Re: [ccp4bb] S=O converted to S-OH during refinement

[Peat, Tom (Manufacturing, Parkville)]

Hello Shipra,

If you have defined the small molecule with a cif dictionary file (used for 
refinement in REFMAC), then take a look at that file and see whether it is 
correctly defined.
You can manually edit these files or remake them using any number of programs 
to get the parameters you think are correct.
Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Shipra Bijpuria 

Sent: Friday, June 25, 2021 7:04 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] S=O converted to S-OH during refinement

Hello everyone,

I am trying to refine a protein-ligand complex structure.

The ligand is a small molecule and at one end has Sulfur that has three 
branches of O, NH and CH3.
Sulfur is attached to oxygen by a double bond (S=O). After fitting the ligand, 
I did refinement using Refmac5 with default settings.

But after the refinement the S=O gets converted to S-OH. Please let me know how 
can I retain the S=O during refinement.

Thanks,
Shipra



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Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

[Peat, Tom (Manufacturing, Parkville)]

I agree with Roger that human CAII is easy to express in E. coli at high level 
and does not need a tag for purification- and that it is a good lesson for 
students to purify proteins without tags (they sometimes have better activity 
and crystallise better without having the tag).
It is also easy to find things in a catalogue for binding studies (many small 
molecules with a sulfonamide moiety will bind) and assays are relatively 
straightforward to perform.
Good recommendation!
cheers, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Roger Rowlett 

Sent: Thursday, June 17, 2021 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

Human carbonic anhdydrase II is very expressible in E. coli, and purifiable in 
one step via affinity chromatography with para-aminobenzenesulfonamide affinity 
resin (which is relatively easy to make, and reusable for many years.) It can 
be assayed by stopped-flow spectrophotometry for CO2 hydration, by a timed 
colorimetric assay, or you can investigate it's esterase activity with 
p-nitrophenylacetate. This enzyme, as well as most other carbonic anhdydrases, 
is also easy to purify by a classical combination of anion exchange 
(Q-sepharose), hydrophobic interaction (butylsepharose), and gel exclusion 
polishing. The latter would be a good exercise for students in general protein 
purification optimization, which is an increasingly lost art. (Just had a 
conversation with one of the protein chemists ast BioGen who pretty much 
observed the same thing.) We routinely did classical purifications on tagless 
overexpressed proteins for crystallography work. The time saved in His-Tag 
purification is sometimes lost in cleaving the tag to make tagless protein for 
crystallography.

A paper describing the purification procedure can be found in J. Chem. Ed. 
(https://doi.org/10.1021/ed075p1021) for the similar bovine carbonic anhydrase. 
An fun long-term undergraduate research training project might involve 
improving the esterase activity through student-initiated point mutations.

I did this kind of parallel protein mutation project with my students in a 
biochemistry research training studio course I taught, often  with one of my 
research target proteins. Teaching lab students can do all sorts of crazy 
things you might never prioritize in your funded research. Some of these crazy 
things turn out to be fun and interesting. One of my students insisted on 
making a mutation in a protein that seemed to have low chances of leading to a 
successful publication based on prior work. Lo and behold, that mutation turned 
out to be gold, and he was published within the year. I still can't believe it 
not only worked, but crystallized easily from the first screen and optimization 
for structure determination. Go figure.

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

email: rrowl...@colgate.edu

On Wed, Jun 16, 2021 at 7:09 PM Chun Luo 
mailto:c...@accelagen.com>> wrote:

Many phosphatases, such as lambda phosphatase, have good soluble expression in 
E. coli. Their activity can be shown by simply colorimetric assay.



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of P. H
Sent: Wednesday, June 16, 2021 3:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Looking for proteins for undergraduate biochemistry lab



Hello All,



We are looking for some candidate proteins for an undergraduate level advanced 
biochemistry lab. They should be expressed in bacteria, simple enough to purify 
and it will be nice to perform some simple characterization experiments(binding 
assays, enzymatic assays).

Any suggestions?



Thank you in advance.

Prerna gupta





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Re: [ccp4bb] H-bond modelling

[Peat, Tom (Manufacturing, Parkville)]

Hello Vivek,

As Brian has mentioned, the angle is an important aspect, but most people 
consider distances of 2.4 to 3.2 (although there is some variability here to go 
slightly longer/ shorter, say 2.3 to 3.3) Angstrom to be a hydrogen bond 
distance between two 'heavy' atoms like oxygen and nitrogen. If you are 
interested in 'seeing' the hydrogens, you can add these to your model to see 
where they are automatically placed.
>From your figure, your density is not perfect and I suggest that you drop the 
>last digit (2.61 should be 2.6) as you have at least 0.1 Angstrom error in 
>these positions. On first inspection without knowing anything other than the 
>figure you sent, it looks like it is a likely hydrogen bond distance and a 
>likely pair of side chains that are positioned to make that hydrogen bond.

Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of vivek sharma 

Sent: Monday, June 7, 2021 6:05 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] H-bond modelling

Dear all,

How does one validate if 2 atoms (non-hydrogen) which are close enough, 
actually participate in H-bonding?
I have a recent data that i am currently working on, the NH2 of ARG is at 2.61A 
from ligand's oxygen atom (refer to attached image), since there is no electron 
density for hydrogens, how can i be sure if i am modelling ligand correctly?

thanks



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Re: [ccp4bb] Co crystalization with less soluble ligand.

[Peat, Tom (Manufacturing, Parkville)]

Hello Gourab,

DMSO is not the only possible solvent- there are others to try.
I don't want to sound negative, but 40 micromolar is not a very tight binding 
compound. It would also depend on how that binding constant was measured- how 
did someone get enough in solution to measure that?
Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Gourab Basu 
Choudhury 
Sent: Saturday, April 24, 2021 12:46 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Co crystalization with less soluble ligand.

Hello everyone,

I am finding it difficult for getting a ligand density inside the protein as 
the ligand is very much insoluble. It's only soluble in 100% DMSO. I tried for 
co crystalization. Kd value of the ligand is near 40um. Any suggestion what to 
do?



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Re: [ccp4bb] crystallizing fusion proteins

[Peat, Tom (Manufacturing, Parkville)]

Hello Herman,

If you have plenty of the fusion protein, there is probably no reason not to 
set it up in crystallisation trials and see if you get something.
There are published reports of proteins crystallising with fusion partners, but 
I suspect there are a whole lot of unpublished results of this not working as 
well.
As Artem has already stated, it could be that your protein of interest just 
doesn't like the buffer conditions when it finds itself alone in solution after 
cleavage, so that is an area to explore.
Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Schreuder, 
Herman /DE 
Sent: Monday, March 15, 2021 8:07 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] crystallizing fusion proteins


Dear Bulletin Board,

Sorry for the slightly off-topic question, but we are struggling with a 
receptor domain that expresses well as a fusion protein, but gets lost the 
moment it is cleaved from the fusion partner. It could be that the receptor 
domain is not or misfolded, but it could also be a solubility problem.



I have seen some crystal structures of fusion proteins with MBP and for 
membrane proteins, T4-lysozyme fusions are often crystallized. What is your 
experience? Would it be worth trying to express and crystallize a fusion 
protein, or would it be better to look for other constructs, e.g. to include 
more receptor domains?



Thank you very much for your advice!

Herman









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Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

[Peat, Tom (Manufacturing, Parkville)]

Speaking of Linux, but somewhat tangential to the thread:
Ubuntu has recently released their newest version 20.04 (Focal Fossa).
Has anyone implemented this and is there anything that doesn't work? Any 
gotchas that one might want to be aware of?

Cheers, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board on behalf of Tim Gruene
Sent: Sunday, February 21, 2021 2:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS 
still a good choice?

Hi Matthias,

I have been using Debian for more than a decade. Every stable release
is supported for at least 5 years.
Many crystallographic libraries and some programs are part of the
standard repository, like raster3d, pymol, shelxle, libccp4,
libclipper, ...

Debian is particularly stable, and requires little maintenance.

Cheers,
Tim

On Fri, 19 Feb 2021 21:35:46 +0100
Matthias Zeug  wrote:

> Hi all,
>
>
>
> I just came across the (already quite old) news that Red-Hat switches
> their support-policy for CentOS to a rolling preview model (replacing
> CentOS Linux by CentOS Stream):
>
> https://www.zdnet.com/article/why-red-hat-dumped-centos-for-centos-stream/
>
> https://www.enterpriseai.news/2021/01/22/red-hats-disruption-of-centos-unlea
> shes-storm-of-dissent/
>
>
>
> I wondered if that has any implications for the community, as
> scientific programs - maybe except the big ones like coot, Phenix,
> and ccp4 - are often not *that* well maintained for an extended
> period. I had the impression CentOS was liked especially for its
> "unbreakability,"  and it seems to be the main developing platform
> for some widely used smaller programs (e.g., adxv).
>
>
>
> Do you think it would be advisable to switch to a Ubuntu-distro when
> setting up new workstations in the future, or is it safe to stick to
> CentOS?
>
>
>
> Please let me know what you think :-)
>
>
>
> Best,
>
>
>
> Matthias
>
>
>
>
>
> Matthias Zeug
>
> Buchmann Institute of Molecular Life Sciences
>
> Goethe University Frankfurt
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of 
> www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & 
> conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/



--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Peat, Tom (Manufacturing, Parkville)]

Although they can now get the fold correct, I don't think they have all the 
side chain placement so perfect as to be able to predict the fold and how a 
compound or another protein binds, so we can still do complexes. I don't know 
what others end up spending their time doing, but much of my work has been 
trying to fit ligands into density, which may take another few years of 
algorithm development, which is fine for me as I can retire!
cheers, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, December 4, 2020 9:55 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Thanks all, very interesting, so our methods are just needed to identify the 
crystallization impurities, when the trays have been thrown away ;-

Cheers, Jon.C.

Sent from ProtonMail mobile



 Original Message 
On 3 Dec 2020, 22:31, Anastassis Perrakis < a.perra...@nki.nl> wrote:

AlphaFold - or similar ideas that will surface up sooner or later - will beyond 
doubt have major impact. The accuracy it demonstrated compared to others is 
excellent.

“Our” target (T1068) that was not solvable by MR with the homologous search 
structure or a homology model (it was phased with Archimboldo, rather easily), 
is easily solvable with the AlphaFold model as a search model. In PHASER I get 
Rotation Z-score 17.9, translation Z-score 26.0, using defaults.


imho what remains to be seen is:

a. how and when will a prediction server be available?
b. even if training needs computing that will surely unaccessible to most, will 
there be code that can be installed in a “reasonable” number of GPUs and how 
fast will it be?
c. how do model quality metrics (that do not compared with the known answer) 
correlate with the expected RMSD? AlphaFold, no matter how impressive, still 
gets things wrong.
c. will the AI efforts now gear to ligand (fragment?) prediction with similarly 
impressive performance?

Exciting times.

A.




On 3 Dec 2020, at 21:55, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hello. A quick look suggests that a lot of the test structures were solved by 
phaser or molrep, suggesting it is a very welcome improvement on homology 
modelling. It would be interesting to know how it performs with structures of 
new or uncertain fold, if there are any left these days. Without resorting to 
jokes about artificial intelligence, I couldn't make that out from the CASP14 
website or the many excellent articles that have appeared. Best wishes, Jon 
Cooper.


Sent from ProtonMail mobile



 Original Message 
On 3 Dec 2020, 11:17, Isabel Garcia-Saez < 
isabel.gar...@ibs.fr> wrote:

Dear all,

Just commenting that after the stunning performance of AlphaFold that uses AI 
from Google maybe some of us we could dedicate ourselves to the noble art of 
gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or 
everything together (just in case I have already prepared my subscription to 
Netflix).

https://www.nature.com/articles/d41586-020-03348-4

Well, I suppose that we still have the structures of complexes (at the moment). 
I am wondering how the labs will have access to this technology in the future 
(would it be for free coming from the company DeepMind - Google?). It seems 
that they have already published some code. Well, exciting times.

Cheers,

Isabel


Isabel Garcia-Saez PhD
Institut de Biologie Structurale
Viral Infection and Cancer Group (VIC)-Cell Division Team
71, Avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9
France
Tel.: 00 33 (0) 457 42 86 15
e-mail: isabel.gar...@ibs.fr
FAX: 00 33 (0) 476 50 18 90
http://www.ibs.fr/




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Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Peat, Tom (Manufacturing, Parkville)]

Hello Jon,

We had a novel structure and it did very well. I haven't tried the MR to see if 
the model would work, but it was so close that I can't imagine it not working. 
Our protein was ~185 residues and the closest PDB structures were about 4 
Angstrom rmsd over about 70 residues over just one part of the structure (the 
beta-sheet running through the middle), so pretty different to all the known 
structures.
So I agree with others, the predictions were much better this year.
cheers, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, December 4, 2020 7:55 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Hello. A quick look suggests that a lot of the test structures were solved by 
phaser or molrep, suggesting it is a very welcome improvement on homology 
modelling. It would be interesting to know how it performs with structures of 
new or uncertain fold, if there are any left these days. Without resorting to 
jokes about artificial intelligence, I couldn't make that out from the CASP14 
website or the many excellent articles that have appeared. Best wishes, Jon 
Cooper.


Sent from ProtonMail mobile



 Original Message 
On 3 Dec 2020, 11:17, Isabel Garcia-Saez < isabel.gar...@ibs.fr> wrote:

Dear all,

Just commenting that after the stunning performance of AlphaFold that uses AI 
from Google maybe some of us we could dedicate ourselves to the noble art of 
gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or 
everything together (just in case I have already prepared my subscription to 
Netflix).

https://www.nature.com/articles/d41586-020-03348-4

Well, I suppose that we still have the structures of complexes (at the moment). 
I am wondering how the labs will have access to this technology in the future 
(would it be for free coming from the company DeepMind - Google?). It seems 
that they have already published some code. Well, exciting times.

Cheers,

Isabel


Isabel Garcia-Saez PhD
Institut de Biologie Structurale
Viral Infection and Cancer Group (VIC)-Cell Division Team
71, Avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9
France
Tel.: 00 33 (0) 457 42 86 15
e-mail: isabel.gar...@ibs.fr
FAX: 00 33 (0) 476 50 18 90
http://www.ibs.fr/




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Re: [ccp4bb] The BDP and the CCPD

[Peat, Tom (Manufacturing, Parkville)]

Hello Murpholino,

OpenEye Scientific Software may still have a working version of the BDP, but 
you would need to inquire with them.
Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Murpholino 
Peligro 
Sent: Friday, November 27, 2020 8:02 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] The BDP and the CCPD

Do you know if the BDP 
(https://journals.iucr.org/d/issues/2005/12/00/en5128/index.html) and/or the 
CCPD (https://journals.iucr.org/d/issues/2006/06/00/cy5030/) are still 
available?


Thanks



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Re: [ccp4bb] OFF TOPIC question

[Peat, Tom (Manufacturing, Parkville)]

Hello Anamika,

>From the information you gave, you have two different promoters- araC and the 
>lac promoter. LacI is the lac inhibitor. The lac promoter is a two part 
>system- when lactose is not present, the inhibitor sits near the promoter and 
>blocks transcription of genes downstream.
Almost any E. coli system will work the expression of proteins from these 
promoters, excepting those that have been modified in some way to block 
arabinose or lactose use. The BL21 (DE3) system has the T7 system implemented, 
but as you are not using the T7 promoter, there is no particular reason to use 
this version of E. coli.
Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Anamika Singh 

Sent: Thursday, November 26, 2020 8:59 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] OFF TOPIC question

Hi all,

I have two constructs having different ori, p15ori and M13 ori, different 
promoters araC and LacI, and different antibiotic resistance chloramphenicol 
and Ampicillin respectively. I would like to know which expressing E. coli host 
cells will be good for the co-transformation of these constructs?

Thanks

Anamika




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[ccp4bb] a question regarding SIMBAD

[Peat, Tom (Manufacturing, Parkville)]

Hello All,

I would like to run SIMBAD to do a brute force MR on a data set that I have 
(running Contra-Miner didn't come up with any known contaminants and running 
SIMBAD with the Lattice and Contaminants search didn't give me anything).
As I understand the documentation, SIMBAD can be run using the MORDA database 
(which I have on my computer).
I've managed to run SIMBAD doing the Lattice and Contaminants search, but 
haven't managed to get it to run using the MORDA database for the brute force 
MR.
As far as I can tell, the servers only run the L & C and not the brute force MR.
Does anyone have experience (hopefully positive) doing this brute force MR?
cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au



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Re: [ccp4bb] number of frames to get a full dataset?

[Peat, Tom (Manufacturing, Parkville)]

I have no disagreement that anomalous is helpful and very useful data to have. 
So I’m in agreement with you and Bernhard without any reservations whatsoever.
It just so happens that 360 degrees of data in the P1 spacegroup does not give 
you very good anomalous signal. In my limited experience, one needs at least 7 
fold multiplicity/ redundancy to get enough signal to solve structures with 
anomalous (at least with what I will call ‘standard’ anomalous scatterers, not 
things like lanthanides which give very large (beautiful!) signals). And you 
just don’t get that in P1.
In violent agreement again…
Cheers, tom

From: bogba...@yahoo.co.uk 
Sent: Wednesday, 24 June 2020 10:29 AM
To: Peat, Tom (Manufacturing, Parkville) 
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

Well, it can still help. I used to be a great fan of inverse-beam expts! Oh, 
and some of us prefer the word 'multiplicity' ;-0
Jon Cooper

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
 wrote:
I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences.
I'm not a minimalist when it comes to data- redundancy is a good thing to have.
cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] number of frames to get a full dataset?

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit.
Jon Cooper

On 23 Jun 2020 07:29, Andreas Förster  wrote:
Hi Murpholino,

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.
https://doi.org/10.1107/S2059798319003528

All best.


Andreas


(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.



On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:
Hi.
Quick question...
I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':
at least 180 frames if symmetry is X
at least 90 frames if symmetry is Y
at least 45 frames if symmetry is Z
Can somebody point where is *somewhere*?

...also...
what other factors can change n... besides symmetry and radiation damage?

Thanks



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--
Andreas Förster, Ph.D.
Application Scientist Crystallography, Area Sales Manager Asia & Pacific
Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: 
andreas.foers...@dectris.com<mailto:andreas.foers...@dectris.com>
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | 
www.dectris.com<https://www.dectris.com>


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This message was issu

Re: [ccp4bb] number of frames to get a full dataset?

[Peat, Tom (Manufacturing, Parkville)]

I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences.
I'm not a minimalist when it comes to data- redundancy is a good thing to have.
cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] number of frames to get a full dataset?

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit.

Jon Cooper

On 23 Jun 2020 07:29, Andreas Förster  wrote:
Hi Murpholino,

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.
https://doi.org/10.1107/S2059798319003528

All best.


Andreas


(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.



On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:
Hi.
Quick question...
I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':
at least 180 frames if symmetry is X
at least 90 frames if symmetry is Y
at least 45 frames if symmetry is Z
Can somebody point where is *somewhere*?

...also...
what other factors can change n... besides symmetry and radiation damage?

Thanks



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--

Andreas Förster, Ph.D.
Application Scientist Crystallography, Area Sales Manager Asia & Pacific
Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: 
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | 
www.dectris.com


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Re: [ccp4bb] Question about small molecule crystallography

[Peat, Tom (Manufacturing, Parkville)]

Hello Jiyuan,

One small point to note- as Artem says, small molecule crystals are often 
generated out of solvents and these same solvents often melt the standard 
protein crystallisation plates, so be careful what you put into a plastic plate.

As Artem mentioned, synchrotrons are generally overkill for small molecule 
structures (although there are exceptions). In this case, I would like to plug 
for the Australian Synchrotron which has a dedicated small molecule 
crystallographer and a beamline set up for small molecule crystallography (we 
do some protein crystallography there too!). So there is help available for 
those that do want to use synchrotrons for small molecule structures.

cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Artem Evdokimov 

Sent: Tuesday, June 2, 2020 8:07 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Question about small molecule crystallography

Hi

A small organic molecule is typically crystallized from organic solvents (or 
water, if soluble) by means of at least three main techniques:

1. slow evaporation of solvent leading to supersaturation and eventual 
crystallization
2. supersaturation at higher temperature followed by gradual drop in 
temperature causing crystallization
3. counter-diffusion of an incompatible solvent to drop solubility of the 
substance and cause crystallization

Many times, just leaving an NMR tube with a tiny hole in the plastic cap for a 
week or so will cause crystals to form.

Schnobviously, some substances will not crystallize easily - some form oils, 
amorphous precipitates, etc. and others will form liquid hydrated forms or just 
plain decompose. If you have any specific questions please don't hesitate to 
contact me in person. I've spent half of my PhD crystallizing weird small 
molecules for fun and profit.

As to how to solve structures of small molecules - any synchrotron is a massive 
overkill. Just get in touch with a University X-ray lab, many of which still 
have functional small molecule instruments. SHELX is the software of choice - 
of course! (I still have the blue/white polka dot SHELX cup, it's one of my 
more treasured curios).

Artem
- Cosmic Cats approve of this message


On Mon, Jun 1, 2020 at 6:01 PM Jiyuan Ke 
mailto:jiyuan...@h3biomedicine.com>> wrote:
Hi Everyone,

I want to crystallize a small organic molecule. I have very limited experience 
in small molecule crystallography. I found that the Crystal Screen HT from the 
Hampton research is good for both small molecule and macromolecule 
crystallization. Plan to set up a sitting drop screen just like setting up 
protein crystallization. I don’t know if this is the proper way to do it. Is 
the MRC sitting drop 2-well plate (HR3-083) used for protein crystallization 
good for small molecule crystallization? Are there any special plates used for 
small molecule crystallization? Is room temperature ok or not?

For data collection, can I use the beamline for protein crystals to collect 
data on small molecule crystals? Larger oscillation angle, shorter exposure, 
reduced beam intensity?

For structure determination, is SHELXL the preferred software for solving small 
molecule structures?

If anyone has experience in small molecule crystallography, please help.  
Thanks!

Best Regards,

--

Jiyuan Ke, Ph.D.


Research Investigator

H3 Biomedicine Inc.

300 Technology Square, Floor 5

Cambridge, MA 02139

Phone: 617-252-3923

Email: jiyuan...@h3biomedicine.com

Website: www.h3biomedicine.com

[https://docs.google.com/uc?export=download&id=0B1VBLPNVMUntenZVa3RFS3JOcVU&revid=0B1VBLPNVMUntbExRa0hyYWpCZGVNeFhZc0JwVit3bzU5c1Z3PQ]





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Thi

[ccp4bb] linux issue- Ubuntu specific?

[Peat, Tom (Manufacturing, Parkville)]

Hello All,

For some time now I've had some issues with ccp4i starting up. Specifically it 
seems to be the drawing of new windows, so it happens upon starting up the main 
window, any application window, etc. The window starts (a small 'icon' window 
is drawn) and then things just hang. So I'm guessing it is some kind of 
graphics issue. It appears that the latest version of ccp4i with the latest 
updates to Ubuntu 18.04.4 are incompatible as now I don't just wait with 
something eventually coming up, it hangs forever.
I was wondering whether anyone else has had this experience or whether someone 
knows of a fix? I did try a Google search and didn't come up with anything 
relevant. I currently have tcl version 8.6.0+9 which is said to be 'highly 
compatible' with earlier versions (the ccp4 page suggests version 8.4).

cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au





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Re: [ccp4bb] microscope camera

[Peat, Tom (Manufacturing, Parkville)]

There are fairly cheap adapter eye-pieces that can be purchased that will hold 
most of the standard phones (iPhones 5, 6, 7, etc).
They work very well and we have replaced our old microscope camera with these 
and the pictures are great (for one offs, not for taking time courses over many 
drops/plates).
cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Phoebe A. Rice 

Sent: Saturday, November 30, 2019 8:54 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] microscope camera


With a little fiddling and patience, one can just point a cell phone camera 
down the eyepiece.  It doesn’t produce the best pics, but works fine if you 
just want to stick a few in a notebook (or a grant …).



From: CCP4 bulletin board  on behalf of Sergei Strelkov 

Reply-To: Sergei Strelkov 
Date: Thursday, November 28, 2019 at 7:47 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] microscope camera



Moticam 5 has been working well for us for a few years now (installed on a 
Leica binocular)



Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O&N2, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography



From: CCP4 bulletin board  on behalf of Dean Derbyshire 

Sent: Wednesday, November 27, 2019 11:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] microscope camera



Forgive the off topic subject:



Has anyone got any experience with moticam microscope cameras?

We are looking into cheap cameras for record keeping etc and this supplier 
looks good but…



Cheers in advance



Sent from Mail for Windows 10







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Re: [ccp4bb] A crystallisation screen pH query.

[Peat, Tom (Manufacturing, Parkville)]

As was suggested, you can take a small drop and use pH paper to get a rough 
idea of the pH.
The pH will go acidic over time as you have 20% PEG in there. This is an issue 
with all PEG conditions, so your specific pH will not be known by someone 
outside your lab as they don't know how old your screen is (and whether you've 
kept it frozen, in the fridge, at room temp, etc).
Best of luck, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Jon Cooper 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
Sent: Sunday, October 6, 2019 8:09 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] A crystallisation screen pH query.


Does anyone know the pH of JCSG+ condition A3 which is stated as 0.2 M ammonium 
citrate dibasic, 20% (v/v) PEG3350. I can't really measure it myself, so any 
help much appreciated!



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Re: [ccp4bb] challenges in structural biology

[Peat, Tom (Manufacturing, Parkville)]

Yes, but are we poets or scientists?
Wax lyrical in your poetry, but maybe have some standards in our science?
cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Goldman, Adrian 

Sent: Wednesday, July 24, 2019 7:39 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] challenges in structural biology

..and responding in the same vein:

my OED says that its etymology also comes from the Latin sulfur, sulphura in 
the plural.  So there is an etymological basis for the ph, even if it doesn’t 
come from Greek.

Plus, since when has etymological logic has _anything_ to do with English 
spelling?

Finally, it may be how the RSC is spelling it, but I would take a fair bet that 
writers of English prose today (pace America), contemplating an stinky inferno, 
will write “sulphurous flames”, not the unattractive and less stinky “sulfurous 
ones”.

Adrian


On 23 Jul 2019, at 22:21, CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi

Going off at a tangent...

The accepted spelling by the Royal Society of Chemistry (i.e. the professional 
body representing chemists in the U.K.) since at least the early 1990s has been 
"sulfate" too. "Sulphur", etc, has been deprecated for quite some time. Why? 
Well, there's no good etymological reason for the "ph" in "sulphate". My 1984 
copy of Greenwood and Earnshaw's "Chemistry of the Elements", written in 
Yorkshire, uses "sulfur" etc throughout.

"Phosphorus" comes from the Greek, so retains the "ph"s on both sides of the 
pond.

Element 13 appears to have started life as "alumium", mutated to "aluminum", 
and finally (in the English speaking world outside North America) settled down 
as "aluminium".

Harry
--
Dr Harry Powell

On 23 Jul 2019, at 17:12, Engin Özkan 
mailto:eoz...@uchicago.edu>> wrote:

On 7/23/19 3:35 AM, 
melanie.voll...@diamond.ac.uk wrote:
No longer those 20 odd names for ammonium sulphate

You mean ammonium *sulfate*. As it is called across the pond. :)

On a related note on common nomenclature for recording crystallization
experiments that Janet brought up:

I find it odd that we still do not report cryo-protection methods and
conditions in PDB depositions. Given that a large fraction of the small
molecules observed in crystal structures are derived from the
cryo-protectants, one would think that reporting the contents of that
solution (and pH) would be paramount to a PDB deposition. Surely, the
crystallographic experiment has changed since 1990/use of synchrotron
sources, which PDB has adjusted well to in most other aspects (e.g.,
including reporting of synchrotron x-ray optics and all the new
detectors during submission).

Engin




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Re: [ccp4bb] challenges in structural biology

[Peat, Tom (Manufacturing, Parkville)]

I will agree with Artem here-
Having knowledge as to whether crystallisation is likely or not with a given 
protein/ complex would be extremely useful.
If there were a set of screens/ tests/ experiments that one could run to show 
that it was 99% certain that something was not going to work (or conversely 
that something had a good chance of success) would be a goal and substantial 
step forward for the field.
Janet’s point is quite valid here- as we don’t know what people are doing (and 
we don’t have a defined vocabulary for describing experiments), we don’t 
actually know what has happened in the past, so it is hard to learn what should 
be done in the future.
So pulling together a defined way of describing what we do is likely the first 
step to understanding what has been done (and preserving it) so we know what to 
try in the future.

Cheers, tom

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Artem 
Evdokimov
Sent: Monday, 22 July 2019 7:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology

Dear Kay


I disagree that 'magic bullet' is impossible. I think the definition is wrong 
here - magic bullet to me is a rational set of methods that (when executed with 
precision and care) enable crystallization to the maximum possible benefit. 
This includes everything - constructs, crystallization design, etc. Part of the 
magic bullet is also a precise knowledge when crystallization is unlikely (i.e. 
an actual proven predictor that consistently discriminates between "you're 
going to succeed if you work hard" and "it's doomed to fail, don't bother" 
scenarios in crystallization.

The above is not sexy. It does not present itself as a lovely subject on which 
to have international cocktail parties with politicians delivering fancy 
speeches. But that is what is needed, and no one is funding that to the best of 
my knowledge.

What needs to be done is a significant amount of testing, standardization, and 
methods development from the perspective of holistic outcome (i.e. crystals 
that work) - and none of the previously advertised 'magic bullets' work the way 
I just described.

Having written this, I think you're right - this is a bit of a distraction from 
James' original point. However it's a valid opportunity for a lively discussion 
on its own :)

Artem

- Cosmic Cats approve of this message


On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:
Dear Artem,

black or white is not my way of thinking, which is why I don't believe in 
Hannibal's approach when it comes to crystallization.

None of the magic bullets that were advertised over the past decades have 
proven generally applicable.  I believe more in incremental improvement which 
in this case includes a few biophysical characterization methods, possibly 
improved microfluidics or other apparatus, and expanded screens. And a lot of 
hard work, perseverance, intuition, frustration
 tolerance. Nothing that really needs huge funding - of course it does need 
money, but just a  share of what is anyway needed for the usual lab work 
including expression, purification, functional characterization, binding 
studies and the like.

One area where a huge amount of money was burnt is crystallization in space, on 
board of e.g. the spacelab and ISS. This is for me an example of a mis-led 
approach to throw money at a difficult problem, with the expectation of a 
solution. Science does not work like that, and money in this case seems more to 
be the problem than the solution.

This example may illustrate a certain failure of us scientists to resist the 
temptation to promise unrealistic outcomes when confronted with money provided 
for political reasons, which ultimately undermines our credibility. But this 
takes us away from James' points.

best,

Kay

On Sun, 21 Jul 2019 16:06:48 -0400, Artem Evdokimov 
mailto:artem.evdoki...@gmail.com>> wrote:

>Dear Kay,
>
>Even the small, badly diffracting and 'messed up' crystals are still
>crystals. There is literally a phase transition (pun very much intended)
>between growing *usable crystals* versus *having no crystals* (or having
>crystals that do not qualify as 'diffraction quality' even under the most
>favorable light). Points 2-9 fall into the 'I have crystals' bucket and
>everything else is in the 'I have no crystals' bucket.
>
>I am being deliberately black and white of course.
>
>As to whether huge funding would help to bridge the 'phase gap' - to me
>this is a purely theoretical question since to the best of my knowledge
>there never was a 'huge funding' for this particular problem :) And if it
>is true that the general belief in the art is that crystallization is not
>worth investing into because there's no hope in it then of course it is a
>self-fulfilling prophesy.
>
>There is an unresolved dichotomy buried in the sentiment above: it seems
>that we (the community of structural biologists) more or less believe

Re: [ccp4bb] challenges in structural biology

[Peat, Tom (Manufacturing, Parkville)]

Hello Tim, 

I'm not sure this question is specific to crystallography- I believe the same 
can be asked of any experiment in any field? 
And if one wants to get into true costs- was it worth it to build the Large 
Hadron Collider to statistically prove that the Higgs boson exists? 
I'm guessing it was worth it to the folks that got their name on the paper... 
Cheers, tom 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Grüne
Sent: Tuesday, 16 July 2019 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology

Dear James,

10) are the biological questions that you can answer with a (crystal) structure 
sufficiently relevant to justify the resources?

Best,
Tim



Am 15.07.2019 21:44, schrieb Holton, James M:
> Hello folks,
> 
> I have the distinct honor of chairing the next Gordon Research 
> Conference on Diffraction Methods in Structural Biology (July 26-31 
> 2020).  This meeting will focus on the biggest challenges currently 
> faced by structural biologists, and I mean actual real-world 
> challenges.  As much as possible, these challenges will take the form 
> of friendly competitions with defined parameters, data, a scoring 
> system, and "winners", to be established along with other unpublished 
> results only at the meeting, as is tradition at GRCs.
> 
> But what are the principle challenges in biological structure 
> determination today?  I of course have my own ideas, but I feel like 
> I'm forgetting something.  Obvious choices are:
> 1) getting crystals to diffract better
> 2) building models into low-resolution maps (after failing at #1)
> 3) telling if a ligand is really there or not
> 4) the phase problem (dealing with weak signal, twinning and
> pseudotranslation)
> 5) what does "resolution" really mean?
> 6) why are macromolecular R factors so much higher than small-molecule 
> ones?
> 7) what is the best way to process serial crystallography data?
> 8) how should one deal with non-isomorphism in multi-crystal methods?
> 9) what is the "structure" of something that won't sit still?
> 
> What am I missing?  Is industry facing different problems than 
> academics?  Are there specific challenges facing electron-based 
> techniques?  If so, could the combined strength of all the world's 
> methods developers solve them?  I'm interested in hearing the voice of 
> this community.  On or off-list is fine.
> 
> -James Holton
> MAD Scientist
> 
> 
> ##
> ##
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University 
of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] challenges in structural biology

[Peat, Tom (Manufacturing, Parkville)]

If one were able to crystallise almost all proteins (and complexes) reliably 
and with good diffraction, that would make most people's lives much easier. So 
I would go with 1) as a grand challenge.

Many of the rest follow on from not having 'good' crystals to start with.

cheers, tom


Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au



From: CCP4 bulletin board  on behalf of Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, July 16, 2019 5:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] challenges in structural biology

Hello folks,

I have the distinct honor of chairing the next Gordon Research
Conference on Diffraction Methods in Structural Biology (July 26-31
2020).  This meeting will focus on the biggest challenges currently
faced by structural biologists, and I mean actual real-world
challenges.  As much as possible, these challenges will take the form of
friendly competitions with defined parameters, data, a scoring system,
and "winners", to be established along with other unpublished results
only at the meeting, as is tradition at GRCs.

But what are the principle challenges in biological structure
determination today?  I of course have my own ideas, but I feel like I'm
forgetting something.  Obvious choices are:
1) getting crystals to diffract better
2) building models into low-resolution maps (after failing at #1)
3) telling if a ligand is really there or not
4) the phase problem (dealing with weak signal, twinning and
pseudotranslation)
5) what does "resolution" really mean?
6) why are macromolecular R factors so much higher than small-molecule ones?
7) what is the best way to process serial crystallography data?
8) how should one deal with non-isomorphism in multi-crystal methods?
9) what is the "structure" of something that won't sit still?

What am I missing?  Is industry facing different problems than
academics?  Are there specific challenges facing electron-based
techniques?  If so, could the combined strength of all the world's
methods developers solve them?  I'm interested in hearing the voice of
this community.  On or off-list is fine.

-James Holton
MAD Scientist




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Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

[Peat, Tom (Manufacturing, Parkville)]

Hello Kay, 

Yes, locks the whole machine means it is dead in the water- no mouse, no other 
windows can be activated, no sequence of buttons (e.g. Ctrl-Alt-Del, Ctrl-C, 
etc) to stop or bring anything back to life. What I would call a classic case 
of the machine crashing- the window with the molecule is there, I just can't do 
anything. 
I can look into the magic SysRq system and see if that can help at all. 

Cheers, tom 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: Monday, 15 July 2019 4:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

Hi Tom,

does "locks my whole machine" mean that you cannot open another terminal 
window? If you still can, use the "ps -ef | grep coot" command to find out if 
the coot process still exists, and note its process id ("pid"). If it does, 
remove it with "kill -9 ". 
Or does the window system crash? This would be a bug of the latter.
Or does (the crashed) coot still take input focus, with the effect that you 
cannot use your mouse to activate another window? In that case, try "Alt-tab" 
to switch window focus.
Or can you not even type in another window? For such cases, it pays off to set 
up the machine for the "Alt-SysRq"commands; see 
https://en.wikipedia.org/wiki/Magic_SysRq_key . These can be used to trigger a 
reboot. On Linux I see rarely a need to reset a machine with the power button. 

HTH,
Kay

On Mon, 15 Jul 2019 05:24:38 +, Peat, Tom (Manufacturing, Parkville) 
 wrote:

>Hello again, 
>
>To be more specific- sometimes when Coot crashes, I can just restart Coot. 
>Sometimes it locks my whole machine (maybe 30% of the time) and I need to 
>reboot. 
>The former is just a small pain, the latter is a true pain and I prefer 
>software not to crash the machine in such an untidy way. 
>
...
>
>I'm currently using Ubuntu 18.04.2 LTS and I think I'm reasonably up to date 
>wrt updates... 
>



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Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

[Peat, Tom (Manufacturing, Parkville)]

Hello again, 

To be more specific- sometimes when Coot crashes, I can just restart Coot. 
Sometimes it locks my whole machine (maybe 30% of the time) and I need to 
reboot. 
The former is just a small pain, the latter is a true pain and I prefer 
software not to crash the machine in such an untidy way. 

Cheers, tom 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat
Sent: Thursday, 11 July 2019 4:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ExternalEmail] [ccp4bb] coot crashing

Hello All, 

Just wondering if anyone else is having issues with Coot crashing (regularly, 
not just once in a while). 
I get the following error message: 

/home/pea246/bin/ccp4-7.0/bin/coot: line 318:  2025 Segmentation fault  
(core dumped) $coot_bin "$@"
guile (GNU Guile) 2.2.3
Packaged by Debian (2.2.3-deb+1-3ubuntu0.1) Copyright (C) 2017 Free Software 
Foundation, Inc.

License LGPLv3+: GNU LGPL 3 or later .
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
catching the crash log:
Gtk-Message: Failed to load module "gail"
Gtk-Message: Failed to load module "atk-bridge"
Gtk-Message: Failed to load module "canberra-gtk-module"
coot-exe: "/home/pea246/bin/ccp4-7.0/libexec/coot-bin"
/bin/ls
coot-version: 
/home/pea246/bin/ccp4-7.0/libexec/coot-bin
platform: 
/bin/uname
core: #f
No core file found.  No debugging


I'm currently using Ubuntu 18.04.2 LTS and I think I'm reasonably up to date 
wrt updates... 

Any help would be appreciated if someone has resolved any similar issue. 

cheers, tom 



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