Dear all,
Thank you very much for all of your suggestions and sharing experiences.
As many of you commented, the current small unit cell C2 refinement seems to be
incorrect or correct, and I should put some efforts to crack this question.
- To Phill Jeffrey,
The idea, trying to find high symmet
Excellent!
And now you can test Xtal averaging with models??
Eleanor
On Thu, 10 Jan 2019 at 12:38, Andrew Lovering wrote:
> Dear all,
>
>
>
> Thanks to Vincent, Eleanor, herman and others! It turns out I’ve managed
> to sort it out a different way – the initial TFZ of 10 with cutout density
> a
For two projects in the distant past, we dealt with tNCS by initially telling
lies to the software (1szp and 3pkz). The tNCS was strong enough that there
was a clear weak/dark pattern in the diffraction pattern, so for the initial
molecular replacement we used a data set in the smaller unit cel
On Thursday, January 10, 2019 2:11:52 AM PST Donghyuk Shin wrote:
> Dear all,
>
> I am having tough time with my Xtal data sets those seem to be twinned or
> have translational NCS, and it will be greatly appreciated if you can give me
> some advices or comments!
>
> Data was initially processe
Donghyuk
The combination of two things gives me cause for concern:
1. You've reindexed something that apparently scaled OK in point group
622 into point group 2, with a smaller cell. Since it's hard to fake
that sort of data agreement in 622, I assume your data is at the very
least pseudo-62
Dear Donghyuk,
Unfortunately, everything is possible when NCS, twinning etc. get into the
game. I do not have answers, but some questions for you to think about:
- Do you really have 6 twinning operators, or only one operator and are the
other operators generated by (non)crystallographic symmetr
Dear Jacob Keller and Vipul,
Thank you both very much for the reply.
Regarding the R-values, I am just wondering whether the huge gap between
refinements w/ w/o twin operator can be possible even the crystal is not
twinned?
Best wishes,
Donghyuk
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>>I feel you went ahead with right strategy.
I agree with this part regarding lowering symmetry.
>>For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong
>>indicator, i believe.
This is not true—even non-twinned data will improve in R values with twinning
operators added as parame
Dear all,
Thanks to Vincent, Eleanor, herman and others! It turns out I've managed to
sort it out a different way - the initial TFZ of 10 with cutout density and
resultant map was a bit underwhelming and indicative of an issue - so I cut my
~140ang long molecule in half and searched with densit
Hi Donghyuk,
I feel you went ahead with right strategy.
For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong
indicator, i believe.
If you have already build all possible model, using tls can be of further
help.
Cheers,
Vipul
On Thu 10 Jan, 2019, 3:52 PM Donghyuk Shin Dear all,
Dear Andy,
for the I222 crystal, you mention a large difference in diffracting
resolution, but staraniso doesn't help. Maybe you simply don't have
anisotropy, but rather lack of completeness in high resolution shells, a
different problem. How much is the anisotropy value given by Phaser?
I g
Ok - small oversight - I can see now that phenix has the atoms placed/saved
during cutout stage - so how best to use PHASER output to shift this file?
Andy
From: Andrew Lovering (School of Biosciences)
Sent: 10 January 2019 10:48
To: 'ccp4bb@jiscmail.ac.uk'
Subject: RE: complex multi-crystal ave
Thanks everyone for the pointers. I should clarify - my issue here is the
multiple stage "disconnect" between PDB in xtal1 -> cutout density (into a
"interim cell" just for this stage) -> phaser MR with density search model into
xtal2
Hence, do I just simply pop the model from (1) into the "int
Dear colleagues,
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