Re: [ccp4bb] To Trim or Not to To Trim

[Huw Jenkins]

> 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 this interesting debate is 
how do you ensure that none of the atoms in these conformations gets moved by 
the refinement program such that one plausible conformation becomes a rotamer 
outlier after refinement? I would think that most structural biologists would 
agree that a rotamer that is an outlier and is unsupported by electron density 
is hard to justify.


Huw 


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Re: [ccp4bb] To Trim or Not to To Trim

[Huw Jenkins]

> 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 cryoEM maps (assuming you mean SPA) are not 
calculated with phases derived from the model shown built into the map?

Most maps shown to convince the reader of the validity of the authors 
interpretation of the electron density in X-ray crystallography papers use some 
attempt at removing bias from 2Fo-Fc or Fo-Fc density when the phases have at 
some point in the refinement been derived from a model including the region of 
interest. Few are “discovery maps” to use Dale Tronrud’s term: 
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg04276.html


Huw 


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Re: [ccp4bb] To Trim or Not to To Trim

[Guillaume Gaullier]

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 scientists understand the difference between observed 
data and interpretation, I believe the best way to educate non-expert users of 
macromolecular models would be for the PDB to systematically show a map. An 
overview consisting of a still image with map and model is already in 
validation reports, so it could be displayed on the entry page on the web as 
well. We now have in-browser interactive map and model viewers, so the PDB 
should make use of this capability and show the map by default, and use a 
legend that would be clear for non-experts (with terms like "observed density" 
and "atomic model interpretation of the density" or whatever explains it best 
in easy words).

We could also all get into the habit of showing a map (or even only the region 
of interest in a map) in a main figure in our papers, instead of keeping it 
hidden deep in the supplementary figures. 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. I hope the cryoEM field will keep doing this, and I hope the MX field 
would start showing more maps in their papers again. Think of a scatter plot 
analogy: what sense would it make to only show the fit line? and leave the data 
points in a supplementary figure or in some database fairly obscure for 
non-experts? This is what we are doing when we only show an atomic model. Then 
no wonder non-expert readers are confused.

Showing maps would go a long way to getting more people "structurally minded", 
until the root problem is fixed with better representations for macromolecular 
models (and viewer programs able to present all the info), like Dale suggested.

Cheers,

Guillaume


On 17 Mar 2023, at 12:25, Subramanian, Ramaswamy 
mailto:subra...@purdue.edu>> wrote:

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 reviewers' comments.   The reviewer insists 
that there is a crystal structure that clearly shows the conformation is XXX in 
the pdb and our interpretation of the biochemical data is wrong.  The B-factors 
of the atoms that he says contradict our results are over 100, and there is no 
density for them in the ED map.   I am writing with a justification, explaining 
all these - but I will see if it is accepted.  But the fact remains that this 
person who is an expert in a different field - still uses it and makes poor 
interpretations.

Are we doing a dis-service to the large group of non-experts, who think the 
positions are experimental results and interpret data?  They are often the 
audience for who we generate and deposit the data.

Thanks, and cheers!



Rams
subra...@purdue.edu



On Mar 17, 2023, at 4:57 AM, Manfred S. Weiss 
mailto:manfred.we...@helmholtz-berlin.de>> 
wrote:

 External Email: Use caution with attachments, links, or sharing data 


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. When you have crystallized your protein, and collected data
from it, the obvious assumption is that it is still intact. Unless you
have additional information, e.g. from mass spec, that some
side chains are cleaved off, they are there.

2. Absence of evidence (meaning missing electron density)
is NOT evidence of absence 

3. If you trim, you give the impression that the respective atoms
are not there. This means that the solvent model will be incorrect,
because the area will be defined as solvent.

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.

All the best
Manfred
































































































--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. 

[ccp4bb] ccp4 on cluster

[Rafiga Masmaliyeva]

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



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Re: [ccp4bb] To Trim or Not to To Trim

[mesters@biochem]

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 position in space and with this, are effectively 
indistinguishable (contrast loss i.e. similar contribution to diffraction) from 
one another?

- are current solvent models comprehensive enough in that modelling of atoms 
with very high B factors is really mutually beneficial for bulk and structure 
model?

- is model bias (overfitting) not increased by modelling highly disordered 
side-chain atoms (Rfree will probably not increase but R will drop)?

- analogous to the disordered side-chain atoms, bulk solvent atoms are of 
course also present in the crystal, so why not fill the AU with solvent 
molecules and let refinement take care of them?
(published methodology, see https://doi.org/10.1107/S0907444906021627 
)


Trimming or non-evidence-based placement and refinement are somehow halfhearted 
options with split opinions among the community as the discussions demonstrate.

Adding/Modelling a plausible side-chain rotamer with zero occupancy still has 
its charm and better reflects the situation "the side-chain atoms must be there 
but we do not know exactly where"……..

Cheers

Jeroen





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Re: [ccp4bb] To Trim or Not to To Trim

[Subramanian, Ramaswamy]

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 reviewers' comments.   The reviewer insists 
that there is a crystal structure that clearly shows the conformation is XXX in 
the pdb and our interpretation of the biochemical data is wrong.  The B-factors 
of the atoms that he says contradict our results are over 100, and there is no 
density for them in the ED map.   I am writing with a justification, explaining 
all these - but I will see if it is accepted.  But the fact remains that this 
person who is an expert in a different field - still uses it and makes poor 
interpretations.

Are we doing a dis-service to the large group of non-experts, who think the 
positions are experimental results and interpret data?  They are often the 
audience for who we generate and deposit the data.

Thanks, and cheers!



Rams
subra...@purdue.edu



On Mar 17, 2023, at 4:57 AM, Manfred S. Weiss 
 wrote:

 External Email: Use caution with attachments, links, or sharing data 


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. When you have crystallized your protein, and collected data
from it, the obvious assumption is that it is still intact. Unless you
have additional information, e.g. from mass spec, that some
side chains are cleaved off, they are there.

2. Absence of evidence (meaning missing electron density)
is NOT evidence of absence 

3. If you trim, you give the impression that the respective atoms
are not there. This means that the solvent model will be incorrect,
because the area will be defined as solvent.

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.

All the best
Manfred
































































































--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

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[ccp4bb] Structural biology facility manager post at Imperial College London

[Bubeck, Doryen A]

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 interested in 
acquiring new skills in cryo electron microscopy. The post is shared across 
both the X-ray crystallography and cryo-electron microscopy (cryoEM) facilities 
and offers an exciting opportunity for training in the field of cryoEM. The 
post will be responsible for managing the crystallisation and X‑ray 
crystallography facility within the CSB, including the training of facility 
users. The post-holder will work closely with users to support crystallisation 
experiments and X-ray crystallographic data collection, both within the CSB and 
at synchrotrons (primarily at the Diamond Light Source). The post will support 
the operation of and training for biophysical equipment within CSB and will 
work closely with the cryoEM facility manager to support the training needs of 
the CSB user community. By joining the CSB Facilities team, the candidate will 
benefit from a comprehensive package of career development opportunities, 
including Imperial’s Leadership and Management Development, and Training the 
Trainer Programmes. You will also have the opportunity to engage in 
collaborative research projects.


To apply please see the link below:



https://www.imperial.ac.uk/jobs/description/NAT01410/structural-biology-facility-manager

Best wishes,

Doryen
_

Dr. Doryen Bubeck
Director Centre for Structural Biology
Department of Life Sciences
Imperial College London

https://www.imperial.ac.uk/people/d.bubeck
@bubecklab



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Re: [ccp4bb] To Trim or Not to To Trim

[Goldman, Adrian]

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 truncated gamma-deta resolvase crystallised in *exactly* the 
same crystal form, with two entire DNA-binding domains waving in the breeze as 
far as anyone could tell from dissolving the crystals.  For the 
build-all-the-sidechains approach to be intellectually consistent, as Esko 
pointed out you must do that for all disordered loops and domains, and the N- 
and C-termini unless you have cast-iron evidence (MS on the crystals) that 
these atoms are indeed not present.  If you are working on a glycosylated 
protein, you need to model at the very least all of the first attached NAG and 
NAM and (for preference) run detailed MS on the crystal(s) to identify which 
sites have what levels of glycosylations and model out to the minimal 
identified conserved core. Complete intellectual consistency would require a 
detailed analysis of the fractional extensions at each glycosylation site and 
partial occupancies for those atoms.

At least in the academic circles I have worked in, even some modellers will 
insist on starting from a PDB model with high ADP sidechains as if there is an 
implied truth to them - and often (again my experience, YMMV) turn to you with 
a great cry of ah-ha! that the MD says that they are wrong, so what use is 
crystallography anyway?  Their complete absence sends a rather clear signal to 
the people using the model that the people solving the structure haven’t a clue 
as to where those atoms are.

Operationally, our job is to come up with an accurate model for the atoms that 
we can see. At least that’s my belief. Everything else we can leave to the 
hallucinations (I use the word advisedly) of AlphaFold2 and its offspring.  So 
let’s live and let live?  You put yours in with high ADPs: I take them out.

In both cases, the (protein structural) world is not going to come to an end.  
We can rely on the Voldemort of modern diplomacy for that.

Adrian

On 17 Mar 2023, at 11:50, Esko Oksanen 
<533d495de740-dmarc-requ...@jiscmail.ac.uk>
 wrote:

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 don’t know what reactions can 
happen during crystallisation or even data collection. I would also argue that 
the model should not primarily represent the chemical composition as such, but 
rather those atoms that are actually ordered. So if there is no electron 
density, it is not evidence of that particular atom being absent, but it that 
doesn’t mean we should model it. If one would apply the same logic to hydrogen 
atoms we should include them in the model since there is no evidence of their 
absence. Similarly we could explicitly model water molecules in the disordered 
solvent and just let them refine to high ADPs, since we have no evidence of the 
absence of water molecules. Or any disordered region of the protein such as 
termini. By not modelling these termini, hydrogens or water molecules we could 
also give the impression that they are not there, but I think the users of the 
models can and should be expected to understand the limitations of the model. I 
would find it more misleading to model things that we don’t see but assume to 
be there versus not modelling them. I think if the “end users" of the model are 
educated enough that they notice unphysically high ADPs they will also 
understand a truncated lysine side chain.

  Just my 2c,
  Esko

On 17 Mar 2023, at 09:57, Manfred S. Weiss 
mailto:manfred.we...@helmholtz-berlin.de>> 
wrote:


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. When you have crystallized your protein, and collected data
from it, the obvious assumption is that it is still intact. Unless you
have additional information, e.g. from mass spec, that some
side chains are cleaved off, they are there.

2. Absence of evidence (meaning missing electron density)
is NOT evidence of absence 

3. If you trim, you give the impression that the respective atoms
are not there. This means that the solvent model will be incorrect,
because the area will be defined as solvent.

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 

Re: [ccp4bb] To Trim or Not to To Trim

[Esko Oksanen]

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 don’t know what reactions can 
happen during crystallisation or even data collection. I would also argue that 
the model should not primarily represent the chemical composition as such, but 
rather those atoms that are actually ordered. So if there is no electron 
density, it is not evidence of that particular atom being absent, but it that 
doesn’t mean we should model it. If one would apply the same logic to hydrogen 
atoms we should include them in the model since there is no evidence of their 
absence. Similarly we could explicitly model water molecules in the disordered 
solvent and just let them refine to high ADPs, since we have no evidence of the 
absence of water molecules. Or any disordered region of the protein such as 
termini. By not modelling these termini, hydrogens or water molecules we could 
also give the impression that they are not there, but I think the users of the 
models can and should be expected to understand the limitations of the model. I 
would find it more misleading to model things that we don’t see but assume to 
be there versus not modelling them. I think if the “end users" of the model are 
educated enough that they notice unphysically high ADPs they will also 
understand a truncated lysine side chain.

  Just my 2c,
  Esko

On 17 Mar 2023, at 09:57, Manfred S. Weiss 
mailto:manfred.we...@helmholtz-berlin.de>> 
wrote:


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. When you have crystallized your protein, and collected data
from it, the obvious assumption is that it is still intact. Unless you
have additional information, e.g. from mass spec, that some
side chains are cleaved off, they are there.

2. Absence of evidence (meaning missing electron density)
is NOT evidence of absence 

3. If you trim, you give the impression that the respective atoms
are not there. This means that the solvent model will be incorrect,
because the area will be defined as solvent.

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.

All the best
Manfred
































































































--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

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Re: [ccp4bb] To Trim or Not to To Trim

[Manfred S. Weiss]

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. When you have crystallized your protein, and collected data
from it, the obvious assumption is that it is still intact. Unless you
have additional information, e.g. from mass spec, that some
side chains are cleaved off, they are there.

2. Absence of evidence (meaning missing electron density)
is NOT evidence of absence 

3. If you trim, you give the impression that the respective atoms
are not there. This means that the solvent model will be incorrect,
because the area will be defined as solvent.

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.

All the best
Manfred
































































































--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

Diese E-Mail kann vertrauliche und/oder rechtlich geschützte Informationen 
enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben, informieren Sie 
bitte sofort den*die Absender*in und vernichten Sie diese Mail. Das unerlaubte 
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[ccp4bb] Save the date! “Not the GRC” on Diffraction Methods in Structural Biology 2024

[Winter, Graeme (DLSLtd,RAL,LSCI)]

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 will have seen from a message from James Holton last year, the GRC have 
decided that the 2024 meeting on Diffraction Methods will not be further 
supported.

We are not deterred!

A number of the GRC ex-chairs and those nominated for chairing the next meeting 
feel that this opportunity for the diffraction methods community to come 
together is important enough that it should continue to happen, even without 
GRC support. We are therefore delighted to launch the “Not-the-GRC Diffraction 
methods in Structural Biology”. The topic of the meeting will be “Experiments 
and Measurements” and we have a great lineup of speakers in mind.

Where:

https://www.harnackhaus-berlin.mpg.de/en

When:

21st - 27th July 2024

i.e. about when the next diffraction methods meeting would have been. Starting 
with the model of the GRC, since we collectively believe it is a fantastic 
meeting, we plan to make a few improvements (better accommodation and 
acoustics, fewer minimum attendees to keep the feel of a small meeting) and we 
will keep the equivalent of the GRS before the main meeting, as well as the 
free afternoons for collaborative discussion, and the strong emphasis on being 
able to talk to everyone. We will also keep the focus on new ideas and so 
follow the protocol of not recording presentations and encouraging the 
presentation of unpublished data and ideas. 

With that in mind, this will be a small meeting (100-120 maximum) so there will 
be an application process and we will open registration in January 2024. We 
also want as many early career people as possible - the last GRC was refreshing 
and fun with a lot of new faces, and this is something we want to build on.

So, please hold the date in your calendar and we look forward to sharing the 
scientific programme with you in the coming months and seeing many of you in 
Berlin next summer. 

All the best Graeme, Kunio, Helena, Ali, Arwen and Ashwin


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Re: [ccp4bb] anomalous data usage

[Eleanor Dodson]

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
detail like  how fom falls off with resolution.

Then sometimes one has three data sets from “identical” crystals and it
would be nice to inspect how identical they are. cAD allows you to gather
them together with appropriate column names and I can find that useful.

Then there is the question of anomalous differences. We do much less
expensive phasing now where SAD or MAD datasets are important but I almost
always check the anom diff map at the end of refinement to make sure I
haven’t called SO4 a low bfacter water and that the MET residues really fo
have a SD atom.  Even when the anomsignal is insignificant these often show
up.

On Thu, 16 Mar 2023 at 09:00, Paul Bond <
30b0cd59fccb-dmarc-requ...@jiscmail.ac.uk> wrote:

> I believe there are many advantages to storing things *internally* as
> data objects with metadata instead of as columns of an MTZ file. How many
> students know what FP,SIGFP mean? And how many know that the FP,SIGFP
> columns in Refmac's HKLIN are not the same as the FP,SIGFP columns in
> HKLOUT? In an interface you can give these much more friendly names such as
> "observed amplitudes" and "amplitudes scaled by Refmac". The problem is
> that people should not need to access the *internal *i2 files to get to
> this data. Currently, you can export mini MTZs (containing only one data
> object) at the bottom of each report and you can export a full MTZ from
> Refmac using the Export MTZ button at the top of the interface, but
> probably this issue can be solved by doing the following:
>
>1. Making sure that reflection data objects have sensible names
>2. Expanding the "Export MTZ" functionality to have a customisable
>selection of any data objects (and allowing customisation of column labels
>as there may be clashes)
>
> Kind regards,
> Paul
>
> On Thu, 16 Mar 2023 at 07:14, Jan Dohnalek  wrote:
>
>> We are hitting the same problems also with students (so no rigidified
>> brains I think) ... the concept of "files" seems absolutely natural (also
>> to them) and when they ask about solving more tricky problems in i2 ... we
>> do the obvious, go back to ccp4i.
>>
>> I2 is fine when things are smooth and easy.
>>
>> Jan
>>
>>
>> On Wed, Mar 15, 2023 at 3:52 PM Randy John Read  wrote:
>>
>>> Hi Jon,
>>>
>>> My understanding of the philosophy is that new users would prefer to
>>> think about crystallographic data objects, rather than worrying about the
>>> arcana of MTZ files and the many different flavours of columns. There are
>>> tradeoffs — it can indeed be more difficult to find the bits of information
>>> you need, but you should be thinking in terms of the stored objects from
>>> the imports at the beginning of the project, rather than the files that
>>> hold them.
>>>
>>> Personally, I find multicolumn MTZ files easier to think about, but my
>>> brain probably rigidified a decade or two ago!
>>>
>>> Best wishes,
>>>
>>> Randy
>>>
>>> > On 15 Mar 2023, at 13:09, Jon Cooper <
>>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> >
>>> > Hello Ian,
>>> >
>>> > if I understand you and Eleanor correctly, this is the philosophy of
>>> the mini-MTZ, i.e. if you are doing anything independent of i2, you have to
>>> dig around a bit to find which output file contains the columns you need.
>>> >
>>> > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>> >
>>> > Sent from Proton Mail mobile
>>> >
>>> >
>>> >
>>> >  Original Message 
>>> > On 13 Mar 2023, 23:27, Ian Tickle < ianj...@gmail.com> wrote:
>>> >
>>> >
>>> > Eleanor, which program is doing that and more to the point, why?
>>> >
>>> > -- Ian
>>> >
>>> >
>>> > On Mon, 13 Mar 2023 at 20:17, Eleanor Dodson <
>>> eleanor.dod...@york.ac.uk> wrote:
>>> > fIf you are using ccp4I2 for some forgotten reason the final output
>>> has one reflection with I+ and I-, another with Imean, another with Fmean -
>>> aagghh
>>> >
>>> >
>>> > On Mon, 13 Mar 2023 at 19:40, Ian Tickle  wrote:
>>> >
>>> > Hi Gottfried
>>> >
>>> > AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default.
>>> >
>>> > Cheers
>>> >
>>> > -- Ian
>>> >
>>> >
>>> > On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried 
>>> wrote:
>>> > Dear all,
>>> >   I have a few questions handling (non) anomalous data:
>>> > By default aimless seems to produce Iplus and Iminus columns. Can I
>>> force it to (also) create an Imean column?
>>> > What does refmac do, when it gets Iplus and Iminus (and their sigmas)
>>> as input. Does it take only one of them or does it calculate and use Imean?
>>> > Greetings
>>> >   Gottfried
>>> >
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