Gotta love the extra wood on the fire.
In the bad old days, I agree, we had no real idea.
But these days I usually have mass spec done on most everything and
additionally look at different crystal forms. Often I find that in one space
group more will be seen than in another (and that one isn't
Hi Debanu,In your example, I would guess that models with truncated side chains would probably be problematic too, so would alternative conformations, unmodelled segments, asymmetric unit consisting of only a fraction of the biological/functional unit, etc.I am not sure if it is possible to build
On thus topic, I note that the "ModelCIF" format has been developed which
allows inclusion of appropriate parameters associated with predicted models,
such as those from AlphaFold (e.g. confidence values instead of B-values).
Would it be too much to ask for fields associated with "modelled
Hello All,
I agree with Dale that we don't have a good way to model these things and it
has been a discussion for a very long time with no proper answer.
Two more small points- we (or at least I do this all the time) don't model the
N- or C-terminal residues that I don't see. They are most
Hi
As a frequent contributor to prior discussions on this same topic I
would like to broaden the discussion a bit. I'm sorry to say that most
of the comments on this threat are exactly the same positions that have
been expressed many times over the years. I don't want to spent time,
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
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
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
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
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
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
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
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
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
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
I believe Julia is absolutely right.
The other consideration that I haven’t seen mentioned yet in this thread is the
effect on refinement. If you truncate a side chain or set it to zero occupancy
then the bulk solvent mask would contain that region that is actually occupied
by the flexible
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
building is not to achieve the lowest
Dear all,
Final reminder that the early bird registration for the CCP-EM Symposium closes
today (Friday 10th March). After today the registration fees increase.
Registration link and more conference details here…
https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php
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