Dear colleagues,
An excellent opportunity is available for a Research Officer to join the Cowman
Laboratory in the Infectious Diseases and Immune Defence Division (ID2) at The
Walter & Eliza Hall Institute in Melbourne, Australia.
About the Position
The position, funded by the Gates Foundation,
Hi Derek,
you can do it in Phenix, a matter of one command or in GUI. Let me know
off-list if you need guidance.
Pavel
On Mon, Dec 16, 2024 at 6:39 AM Derek Logan <
ac2332bb2871-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi everyone,
>
> I would like to do a quick rigid-body refinement of a model
Dear Derek,
When using servalcat refine_spa_norefmac, you can:
* fix ADPs with the option --adp fix
* or set very high weight for the ADP restraints:
--adpr_weight ADPR_WEIGHT ADP restraint weight (default: 1.00)
You can also play with jelly body options:
--jellybody
Dear Saniya,
For complexes with antibodies (special case of protein-protein
complexes), you may consider the ProPlex screen and the TCR/pMHC
Optimized Protein crystallization screen.
In general, take also an (at least predicted) pI of your protein(s) into
account when selecting a screen. Your p
I've done that at 6 Å with a large X-ray structure a long while ago and
I think the trick was to define your own groups, by way of example
snipped from the .eff file:
adp {
individual {
isotropic = None
anisotropic = None
}
group_adp_refinement_mode = one_adp_group_per_residue \
Hello Derek,
You might receive more answers if you post cryoEM questions to the CCPEM list:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ccpem
Not sure why you need to refine a B-factor, at this resolution it won't tell
you much, even with only one per chain or per tetramer.
For the rigid-
Hi everyone,
I would like to do a quick rigid-body refinement of a model against a low
resolution (6 Å) cryo-EM map. The model consists of four tetramers and I want
to refine each tetramer as a rigid body, either with one (anisotropic?) ADP per
tetramer or at the most one per chain. I haven't y
Hello Saniya,
For protein-DNA complexes, the set of conditions described in this article has
been helpful in the past: https://doi.org/10.1107/S1744309112025316
You will find more info in a message I posted in a discussion from earlier this
year: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A
Searching a new PhD student for an exciting project on ubiquitin conjugation in
DNA repair. It involves biochemistry, cryo-EM, chemical biology and mass
spectrometry.
We are looking for applicants with a master degree and experience in protein
biochemistry and/or structural biology. Students
Hi 白雪慧
Initially I would try to diffract these crystals befofe any optimisation. A
microfocus beam should give you some clues. You might find out that you have a
super ordered crystal at 1.2 A resolution already, or you crystallized salt or
a contaminant.
Further, have you tried seeding? These
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