All,
Please join us on Wednesday, September 21, 2022 at 9:00am (PDT), 12:00pm
(EDT), 6:00pm (CEST) for a webinar by Michael Grange (The Rosalind Franklin
Institute) and Alexander Rigort (Thermo Fisher). They will present recently
published results.
Webinar will be able be available to watch
You might try this:
https://seq2fun.dcmb.med.umich.edu/DeepFoldRNA/
I’m recommending it with the caveat that I’ve tested it on exactly 1
unpublished structure, and it did a really impressive but far from perfect job.
From: CCP4 bulletin board on behalf of Abhilasha Thakur
Date: Thursday,
Need I mention moleman and moleman2? Not trivial I suppose, but I will miss
them….
From: CCP4 bulletin board on behalf of Paul Emsley
Date: Thursday, September 8, 2022 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDBx-format utilities
A spectre is haunting structural biology - it
I have a set of utilities for handling PDB files, known as "PDB Pipeline". Each
one does a single distinct thing: manipulate the spatial coordinates, reset the
B, pull out a particular subset of residue numbers, fix particular known
problems, etc. There are several dozen. They work very nicely
Hello everyone..
Greetings of the day!!
I am working on RNA and it's structure prediction.
I have a RNA sequence which is about less than 160 nucleotide sequence, I
don't have it's structural information. Please suggest me what kind of
software can be used which can provide me structure with High
A spectre is haunting structural biology - it is the spectre of the PDBx
format.
We at CCP4 are interested in providing tools that are equivalents of
those that one might have trivially made with utilities such as grep or sed.
For example:
delete the hydrogen atoms
extract the
Much of the analysis suggested, like checking B-factors of neighboring
atoms, coordination geometry and atom-atom distances, are implemented here:
https://cmm.minorlab.org/metal_sites
Engin
On 9/8/22 8:27 AM, Eleanor Dodson wrote:
Is that the right way round? Atomic no K 19, Na 11
Call
Mitch,
For discernment of Sodium versus Potassium, you could also look at the bonding
distances and coordination of the metal present. Ran into this problem back in
the day. Check out Figure 6 C,D in the following pub:
https://pubs.acs.org/doi/10.1021/bi060653d
Scott
--
Scott Pegan
You can also look at your anomalous maps. For most
energies/wavelengths used to
collect protein data, f" for K will be just under 2x the f" for S
while for Na f"
will be much less (0.2-0.25 of S). So you can use S atom anomalous as
an internal reference.
If you see anomalous peaks at your S
Apologies for the stupid post about freezing conditions last night – my brain
was clearly very low on glucose when I read that list of temperatures!
From: CCP4 bulletin board on behalf of Phoebe A. Rice
Date: Wednesday, September 7, 2022 at 7:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re:
Cool, typed a long reply but only about 1/3 of it is still relevant and is
given below.
The crystal would have to be capillary mounted for these data collections or
the humidity controlled somehow. Only 253 K would be a good one to use.
Pre-cryo, this used to give good data at SRS! Interested
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
Is that the right way round? Atomic no K 19, Na 11
Call something K when it should be NA - B factor will shoot to reduce the
atom contribution.
Call something Na when it should be K - B factor will become very small..
As you say - check which fits best with the surrounding atoms..
On Thu, 8
Hello, K will always have a higher B-factor for a given piece of density due to
it having a larger atomic number. Is the K B-factor much higher than those of
neighbouring atoms and, if not, it's probably the best interpretation? Cheers,
Jon.C.
Sent from ProtonMail mobile
Original
Dear Community,
Can you tell me. if we fit some metal in X-ray
structure and its geometry and other properties are satisfied but showing
some higher B-factor. does it validate to put that metal-ligand.ligand. At
one site 2 metals such as K and NA fit, but K shows a higher
Hmmm - very puzzling..
One expects the for the atoms to more or less match the Wilson B for
the data sets..
There are some mini bugs which can mislead you.
Is your average a mean or an RMS value? RMS ones can be hugely inflated if
you have a few crazily high Bs and the refinement programs can
Hi Graeme
good to know that I haven’t forgotten everything.
Rgarding the data collection - I don’t think the OP mentioned how many crystals
were used in the data collection (unless, of course, I’ve been reading even
less carefully than normal…).
Harry
> On 8 Sep 2022, at 10:29, Winter,
Hi Harry,
You’re not wrong - “conventional wisdom” these days is pointing to CC of about
0.3 but I suspect that the difference is pretty modest in general
However, in the case, the difference could have an impact as the higher
resolution reflections may have something to say about the overall
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hi folks
I’ve been away from data processing for a while, but am I alone in thinking
that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of useful data? I
seem to remember that AutoProc and xia2.multiplex use a default of >= 0.3.
Harry
> On 7 Sep 2022, at 19:46, Matt McLeod wrote:
>
Hello:
this may not be 100% relevant to the discussed issue but to add a data
analysis perspective: to be able to compare B factors in different
structures, they need to be scaled. We used primitive but in my opinion
functional linear scaling from 1 to 100 (Schneider et al. Acta Cryst D,
Hi Matt,
You mention that you process with DIALS - one thing I would recommend is
scaling all the data together then merging each temperature point separately -
I could do with preparing a HOWTO on this [1] - this would then mean that they
are being scaled to be as similar as possible before
Dear Pavel,
sorry for the late reply.
You might look at the tyrosine-phenol lyase structures, in which a small
domain in one of the two crystallographically independent protein subunits
is discretely disordered, PDB IDs 6DUR and 6ECG.
Actually, modeling the small domain in the two discretely
Dear colleagues,
I would like to inform you that the EMBL Hamburg Unit is currently
advertising for a Group/Team leader position.
*Reference Number HH00216*: Group/Team leader - Integrated structural
biology by Small Angle X-ray Scattering
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Further
In a similar vein, there could be effects of variation in humidity. How is
humidity controlled at these different temperatures? It can drastically
affect crystal ordering, which is of course a key determinant of the
eventual Wilson B of a dataset and should be distinguished from a property
of the
There could be a release of sum stress in the crystal with increasing
temperature which could even lead to better ordering I can imagine.
But that would need a very close inspection and mainly - are the structures
completely isomorphous?? I.e. are there changes at all?
If not then I am puzzled.
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