uitin Signalling Division
elechtenber...@wehi.edu.au <mailto:lechtenber...@wehi.edu.au>
T +61 3 9345 2217
*From:*CCP4 bulletin board on behalf of Rhys
Grinter <22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
*Date:*Friday, 10 March 2023 at 12:26 pm
*To:*CCP4BB@JISCMAIL.AC.UK
*
> T +61 3 9345 2217
>
>
> From: CCP4 bulletin board on behalf of Rhys Grinter
> <22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
> Date: Friday, 10 March 2023 at 12:26 pm
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] To Trim or Not to To Trim
>
> Hi All
The most pertinent question is, of course, what is the average frequency of
the disordered chain controversy flareup. Once we figure that out, some
profound mysteries of the Universe will reveal themselves. I am betting
it's a simple combination of the solar cycle, inflation adjusted price of a
b
On Tue, Mar 28, 2023, James Holton wrote:
Members of an ensemble spread out over a supercell are equivalent to a
conventional multi-conformer model, but only when it comes to the
density derived from the coordinate atoms alone. They are not the
same when it comes to bulk solvent and also not
d probably give more overfitting. Alt confs can easily be
converted to an ensemble (if done properly…).
Thanks,
Nick
———
Nicholas Pearce
Assistant Professor in Bioinformatics & DDLS Fellow
Linköping University
Sweden
------------------------
*From
r to what Nick said was published around
2002-2003. I was reviewing it. I did not understand then what the
author was trying to achieve and kept thinking about it for few
months. The author split model into 20 each with 5% occupancy. After
refinement he got an ensemble that looked like NMR structures.
ds to
>> the protonation state of that His. This kind of sensitivity is really
>> attractive if you are looking for low-lying features, such as
>> partially-occupied ligands. Some may pooh-pooh R factors as "cosmetic"
>> features of structures, but they are, in fact, not
, which is a typical experimental error in
> crystallographic data, anything bigger than one electron is clear.
>
> -James Holton
> MAD Scientist
>
>
>
> On 3/18/2023 2:10 PM, Nicholas Pearce wrote:
>> Not stupid, but essentially the same as modelling alt confs, tho
ything bigger than one electron is clear.
>
> -James Holton
> MAD Scientist
>
>
>
> On 3/18/2023 2:10 PM, Nicholas Pearce wrote:
>
> Not stupid, but essentially the same as modelling alt confs, though would
> probably give more overfitting. Alt confs can easily be
Yes, I meant maps from SPA. This is the great thing about cryoEM: most maps are
discovery maps!
I agree that showing crystallographic maps requires more careful explanations
for non-experts, but I still believe we, as a field trying to make our nerdy
technical things more approachable to others
Professor in Bioinformatics &
DDLS Fellow
Linköping University
Sweden
From: CCP4
bulletin board on behalf of
benjamin bax
Sent: Saturday, March 18, 202
Linköping University
Sweden
From: CCP4
bulletin board on behalf of
benjamin bax
Sent: Saturday, March 18, 2023 10:07:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject:
--------------------------
*From:* CCP4 bulletin board on behalf of
benjamin bax
*Sent:* Saturday, March 18, 2023 10:07:26 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] To Trim or Not to To Trim
Hi,
Probably a stupid question.
Could you multiply a, b and c cell
00968307750321-dmarc-requ...@jiscmail.ac.uk>
*Reply-To: *Bernhard Lechtenberg
*Date: *Friday, March 10, 2023 at 05:07
*To: *"CCP4BB@JISCMAIL.AC.UK"
*Subject: *Re: [ccp4bb] To Trim or Not to To Trim
I found the poll I wrote about earlier. This actually is way older
than I had expecte
On Behalf Of benjamin bax
Sent: Saturday, March 18, 2023 5:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] To Trim or Not to To Trim
Hi,
Probably a stupid question.
Could you multiply a, b and c cell dimensions by 2 or 3 (to give 8 or 27
structures) and restrain well defined parts of
eden
From: CCP4 bulletin board on behalf of benjamin bax
Sent: Saturday, March 18, 2023 10:07:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] To Trim or Not to To Trim
Hi,
Probably a stupid question.
Could you multiply a, b and c cell dimensions by 2 or 3 (to
Hi,
Probably a stupid question.
Could you multiply a, b and c cell dimensions by 2 or 3 (to give 8 or 27
structures) and restrain well defined parts of structure to be ‘identical’ ? To
give you a more NMR like chemically sensible ensemble of structures?
Ben
> On 18 Mar 2023, at 12:04, Helen Gi
Models for crystallography have two purposes: refinement and
interpretation. Here these two purposes are in conflict. Neither case is
handled well by either trim or not trim scenario, but trimming results
in a deficit for refinement and not-trimming results in a deficit for
interpretation.
Ou
-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/
<http://www.icm.uu.se/structural-biology/griese-lab/>
*From: *CCP4 bulletin board on behalf of
Bernhard Lechtenberg <968307750321-dmarc-requ...@jiscmail.ac.uk>
*Reply-To: *Bernhard Lechtenberg
*Date: *Friday, March
> On 17 Mar 2023, at 08:57, Manfred S. Weiss
> wrote:
>
> In my view, the best approach is to build the side chains in their
> most plausible conformation, or maybe in 2 or 3 or 5 different
> conformations, and let the ADPs refine freely.
One point I don’t think has been mentioned so far in thi
> On 17 Mar 2023, at 15:01, Guillaume Gaullier
> wrote:
>
> CryoEM papers often show a map in a main figure, and as a reader I think it
> is very nice to show me the map that convinced you of some finding before
> showing me your interpretation of this map.
Surely a key difference is that cry
Hello,
I think Rams’ last remark is very important. People with every preference
regarding modelling (trimmed, zero-occupancy or high-B), past their
disagreement on this particular question, are all concerned about how their
models will be interpreted by non-experts.
Since all experimental sci
Dear all,
to trim or not to to trim….
- what is the difference between highly disordered side-chain atoms versus
disordered bulk-solvent atoms? Do not both represent a continuum function with
a comparable electron-density distribution? Have not solvent and side-chain
atoms merged/mixed at this
Dear All,
I am kind of in agreement with Manfred, but I also have concerns.
The RCSB and the databases are public databases used by non-structural biology
experts a lot. They take the model as if it is an experimental result - rather
than it being a model.
Example: I just got a paper with re
I would add that those who insist on modelling the atoms that they can’t see
display a quasi-religious fervour about it, as if there is only one right way.
Sorry about the snark.
One example I remember from my graduate student days is this:
https://tinyurl.com/bddefd3t
where intact and truncate
Dear Manfred,
In addition to personal preference I think there are some philosophical
differences in what the model actually means. I would argue that what we see in
the density is stronger evidence of the chemical identity than what we believe
we have used as a starting material. After all we
Dear all,
many views have been expressed in this thread, which I have been
following with great interest. Unfortunately, I have to say that many
of the views are more based on personal preferences, than on the
scientific evidence behind.
Here are some facts, that one may want to consider:
1. W
,
Robbie
From: CCP4 bulletin board On Behalf Of Rudolph, Markus
Sent: Tuesday, March 14, 2023 15:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [Sender Not Verified] Re: [ccp4bb] To Trim or Not to To
Trim
Hello Adrian,
Provided a crystal contains the intact protein, as measured by mass
8:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] To Trim or Not to To Trim
You don't often get email from jxb...@case.edu. Learn why this is
important<https://aka.ms/LearnAboutSenderIdentification>
Well Tom,
Your missing N-terminus might just be degraded same with the C-terminus t
gt; http://www.icm.uu.se/structural-biology/griese-lab/
> <http://www.icm.uu.se/structural-biology/griese-lab/>
>
> *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
> Bernhard Lechtenberg <968307750321-dmarc-requ...@jiscmail.ac.uk>
> *Repl
gt;> --
>> Dr. Julia Griese
>> Associate Professor (Docent)
>> Principal Investigator
>> Department of Cell and Molecular Biology
>> Uppsala University
>> BMC, Box 596
>> SE-75124 Uppsala
>> Sweden
>> email: julia.gri...@icm.uu.se
>> phone: +
e don't
see something, the conservative approach is to probably avoid putting it in,
otherwise it will get propagated forever.
My two cents. cheers, tom
From: CCP4 bulletin board on behalf of Dale Tronrud
Sent: Saturday, March 11, 2023 7:15 AM
To: CCP4BB@JIS
rd on behalf of
Bernhard Lechtenberg <968307750321-dmarc-requ...@jiscmail.ac.uk>
*Reply-To: *Bernhard Lechtenberg
*Date: *Friday, March 10, 2023 at 05:07
*To: *"CCP4BB@JISCMAIL.AC.UK"
*Subject: *Re: [ccp4bb] To Trim or Not to To Trim
I found the poll I wrote about earli
Hi Phil,
I don't think that this is model cosmetics, but I certainly didn't claim that
this isn't controversial. That's why we're having this discussion again and
again after all.
Have you tried to model a disordered Arg with 10 (why only 10?) alternate
rotamers? Did it refine to something sen
Surely not if the locations of those other atoms are strongly supported by
density? And surely you would always select a rotamer that does not clash with
its surroundings?
On 3/10/23, 17:32, "CCP4 bulletin board on behalf of Goldman, Adrian"
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of
adrian.g
As with Jurgen, I’ve never trimmed a residue.
In my view the trimmed residues do not exist.
If we were to build models consisting of only atoms defined by the experimental
density, then I wonder what the original model of the DNA double helix would
have looked like.
BTW, hey Jurgen, long time no
I’m sure James H. Is preparing a philosophical dissertation on the "State of
the atoms to B or not to B that is not only a refinement question” that he will
share momentarily with the board.
Jürgen
> On Mar 10, 2023, at 12:06 PM, DEBANU DAS
> wrote:
>
> Yes, zero occupancy would reflect tha
Hi Jürgen
You might think so, but I’d disagree. Not going too far away from your line of
reasoning I could also put in a completely fictitious ligand or cofactor and
assign its occupancies to zero (I really, really knew it was there but I just
couldn’t find any evidence… :-))
Harry
> On 10 Ma
Yes, zero occupancy would reflect that. But not the coordinates in any
proper way. Then what would be the point of associating occupancy and
B-factors with totally incorrect coordinates?
Debanu
On Fri, Mar 10, 2023 at 8:58 AM Jurgen Bosch wrote:
> Going back to RIP phasing methods :-)
> So Harry
Going back to RIP phasing methods :-)
So Harry in your particular case occupancy of zero would actually reflect
reality for those “combusted” atoms.
Jürgen
> On Mar 10, 2023, at 11:56 AM, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi folks
>
> One other thing t
Hi folks
One other thing that I haven’t noticed anyone mentioning yet (sorry to those
who have mentioned it!!) is that you may not see your sidechain atoms in
density because they are not there at all, in spite of what you may have had in
the original protein, or even if the atoms were really t
Are downstream users of models with poorly resolved regions more likely to
spot them if they have huge B-factors or zero occupancy? If the answer is
'neither', then perhaps we need to develop a different solution.
On Fri, 10 Mar 2023 at 16:33, Goldman, Adrian
wrote:
> Maybe simplest just to trim
Maybe simplest just to trim it back. I do worry that the presence of a wrong
conformation will lead to inaccurate vdw clashes that could negatively affect
other atoms.
Sent from my iPhone
> On 10 Mar 2023, at 18:25, Phil Jeffrey wrote:
>
> On 3/10/23 4:05 AM, Julia Griese wrote:
>> Hi all,
On 3/10/23 4:05 AM, Julia Griese wrote:
Hi all,
My impression has been that the most common approach these days is to
“let the B-factors take care of it”, but I might be wrong. Maybe it’s
time to run another poll?
Personally, I call any other approach R-factor cosmetics. The goal in
model b
Lechtenberg
> <968307750321-dmarc-requ...@jiscmail.ac.uk
> <mailto:968307750321-dmarc-requ...@jiscmail.ac.uk>>
> Reply-To: Bernhard Lechtenberg <mailto:lechtenber...@wehi.edu.au>>
> Date: Friday, March 10, 2023 at 05:07
> To: "CCP4BB@JISCMAIL.
K"
Subject: Re: [ccp4bb] To Trim or Not to To Trim
I found the poll I wrote about earlier. This actually is way older than I had
expected (2011). You can see the poll results (which was run by Ed Pozharski)
and discussion at the time here in the CCP4BB archive:
https://www.mail-ar
bulletin board on behalf of Debanu Das
Date: Friday, 10 March 2023 at 2:56 pm
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] To Trim or Not to To Trim
We dealt with this in-depth during structural genomics days when we deposited
over 1500 novel, high-quality, experimentally-phased structures into
gt;
>> Bernhard
>>
>> *Bernhard C. Lechtenberg* PhD
>> NHMRC Emerging Leadership Fellow
>> Laboratory Head
>> Ubiquitin Signalling Division
>> E lechtenber...@wehi.edu.au
>> T +61 3 9345 2217
>>
>>
>>
>> *From: *CCP4 bulleti
rging Leadership Fellow
> Laboratory Head
> Ubiquitin Signalling Division
> E lechtenber...@wehi.edu.au
> T +61 3 9345 2217
>
>
>
> *From: *CCP4 bulletin board on behalf of Rhys
> Grinter <000022087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
> *Date: *Fr
087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
> Date: Friday, 10 March 2023 at 12:26 pm
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] To Trim or Not to To Trim
>
> Hi All,
>
> I'm trying to crowdsource an opinion on how people deal with modelling side
> chains with
rinter
<22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
Date: Friday, 10 March 2023 at 12:26 pm
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] To Trim or Not to To Trim
Hi All,
I'm trying to crowdsource an opinion on how people deal with modelling side
chains with poorly resolved electron or cr
Hello, yes, the trimming and occupancy tricks can be confusing and they can be
a bit of a cheeky way to improve the model statistics. I prefer to build the
whole side chain and if you can't see all or part of it, then that's just too
bad, but I have erred.
Best wishes, Jon Cooper. jon.b.coo...@
Hi All,
I'm trying to crowdsource an opinion on how people deal with modelling side
chains with poorly resolved electron or cryoEM density.
My preference is to model the sidechain and allow the B-factors to go high
in refinement to represent that the side chain is flexible. However, I'm
aware tha
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