hello Randy,
I'm chiming in about the last sentence in your reply:
> Finally, I would suspect that getting a significantly lower LLG for two
> copies of a dimer means that the dimer in your structure is slightly
> different from the dimer in the model.
>
Will you please be more specific about
Yes, I can see how that message would be confusing!
This comes from a new feature. Phaser now does a relatively liberal packing
test as part of rescoring the fast translation results with the full likelihood
function. Peaks that are rejected at this stage aren’t counted for the top
peak
Regarding the warning message "The top solution from a TF rescoring did not
pack”, I get this on all the PHASER jobs that I have run recently, but looking
through the PHASER log file I cannot see any evidence for packing failure.
It may be that the failure is buried in an obscure place in the
You need to provide a bit more information.
First of all about the data processing..
Is the space group correct?
ways of being misled are:
Non-crystallographic translations with a shift of ~0.5 along an axis - say
a. This will generate absences in the odd h 0 0 reflections and can make
the
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