Yes, I agree this is a good point. We had an example at a CCP-EM workshop where
the participant’s map turned out to have the wrong hand. I’m embarrassed to say
that it took Tristan Croll (sitting next to me) to notice that the helices were
left-handed! Anyway, flipping the hand was quick and eas
p
>
> HTH
> m
>
> -Original Message-
> From: CCP4 bulletin board On Behalf Of Randy John Read
> Sent: 27 November 2024 08:40
> To: ccp4bb
> Subject: Re: [ccp4bb] cryoEM molecular replacement
>
> Hi Gloria,
>
> Guillaume already mentioned emplace_local, so
Hi Gloria,
Guillaume already mentioned emplace_local, so I’ll just mention that if you get
a recent nightly build of Phenix and the latest version of ChimeraX (plus the
Phenix UI plugin from the toolshed), you can tell it your map has symmetry,
place a monomer, and then it will detect the symme
hoc’ input parameter T of Relion, still required as user input
> in the current version for 3D classification, corresponds to the inverse of
> this correction factor
> Best wishes, Chuck
> From: CCP4 bulletin board on behalf of Randy
> John Read <eafc0efa8263-dma
rom over.
>>
>> -James Holton
>> MAD Scientist
>>
>> On 10/9/2024 10:25 AM, Frank von Delft wrote:
>>> So Randy, what should we be saying/using, and where do we find it... and
>>> (not least!), when in the experiment-to-final-model process?
>>>
&g
y-to-day parlance.
>
> (A very interesting discussion, thanks!)
>
>
> On 08/10/2024 09:05, Randy John Read wrote:
>> Dear Marin,
>>
>> In crystallography we do have the information gain measure (based on
>> Kullback-Leibler divergence) that my group put
Dear Marin,
In crystallography we do have the information gain measure (based on
Kullback-Leibler divergence) that my group put forward and implemented in our
Phaser program (https://doi.org/10.1107/s2059798320001588). Signal and noise
aren’t isotropic, so information gain isn’t isotropic eithe
Maybe someone else will have a different opinion, but I suspect that the very
best method to predict secondary structure at the moment is to predict the
tertiary structure using AlphaFold or another machine-learning structure
prediction method, and then observe the secondary structure in the pre
Dear Marco,
You don’t mention here or in the earlier thread whether you tried AlphaFold
models and, if you did, how you prepared them for MR. I’m happy to hear of any
case where we still need experimental phasing methods to solve new protein
structures, but we’ve seen very few examples where Al
ese loops?
> Because that's the only way this will be achieved systemically.
>
> Presumably ccp4i2 can be wrangled into making it happen magically. (Apologies
> if it does already, if so, a comment here would help the discussion...)
>
> Frank
>
>
>
> On 18/04/2024 11:02,
I’d like to add my strong agreement to what Robbie said, but also point out a
wrinkle. When the PDB runs validation, it just takes the data that are in the
first reflection loop of the reflections.cif file. So if you want the
validation statistics to match your reported refinement statistics, th
4, at 11:49, Randy John Read wrote:
>>
>> Why would we want to impose an arbitrary restriction on users for this
>> relatively common scenario.
>
> If the user has the unmerged data this can be imported into CCP4i2 via the
> data reduction task and merged in P1.
In the recent crystallography workshop in Thailand, we had at least 3 cases
brought by participants where we had reason to suspect that the data had been
over-merged because of undetected twinning. Often there is more than one
possible twinning operator and (as potentially in one of the cases br
Hi,
This is also one of my favourite methods, although I hadn’t realised that you
could just say “labin F=FC” instead of making fake intensities!
However, at a recent workshop I ran into a case where pointless misled me. This
was a case with tNCS where one of the translation components was half
0
>> Most likely data problems - a axis ~ = b axis so twinning is possible
>>
>> I could add more comments if either you could share the unmerged data, or at
>> least a pointless logfile..
>> Cheers Eleanor
>>
>>
>>
>>
>>
>>
is ~ = b axis so twinning is possible
>
> I could add more comments if either you could share the unmerged data, or at
> least a pointless logfile..
> Cheers Eleanor
>
>
>
>
>
> On Wed, 21 Feb 2024 at 11:06, Randy John Read wrote:
> Hi Marco,
>
> To add
Hi Marco,
To add to what Kay has said:
The intensity moments from Phaser (between 1.5 and 2 for the second moments
after correcting for anisotropy) are indicative of likely twinning. With the
cell dimensions, it might be possible to have pseudomerohedral twinning in an
orthorhombic space group
Hi Marco,
I was just about to write with a different suggestion when Kay’s reply came in.
What Kay suggests sounds like the best thing to do first!
However, if that isn’t the issue, then I’m wondering if it could be a problem
with incorrectly diagnosed translational non-crystallographic symmetr
Hi,
Hendrickson-Lattman coefficients are just a way of storing phase probability
information, and they can come from different sources including atomic models.
Phaser puts in HL coefficients because they could be handy under some
circumstances for combining the phase information from experiment
Hi,
I’m happy to report that this goniometer head has now found a good new home!
Best wishes,
Randy
> On 27 Jan 2024, at 19:23, Randy John Read wrote:
>
> Hi,
>
> Now that we don’t have a home lab source any more, there’s no need for the
> goniometer head that we used to
Hi,
The current policy of the PDB is that you can deposit a re-refinement of a
structure deposited by someone else only if you publish a new paper about it,
so that there is a citation associated with the structure. Of course, echoing
Eleanor, if you find an issue with someone else’s structure
Hi,
Now that we don’t have a home lab source any more, there’s no need for the
goniometer head that we used to mount crystals on it. I’d be happy to give it
to someone who still has a home source and could make good use of it!
Preference would be given to people in the UK, mostly because that w
Hi,
I think the point about an R-factor of 42% is a bit more subtle than it comes
across in Martin’s reply. For random data without measurement errors (i.e.
coming from a Wilson distribution of intensities), the expected R-factor for
acentric data is something like 59%. The 42% in Evans & Mursh
For anyone who is confused:
Unfortunately, the link given here (https://phenix-online.org/download/) says
that the latest release is 1.19.2-4158! That’s very odd because the same URL
without the trailing slash (https://phenix-online.org/download) gets to a
different page with the right informat
I think we’ve strayed a bit from Doeke’s original question involving crystals
A, B and C, where I think the consensus opinion would be that we would refer to
crystal C as not being isomorphous to either A or B.
On the question of what “isomorphous” means in the context of related crystals,
I’m
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. Unl
Hi,
At 1.9A resolution there should be lots of possibilities, depending on the
details.
You imply you have partial sequence information for chain B. Is there a genome
for your plant or a relative of it? You could search for possible matches to
your sequence, and then test all the AlphaFold mod
For anyone who knew Michael James (who was my PhD supervisor), you might be
interested in looking at two recent obituaries. One is in the current issue of
ACA Reflexions (https://www.amercrystalassn.org/aca-reflexions), and the other
was published in the October issue of Acta Cryst D (Structural
I’ve just been playing with a difference map to check something. If you fail to
set the map as a difference map (either when opening the map initially, or
using Calculate->Map Tools->Set map is a difference map), there’s nothing in
the Display Manager->Properties window that tells you. I was won
I get the impression that these days you can patent just about anything, and
instead of challenging your claims the patent examiners leave it to be settled
later. A few years (probably one or two decades!) ago someone managed to patent
the idea of a difference Fourier to detect binding, ignoring
I’m not sure about other methods, but AlphaFold does predict peptides in both
cis and trans configurations. In a recent paper, Osnat Herzberg and John Moult
show that it was pretty successful in predicting proline cis-peptides, among
the novel structures in the CASP15 set of targets
(https://ww
Also, we’re hoping that the next CCP4 update will include the changes to fix
the same issue in CCP4, so please install it when it’s announced!
Randy Read
> On 5 Jul 2023, at 17:40, Luca Jovine
> <9d27029f2b4b-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi Firdous, for Phaser the solution is s
So have I! They’ll learn not to disrespect one of our favourite people.
Randy
> On 24 May 2023, at 10:44, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi Gerard
>
> I’ve mentioned it to the organiser - we shall see how long the Garmen will be
> there!
>
> Harry
>
>>
Hi Harry,
My advice would be to use one of those new-fangled predicted models. You can
find a model in the AlphaFold database at the EBI
(https://alphafold.ebi.ac.uk/entry/P01132). If you look at it, there are parts
(likely corresponding to the constructs that were crystallised) that look
conf
There’s also this preprint with Tom Terwilliger as lead author:
https://www.biorxiv.org/content/10.1101/2022.11.21.517405v1. The title is
“AlphaFold predictions: great hypotheses but no match for experiment”.
Best wishes,
Randy
> On 1 Apr 2023, at 18:18, Savvas Savvides
> <9d24f7f13e09-dm
Hi Jon,
My understanding of the philosophy is that new users would prefer to think
about crystallographic data objects, rather than worrying about the arcana of
MTZ files and the many different flavours of columns. There are tradeoffs — it
can indeed be more difficult to find the bits of inform
Also, this might be a good time for the regular reminder *never* to use the MTZ
output by Refmac as input for anything else, because the FOBS coming out of
Refmac is not the same as the FOBS going in. It might well have had various
corrections applied, including a correction for twinning. I thin
We don’t have any computers with Apple silicon in our group yet to test Phaser
on ourselves. When preparing the Phenix distribution, Billy Poon has run tests
and when Phaser is compiled for Intel and run through Rosetta 2, it’s generally
faster than on a recent Intel Mac. However, there have bee
Just to add one point that I don’t think I’ve seen yet. If what the referee
wants is a data-free assessment of the expected quality of the model, I think
that the best assessment at the moment is the one done by AlphaFold2 (or indeed
RoseTTAFold if you’re using one of their models). The machine-
sage. By the way, Phaser output suggested " SYNTAX ERROR: Use
> SERIAL". What is the usage of "SERIAL"? I can't find that keyword in the
> manual.
>
> Thanks,
>
> Yong
>
> -Original Message-
> From: CCP4 bulletin board On Be
Hi Yong,
If you make an ensemble with ensembler, the models are numbered from 1 to n, so
there’s no requirement to start from 0. Did you use ensembler to make your
ensemble model file? If you did and Phaser is failing, could you send me the
file so we can figure out the problem? Otherwise, t
servation and the 100-pixel experiment should give
expectation value of 2 and variance of 2? I wouldn't.
Best wishes,
Kay
On Thu, 21 Oct 2021 09:00:23 +, Randy John Read
mailto:rj...@cam.ac.uk>> wrote:
Just to be a bit clearer, I mean that the calculation of the expected value a
same length of exposure, or
the sum from the same pixel measured for smaller time slices adding up to the
same total exposure.
On 21 Oct 2021, at 09:54, Randy John Read
mailto:rj...@cam.ac.uk>> wrote:
I would think that if this problem is being approached correctly, with the
right prior, i
I would think that if this problem is being approached correctly, with the
right prior, it shouldn't matter whether you collect the same signal
distributed over 100 smaller pixels or the same pixel measured for the same
length of exposure but with 100 time slices; you should get the same answer.
ote:
>
> Hi,
> Any chance this will be recorded for those of us in a different dimension?
>
> J
>
> -Original Message-
> From: phenixbb-boun...@phenix-online.org
> On Behalf Of Randy John Read
> Sent: Friday, 27 August 2021 6:27 am
> To: CCP4BB@jisc
9 am CEST (Norway). Pretty early for our North American colleagues, especially
those on the west coast!
> On 27 Aug 2021, at 05:18, Robert Rose wrote:
>
> Does the workshop start on August 31 at 9 am GMT?
>
> On Thu, Aug 26, 2021 at 2:27 PM Randy John Read wrote:
> Hi,
>
Hi,
I’ve just learned that this online workshop is generally open, not just to
members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s
free! Information, including the current programme and a link to registration,
can be found here:
https://www.nora.ai/events/AlphaFoldv2
What the DeepMind people say about this is that when part of a predicted
structure has a low predicted lDDT (a CASP measure of model quality), this is a
good indicator that it may be intrinsically disordered.
Best wishes,
Randy Read
> On 17 Aug 2021, at 17:13, Sorin Draga wrote:
>
> Dear al
Yes, I should have mentioned the truncation by estimated RMS error, which was
part of the protocol we used in the paper with David Baker’s group. The error
estimates are calibrated, I believe, for just the C-alpha atoms, so they are
probably generally underestimates of the errors in the rest of
If there isn’t already a suitable model, this looks like a good opportunity to
try out the powerful new RoseTTAFold deep learning algorithm by Minkyung Baek
in David Baker’s lab. It can be used through the Robetta server
(http://robetta.bakerlab.org, choose Structure Prediction->Submit and then
I agree with Kay that, with a good model, solving in P1 is likely to be the
easiest comprehensive solution. If that doesn’t work, Phaser starts every
MR_AUTO job by making a list of all the subgroups, including the different
potential indexings (represented by Hall symbols), so you could also w
It’s also important to keep in mind that, in this equation, u is the component
of the displacement *in the direction of the diffraction vector*. If you
assume isotropic displacements and you know the mean-squared value of the
overall xyz vector displacement, you have to divide that mean-squared
ndy John Read wrote:
>
> Hi,
>
> I had a hard time tracking down the data in the legacy CCP4 site but
> eventually found it! Then I tried solving the MR tutorial case with Phaser.
>
> Instead of using the tutorial domain 1, 2 and 3 files, I prepared them from
> the
Hi,
I had a hard time tracking down the data in the legacy CCP4 site but eventually
found it! Then I tried solving the MR tutorial case with Phaser.
Instead of using the tutorial domain 1, 2 and 3 files, I prepared them from the
deposited PDB file using a sequence alignment followed by using s
Hi Jessica,
The suggestion by Eleanor and Thierry to break the model into two parts for
molecular replacement should work. However, if it doesn’t there’s another
option, which can work well in marginal cases. Fix the domain that’s
well-placed. Make a note of the Euler angles from the MR solu
Yes, I agree with Eleanor. But if there’s translational NCS, either the
off-origin Patterson peak is below 20% of the origin peak so that Phaser is
missing it, or perhaps you’re turning off the tNCS correction? If Phaser
detects tNCS it will place two copies at once.
We’ve had cases where, as
Dear John,
It’s hard to be absolutely certain from the reproduction, but it looks like you
have equally high 2-fold axes all around the xy plane in the self-rotation
function. Do you have an explanation for that?
It would be helpful to know the heights of the Patterson peaks relative to the
o
Dear Luca,
I think all of those orientations are symmetry-related copies of the same
orientation. This would imply that there is tNCS, but it doesn’t look like
Phaser is applying tNCS. The second and fourth molecules are in the same
orientation, but differing by 1/6 of the a-axis cell transla
Hi Phil,
It’s always a difficult balance between looking hard in a difficult case and
possibly finding an answer with a weak signal, and stopping when the search is
really unlikely to succeed. Phaser perhaps errs too much toward trying really
hard.
There’s one really blunt tool in Phaser, the
Several people have mentioned lack of peer review as a reason to doubt the
significance of the AlphaFold2 results. There are different routes to peer
review and, while the results have not been published in a peer review journal,
I would have to say (as someone who has been an assessor for two
Hi Frank,
Yes, until CASP7 (back in 2006), I used to like saying that there are many more
ways to make a homology model worse than the starting template than to make it
better, and that homology modelling programs were very good at finding them!
After seeing that at least some models (e.g. fro
Hi James,
One really interesting (and to me surprising) aspect of how well AlphaFold2
does is that it does really well without actually understanding chemistry and
physics. (John Jumper from DeepMind talked about choices of deep learning
model types and how they affect the “inductive bias” tha
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