> 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
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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
The Centre for Structural Biology (CSB) is looking to recruit a full-time
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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
Good morning all,
“Not the Gordon Research Conference” on Diffraction Methods in Structural
Biology 2024 - Experiments and Measurements
Organisers:
Graeme Winter, Kunio Hirata (NTGRC-chairs)
Helena Taberman, Ali Ebrahim (NTGRS-chairs)
Local organisers - Arwen Pearson, Ashwin Chari
As you wil
Oh dear - I didn’t mean to start this discussion - just to have a private
moan to Ian tickle, but there are some reasons for the regret.
First of all - column names had a meaning . For example a refmac hklout has
labels
f sigf Phic from delfphwt etc and just occasionally one likes to see some
deta
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