Knowing the author as I do, I checked the date and time, and wasn't fooled.
From: CCP4 bulletin board on behalf of Carter, Charlie
Sent: Saturday, April 1, 2023 4:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] new PDB file format
I fell for this
I fell for this momentarily, hence compliments to James. I was fooled by the
absolutely sensible intro.
Charlie
> On Apr 1, 2023, at 12:34 AM, James Holton wrote:
>
> Anyone who has ever had to lecture a student for writing their unit cell
> lengths to dozens of decimal places is going to lov
I think this is all true - and I’ve been putting things like this into my
(failing) grants - but I get the dispiriting sense that the medics think (to
borrow a line from hamlet) “the applicant doth protest too much methinks”.
Well if as per James H today ;), we deposit coordinates to 1sf, alpha
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
Dear Rams,
I salute you for sharing this.
Just a week ago, I also received a remark along these lines on a declined grant
application. The remark was the only unfavourable point, which suggested that
it must have weighed disproportionally towards the negative outcome. This was a
two-stage eval
I was afraid of this happening at some point and decided to start a new career
~ten years ago and use structures only as a tool and never put them into the
centerpiece of a grant.
My fall back option is either a cocktail bar or starting a restaurant. The
Triple M’s always work Mojito, Martini,
When I tested alpha fold on some of my proteins, it failed to predict the
intramolecular interactions needed for their functions. Alphafold predicts the
folds and overall structure of single domain and may be simple multi domain
proteins but when conformational changes are needed for protein fun
Hi,
Just ask ChatGPT to write it for you!
Dale Tronrud
On 4/1/2023 5:06 AM, Subramanian, Ramaswamy wrote:
Dear All,
I am unsure if all other groups will get it - but I am sure this group
will understand the frustration.
My NIH grant did not get funded. A few genuine comments - they m
And the good thing is we won’t be needed any more! - as alphafold structures
will be just as good! ;)
Adrian
Sent from my iPhone
On 1 Apr 2023, at 18:06, Kolenko, Petr
<9d229ba2f5a3-dmarc-requ...@jiscmail.ac.uk> wrote:
Dear James,
what a great step forward! I see another point. In our p
Dear James,
what a great step forward! I see another point. In our programs, the
coordinates will no longer need to be floats, doubles or whatever. They can
easily be integers! I believe that this will dramatically speed up the process
of refinement. 😉
Best regards,
Petr
Ian,
Thank you. This is not an April fools..
Rams
subra...@purdue.edu
On Apr 1, 2023, at 10:46 AM, Ian Tickle wrote:
External Email: Use caution with attachments, links, or sharing data
Hi Ramaswamy
I assume this is an April Fool's but it's still a serious question because many
Hi Ramaswamy
I assume this is an April Fool's but it's still a serious question because
many reviewers who are not crystallographers or electron microscopists may
not fully appreciate the difference currently between the precision of
structures obtained by experimental and predictive methods, thou
" Is there a canned consensus paragraph that one can add with references to
grants "
How about:
“In general we look for a new law by the following process. First we guess it.
Then we compute the consequences of the guess to see what would be implied if
this law that we guessed is right. Then w
Dear All,
I am unsure if all other groups will get it - but I am sure this group will
understand the frustration.
My NIH grant did not get funded. A few genuine comments - they make excellent
sense. We will fix that.
One major comment is, “Structures can be predicted by alpfafold and other
My suspicions were raised when a post by James to this BB didn't run to several
pages...
Harry
--
Dr Harry Powell
> On 1 Apr 2023, at 08:14, Eleanor Dodson
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Ha ha!
>
>> On Sat, 1 Apr 2023 at 05:34, James Holton wrote:
>> Anyone who
Ha ha!
On Sat, 1 Apr 2023 at 05:34, James Holton wrote:
> Anyone who has ever had to lecture a student for writing their unit cell
> lengths to dozens of decimal places is going to love the new PDB
> format. It is more compact, more realistic, and less misleading to the
> poor, downstream consu
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