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
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
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
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.
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,
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
The Centre for Structural Biology (CSB) is looking to recruit a full-time
Facility Manager on an open-ended permanent contract to work on the Imperial
College South Kensington Campus. We are looking to recruit a candidate with
strong research experience in X-ray crystallography who is
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
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
Dear all,
I need to install CCP4 on my disk in cluster computer. The OS is CentOS Linux
7.
Please instruct me for this.
Thank you in advance.
Best regards,
Rafiga
To unsubscribe from the CCP4BB list, click the
> 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
> 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
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