[ccp4bb] refmac output query

[Emmanuel Saridakis]

Dear All,

A quick question about Refmac on ccp4i. When refining an RNA oligonucleotide 
structure using the findwaters option, the pdb output labels all the atoms as 
HETATM (inluding the original RNA atoms which were not so labelled in the input 
pdb). It is of course trivial to correct this, but I was wondering if there is 
a hidden problem somewhere, that might influence more crucial things.

Many thanks,
Emmanuel

-- 
Dr. Emmanuel Saridakis
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE



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

[Emmanuel Saridakis]

Dear John,
Your article touches all the important points about this breakthrough and its 
caveats.
I would just like to add that the ligand problem is of a different order: it is 
fundamentally not about whether, where and how a ligand is predicted to bind, 
but rather about whether it indeed binds where and in the way it is predicted 
to. So I daresay that it is an irreducibly experimental problem.
Best,
Emmanuel

Dr Emmanuel Saridakis
National Centre for Scientific Research DEMOKRITOS
Athens, Greece
- Original Message -
From: John R Helliwell 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tue, 08 Dec 2020 15:15:14 +0200 (EET)
Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Dear Isabel,
My article in the IUCr Newsletter on DeepMind and CASP14 is released today and 
can be found here:-
https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14
Best wishes,
John 
Emeritus Professor John R Helliwell DSc




> On 3 Dec 2020, at 11:17, Isabel Garcia-Saez  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-SaezPhD
> 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/
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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-- 
Dr. Emmanuel Saridakis
Principal Researcher
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE

tel: +30-2106503793
email: e.sarida...@inn.demokritos.gr



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Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[Emmanuel Saridakis]

And Eleanor Dodson, of course!!! 
E. 


From: "ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ"  
To: "CCP4BB"  
Sent: Thursday, 6 February, 2020 12:15:07 
Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 
2020 


Dear All, 

To strike a more positive note, crystallography (esp. macromolecular) has 
always had a very high representation of women at top levels: Kathleen 
Lonsdale, Dorothy Crowfoot Hodgkin, Rosalind Franklin and Ada Yonath are the 
most famous names that immediately come to mind, but there are many more highly 
distinguished ones like Elena Conti, Naomi Chayen, Elspeth Garman, Petra Fromme 
and scores more. There seems to be no "glass ceiling" for women in 
crystallography so I believe it is one of very few scientific fields where 
gender balance discussions and constraints are irrelevant. 

This might be due to Bragg son, who apparently was a champion of women in 
Science. If this is indeed the case, that would provide strong support to the 
argument that underrepresenation of women in Science (and elsewhere) is due to 
historical reasons that can be easily overturned, rather than to any biological 
predetermination. Crystallography after all is a field which is heavy on maths, 
space visualisation and high-tech instrumentation, which people would 
traditionally more readily associate with males. 

Let me finish with a famous quote by author William Golding: " I think women 
are foolish to pretend they are equal to men. They are far superior and always 
have been." 

Emmanuel 

- 
Dr. Emmanuel Saridakis 
Principal Researcher 
Institute of Nanoscience and Nanotechnology 
National Centre for Scientific Research "DEMOKRITOS" 
15310 Athens 
GREECE 

email: e.sarida...@inn.demokritos.gr 



From: "Bärbel Blaum"  
To: "CCP4BB"  
Sent: Thursday, 6 February, 2020 11:30:36 
Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 
2020 



Dear all, 



yes, there are more male computational crystallographers than females – the 
question we can ask ourselves here is: Do we think there is some biological 
reason for this? Obviously there isn’t. So things are wrong as they stand. Are 
we, nevertheless, ok with this current state of affairs? We are not talking 
some minor issue here – if half of the population is under-represented, that is 
a giant intellectual loss (actually for * all * professions that lack 
diversity, childcare included, and of course the loss is not just on the 
intellectual level). 



If you think you have been lucky to work in a place where there is no bias 
against women it just means you are lucky in not being one. If you care to 
know, simply try and put the other side’s shoes on. Start asking your female 
colleagues, friends, partners, students about their experience, moments they 
witnessed were they felt overlooked or deliberately excluded, treated in sexist 
ways, you name it. You will be surprised. 



Then think about the moments, institutions, relationships that have been 
instrumental in your own careers. University meetings and important talks 
routinely held and given in the evenings. Conferences with no childcare. Many 
male researchers only being able to work as much as they do because some female 
is looking after the house and the kids. Babies being colored-coded by gender, 
mummys at home and daddys at work. Girls being told it’s ok to be bad at math. 
You must be joking if you wonder where all the female scientists are! We all 
grow up and are educated in a world that is heavily biased in terms of which 
roles which gender adopts - how are we supposed to not think that this reflects 
some form of “natural” order? There are plenty of other groups that grow up 
systematically underestimating their potentials, just compare students from 
academic homes with those from working class backgrounds. And there is plenty 
of research on the subject. 



The question is if you care to notice this bias, discrimination, lack of equal 
opportunities, and if you care to do something about it - of course we all have 
other things to attend to. But if teaching is part of our job description then 
we have to think about how to be good teachers, and that does not stop at how 
to explain Fourier transforms or python. The reason I suggested a meeting by a 
female group of scientists as only organizers and speakers is because as long 
as we have these male-dominated environments at workshops and meetings the 
respective younger generation will be presented with this order as being the 
natural way things work * because we taught them so *. If we want these younger 
guys to get things right in ways we did not we have to create alternative 
perspectives and come up with new forms of community work. 



Bärbel 




-- 

Bärbel Blaum, PhD 

Inthera Bioscience AG 

Einsiedlerstrasse 34 

CH-8820 Waedenswil 

Switzerland 

E-Mail: baerbel.bl...@intherabio.com 

Phone: +41 43 477 94 72-- 

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[Emmanuel Saridakis]

Dear All, 

To strike a more positive note, crystallography (esp. macromolecular) has 
always had a very high representation of women at top levels: Kathleen 
Lonsdale, Dorothy Crowfoot Hodgkin, Rosalind Franklin and Ada Yonath are the 
most famous names that immediately come to mind, but there are many more highly 
distinguished ones like Elena Conti, Naomi Chayen, Elspeth Garman, Petra Fromme 
and scores more. There seems to be no "glass ceiling" for women in 
crystallography so I believe it is one of very few scientific fields where 
gender balance discussions and constraints are irrelevant. 

This might be due to Bragg son, who apparently was a champion of women in 
Science. If this is indeed the case, that would provide strong support to the 
argument that underrepresenation of women in Science (and elsewhere) is due to 
historical reasons that can be easily overturned, rather than to any biological 
predetermination. Crystallography after all is a field which is heavy on maths, 
space visualisation and high-tech instrumentation, which people would 
traditionally more readily associate with males. 

Let me finish with a famous quote by author William Golding: " I think women 
are foolish to pretend they are equal to men. They are far superior and always 
have been." 

Emmanuel 

- 
Dr. Emmanuel Saridakis 
Principal Researcher 
Institute of Nanoscience and Nanotechnology 
National Centre for Scientific Research "DEMOKRITOS" 
15310 Athens 
GREECE 

email: e.sarida...@inn.demokritos.gr 



From: "Bärbel Blaum"  
To: "CCP4BB"  
Sent: Thursday, 6 February, 2020 11:30:36 
Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 
2020 



Dear all, 



yes, there are more male computational crystallographers than females – the 
question we can ask ourselves here is: Do we think there is some biological 
reason for this? Obviously there isn’t. So things are wrong as they stand. Are 
we, nevertheless, ok with this current state of affairs? We are not talking 
some minor issue here – if half of the population is under-represented, that is 
a giant intellectual loss (actually for * all * professions that lack 
diversity, childcare included, and of course the loss is not just on the 
intellectual level). 



If you think you have been lucky to work in a place where there is no bias 
against women it just means you are lucky in not being one. If you care to 
know, simply try and put the other side’s shoes on. Start asking your female 
colleagues, friends, partners, students about their experience, moments they 
witnessed were they felt overlooked or deliberately excluded, treated in sexist 
ways, you name it. You will be surprised. 



Then think about the moments, institutions, relationships that have been 
instrumental in your own careers. University meetings and important talks 
routinely held and given in the evenings. Conferences with no childcare. Many 
male researchers only being able to work as much as they do because some female 
is looking after the house and the kids. Babies being colored-coded by gender, 
mummys at home and daddys at work. Girls being told it’s ok to be bad at math. 
You must be joking if you wonder where all the female scientists are! We all 
grow up and are educated in a world that is heavily biased in terms of which 
roles which gender adopts - how are we supposed to not think that this reflects 
some form of “natural” order? There are plenty of other groups that grow up 
systematically underestimating their potentials, just compare students from 
academic homes with those from working class backgrounds. And there is plenty 
of research on the subject. 



The question is if you care to notice this bias, discrimination, lack of equal 
opportunities, and if you care to do something about it - of course we all have 
other things to attend to. But if teaching is part of our job description then 
we have to think about how to be good teachers, and that does not stop at how 
to explain Fourier transforms or python. The reason I suggested a meeting by a 
female group of scientists as only organizers and speakers is because as long 
as we have these male-dominated environments at workshops and meetings the 
respective younger generation will be presented with this order as being the 
natural way things work * because we taught them so *. If we want these younger 
guys to get things right in ways we did not we have to create alternative 
perspectives and come up with new forms of community work. 



Bärbel 




-- 

Bärbel Blaum, PhD 

Inthera Bioscience AG 

Einsiedlerstrasse 34 

CH-8820 Waedenswil 

Switzerland 

E-Mail: baerbel.bl...@intherabio.com 

Phone: +41 43 477 94 72-- 









Von: CCP4 bulletin board  im Auftrag von Susan Lea 
 
Antworten an: Susan Lea  
Datum: Donnerstag, 6. Februar 2020 um 02:21 
An:  
Betreff: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 
2020 





Perhaps so

Re: [ccp4bb] Protein fold and the moonlighting function

[Emmanuel Saridakis]

I believe this is more than a fluke. It looks to me like a very powerful 
evolutionary tool which may have rendered the early stages in the evolution of 
life less improbable.
Best wishes,
Emmanuel Saridakis


- Original Message -
From: "Peter Stogios" 
To: "CCP4BB" 
Sent: Monday, 3 February, 2020 02:18:45
Subject: Re: [ccp4bb] Protein fold and the moonlighting function

I think you’re asking if two proteins with the same fold can have different 
activities.

As was previously mentioned, this is quite common.  The best characterized 
example is the TIM barrel fold - such proteins can be isomerases, transferases, 
hydrolases, lyases, or oxidoreductases, to name a few...



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Re: [ccp4bb] crystallization optimization

[Emmanuel Saridakis]

Dear All, 

Fine-tuning protein and precipitant concentration is of course the first line 
of approach, followed by both rMMS and streak-seeding. 

I would like to remind you of a far less popular but often successful in my 
hands, optimisation technique: It consists in incubating the trial at the 
condition that gives the ugly crystals for some time (shorter than the time it 
takes for the ugly crystals to appear), and then changing the condition to one 
of lower supersaturation for the growth to proceed. That can be done either by 
diluting the reservoir with water (vapour diffusion) or diluting the drop with 
buffer (microbatch), or by just transferring your plate to a different (usually 
higher) temperature. 

Described in more (but perhaps unecessary for most practical purposes) detail 
in: 
E. Saridakis , P.D. Shaw Stewart, L.F. Lloyd and D.M. Blow. Acta Crystallogr. 
(1994) D 50 , 293. 


E E . Saridakis and N.E. Chayen. Protein Science (2000) 9 , 755. 
Best, 
Emmanuel 


De: "Alun R Coker"  
À: "CCP4BB"  
Envoyé: Mercredi 12 Juillet 2017 15:40:10 
Objet: Re: [ccp4bb] crystallization optimization 



Hi Everyone, 

Franks point is really interesting. We routinely reduce the protein 
concentration when we see too many precipitated wells, but we never dilute the 
screen. Has anyone tried this? 

All the best, 

Alun 

On 12/07/17 08:48, Frank von Delft wrote: 




The point I was failing to make: reducing either protein or precipitant 
concentration will indeed reduce nucleation, but often won't get you bigger or 
more single crystals: it will just make the appearance of crystals less 
reliable. 


The way to get big single reliable crystals is to increase protein and greatly 
reduce precipitant. 


(Even better: do seeding. Like Vicky said. Incredible how often people don't 
bother to do seeding, yet it solves so many problems.) 

phx 



On 12/07/2017 07:50, Vicky Tsirkone wrote: 

BQ_BEGIN

Dear Frank, 

I may see in the attached pic several nucleation points and a considerable 
amount of microcrystals. Based to my knowledge decreasing the concentration of 
the precipitant and/or the protein concentration would be a reasonable approach 
to refine the initial hits. 
By checking the diagram as you correctly mentioned you may see that the fine 
tuning of protein and precipitant concetration may lead to the desirable result 
without reaching the precipitation zone. 

Patrick just check your screens. Just a rule of thumb, if you see precipitation 
in the ~60% of your drops then you should definitely reduce the protein 
concentration. 

ps dont forget to try the streak seeding , as well. 

Have a nice day and again good luck. 

Vicky 

On Wed, Jul 12, 2017 at 8:50 AM, Frank von Delft < [ 
mailto:frank.vonde...@sgc.ox.ac.uk | frank.vonde...@sgc.ox.ac.uk ] > wrote: 

BQ_BEGIN



Actually, you should try increasing the protein concentration - a lot. But be 
prepared to drop the precipitant concentration to almost nothing (1 or 2% isn't 
"low"). 


To understand why, look at the phase diagram and what we assume about vapour 
diffusion. (Which I'm assuming is what you're doing.) 



On 12/07/2017 06:28, Vicky Tsirkone wrote: 

BQ_BEGIN

Dear Patrick, 

You may reduce the protein concentation, as well. 
Another option could be the streak seeding by exploiting the drop of your 
initial condition. 

Good luck, 

V.T. 

On Mon, Jul 10, 2017 at 7:17 PM, Patrick Shaw Stewart < [ 
mailto:patr...@douglas.co.uk | patr...@douglas.co.uk ] > wrote: 

BQ_BEGIN


Microseed them into two or three random screens. 

Search for MMS and rMMS online. 

Good luck 

Patrick 




On 10 July 2017 at 15:47, Liuqing Chen < [ mailto:519198...@163.com | 
519198...@163.com ] > wrote: 

BQ_BEGIN
hello everyone! 
I get a condition (10% w/v PEG 6000, 100mm HEPES PH7.0) in which my protein 
grow small needle like crystals, how can i optimize it to get bigger crystals? 
the attach is the crystals figure. 
thanks in advance 
sincerely 
Liuqing Chen 






-- 
[ mailto:patr...@douglas.co.uk | patr...@douglas.co.uk ] Douglas Instruments 
Ltd. 
Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK 
Directors: Peter Baldock, Patrick Shaw Stewart 

[ http://www.douglas.co.uk/ | http://www.douglas.co.uk ] 
Tel: 44 (0) 148-864-9090 US toll-free [ tel:%28877%29%20225-2034 | 
1-877-225-2034 ] 
Regd. England 2177994, VAT Reg. GB 480 7371 36 

BQ_END



BQ_END


BQ_END



BQ_END


BQ_END

-- 
Dr Alun R. Coker
Senior Lecturer
Wolfson Institute for Biomedical Research
University College London
The Cruciform Building
London
WC1E 6BT

Tel: 020 7679 6703 Ext 46703
Web: [ http://www.ucl.ac.uk/pxmed | www.ucl.ac.uk/pxmed ] 

Re: [ccp4bb] Alexander Rich

[Emmanuel Saridakis]

Dear Colleagues,

I do not think it is highly inappropriate that a crucial episode in the 
history of crystallography is described/commmented on in this thread, and I am 
not sure by whom its removal will be highly appreciated, other than by Prof. 
Berger. I do not know any of the protagonists of this episode, except by 
reputation, and the only thing I would be ready to concede is that maybe the 
subject was brought up a bit too close to the sad death of Prof. Rich. But if 
someone is that distinguished, his/her life story will be discussed, for better 
(mostly) or worse (occasionally).

Emmanuel

Dr. Emmanuel Saridakis
PhD Biophysics, MSc History and Philsophy of Science
Institute of Nanscience and Nanotechnology
N.C.S.R. Demokritos
Athens 15310
Greece


- Original Message -
From: Edward A. Berry ber...@upstate.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Saturday, 2 May, 2015 23:30:29
Subject: Re: [ccp4bb] Alexander Rich passed away Monday April 27, 2015

On 05/02/2015 12:23 PM, Imre Berger wrote:
 Dear Edward -

 Would you be so kind and explain why you went ahead to post that comment
 about Alex Rich on CCP4, in a thread which announced the sad news of his
 passing away?

Yes- I realized after posting it that it was inappropriate. If there is any way 
to remove a post, I will be glad to do so. In any case an apology is due.

As for the explanation, I did not intend it to be in any way derogatory.
I have never met Alex Rich, but Prof Sung-Hou Kim was my mentor in 
crystallography, and I have no doubt that their actions were completely 
honorable. As explained on the page I linked, it was all a misunderstanding 
based on poor communications between Kim and Rich, and rapid progress on the 
part of Kim that Rich was not aware of at the previous meeting. There was no 
evidence of actual misconduct on the part of Rich or Kim, as grudgingly 
acknowledged in the final letter from Cambridge. If only I had pointed that out 
in the email, instead of linking to that first accusatory message, it wouldn't 
have looked so bad. I had forgotten how inflammatory that first letter was!

I was thinking this followed in the lines of Bob Sweet's post, that Rich was a 
hard-driving man and maybe not afraid of stepping on some peoples toes in order 
to achieve his goals. I never meant to imply misconduct, although after reading 
back on my post I can see that interpretation.

My sincere apologies to the community and to the memory of professor Rich,
Ed Berry



 I have checked your home page and your CV and it is not obvious to me at
 all what motivation or stake you could possibly have.

 Besides, knowing both Alex Rich and Aaron Klug  and having discussed
 with them years ago, I think it is fair to say that only those two are
 concerned with the issue, and one of them has - very sadly - just died.

 In any case - in my view it is highly inappropriate indeed that you
 placed those comments on CCP4.

 Maybe you could be so kind and remove your contribution from the thread
 - it would be greatly appreciated.

 De mortuis nihil nisi bonum

 Imre

 --

 Imre Berger PhD HDR
 Professor of Biochemistry
 Wellcome Trust Senior Investigator
 Coordinator, EC FP7 ComplexINC project
 The School of Biochemistry, University of Bristol UK
 The European Molecular Biology Laboratory EMBL
 imre.ber...@bristol.ac.uk
 iber...@embl.fr

[ccp4bb] 3D graphics linux compatibility question

[Emmanuel Saridakis]

Dear BB,

We are still a bit confused about compatibility of graphics cards with 3D 
Coot/PyMol in Linux:

(a) In previous CCP4bb discussions, it was stated that only Quadro cards are 
compatible with Linux setups. But could someone tell me what the minimum 
standard really is: is it Quadro FX380, 2000, 3800 or something else ? The 
nVidia site lists Quadro 3700 and 3800 as the two lowest (cheapest) options 
compatible with Linux 3D. However, different CCP4ers have in the past mentioned 
the other two options as working perfectly or with little trouble.

(b) If a monitor such as the ASUS VG278H , which has an in-built nVidia 3D 
vision emitter which takes its stereo synch from a DVI cable is used, can we 
even use the simpler GeForce GTX670 or 680 ?

As you might imagine, we are on a rather tight budget. Any info would be 
greatly appreciated!


Emmanuel Saridakis

N.C.S.R. DEMOKRITOS
Athens 15 310 Greece
esari...@chem.demokritos.gr
tel. +30-210-6503793

Re: [ccp4bb] Temperature and crystallization

[Emmanuel Saridakis]

Dear Acoot,

In the website of the company Centeo, you can find the slides of a short 
presentation I had given three years ago on temperature and macromolecular 
crystalllisation. You may find some info there:

http://www.centeo.com/_fileupload/Temperature%20Control%20in%20PXTL.pdf

There is a lot more on the centeo.com site.

Best,

Emmanuel Saridakis

  - Original Message - 
  From: Acoot Brett 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Monday, November 19, 2012 7:08 AM
  Subject: [ccp4bb] Temperature and crystallization


Dear All,

Will you please give a comment on how the temperature influences on the 
possibility to get protein crystal, and how the temperatures used to get the 
protein crystals of the same protein influences the protein 3-D structures of 
the same protein got based on the crystals of the same protein got at different 
temperatures?

Cheers,

Acoot


   

Re: [ccp4bb] do you think it is interesting?

[Emmanuel Saridakis]

Of course, oligomer (pure Greek) usually does that kind of job, but not in 
this specific case, since oligo means few and in this case we have endless 
chains.
I can only think of the neologism myriomer for this particular case, if 
you want to stick to Greek. Myrioi can mean 1 or countless, depending on 
where you accent the word!


If that catches on, remember you (probably) saw it here first!

Cheers,
Emmanuel


- Original Message - 
From: Tim Gruene t...@shelx.uni-ac.gwdg.de

To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, June 18, 2012 5:43 PM
Subject: Re: [ccp4bb] do you think it is interesting?



-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

[...]

of monomers is called a multimer, not a polymer.

[...]
shiver - what a terrible mixture of languages. 'multi-' has got latin
origin, whereas both poly and mer have got greek origin, and I don't
think one should mix these. Please!!! think of a different _GREEK_
syllable to express what you describe as 'multimer'.

Cheers,
Tim

On 06/18/12 16:21, David Schuller wrote:

Certainly it's interesting, but I think your description is
inaccurate.

Endless linear polymers - Each monomer is a polymer, but a
collection of monomers is called a multimer, not a polymer.

I don't suppose there are any knots? That would be really
interesting.

On 06/18/12 09:49, anna anna wrote:

Hi all! I'd like your opinion about a structure I solved. Apart
from protein structure itself, I think that my protein xtallized
in an odd way! The biological unit is a dimer while the
asymmetric unit is a tetramer (red cartoon in the figure)
resulting from domain swapping between two dimers. The strange
thing is that swapping connects infinite monomers and, rather
than a xtal, my diffracting object seems a multilayer of endless
linear polymers, a kind of papyrus with greek fret-like fibers.
The figure shows the orientation of the polymers in each layer.
I'd like to know if some of you have already seen a similar
pattern or it is weird as I think! I'm further racking my brain
to figure out a biological implication of this behaviour, I
thought something like plaque formation but I can't find support
in literature.

All suggestions are welcome!!

Cheers, Anna







- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP
o034eyZnadpwyQRGXI4FV9w=
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[ccp4bb] Pointless problems

[Emmanuel Saridakis]

Dear All,

I am having problems when trying to run Pointless with input from
Denzo/Scalepack.

(1) Pointless refuses to work from the .sca file. The error message is:

CCP4 library signal mtz:File not identified as MTZ (Error)
CCP4MTZfile: open_read - File missing or corrupted: rn7e222test.sca

or

The program run with command: /programs/CCP4/ccp4-6.1.1/bin/pointless
has failed with error message
child process exited abnormally

(when run from ccp4i)

(2) Scalepack2mtz refuses to convert a Scalepack file produced using the
command: NO MERGE original index (i.e. as instructed by the Pointless
instructions). It fails with the rather tactless message:

*  Resolution Range :
0.002020.00485 ( 22.256 - 14.357 A )
 * Sort Order :
  0 0 0 0 0
 * Space group = 'P 2 2 2' (number 16)

 SCALEPACK2MTZ:  Check your data!

And, no my resolution range is not 22.2-14.3 A!!

(3) Pointless refuses to work with an .mtz file produced by Scalepack2mtz
from a .sca file obtained with the simple NO MERGE instruction (remember
the NO MERGE original index instruction is a no-go for Scalepack2mtz).
The error message in this case is quite simply:

HKLIN is merged and no HKLREF file is defined, SPACEGROUP or REINDEX.

I know the orthodox ccp4 reply would be stop whining and use Mosflm!,
but is there an alternative if I really want to use Denzo/Scalepack? If
not, is there another way to check my point group/spacegroup starting from
Denzo/Scalepack?

Thanks a lot!

Emmanuel

[ccp4bb] DTU vs DTT ?

[Emmanuel Saridakis]

Dear All,

Possibly a trivial question but your experience would be much appreciated:

I recently submitted a structure to PDB containing 3 DTT (dithiothreitol) 
molecules, or so I thought. The molecules had been imported and fitted with 
Coot using the Get Monomer... instruction with the code DTT. The Annotator 
responded, quite rightly as it turns out, as follows:

Please note DTT in your coordinates has been changed to DTU since it
 has incorrect stereochemistry as DTT.
 Please review the stereochemistory in the attached validation report
 summary.

 You can send me corrected stereochemistry for DTT if you want it
 changed back.

 DTU (2R,3S)-1,4-disulfanylbutane-2,3-diol
 C4 H10 O2 S2

 DTT (2R,3R)-1,4-disulfanylbutane-2,3-diol
 C4 H10 O2 S2

So, is the DTT monomer of Coot in fact its stereoisomer known as 
dithioerythritol? Should I import the correct DTT from elsewhere and re-refine 
or is there something else behind this?

Thanks a lot for any suggestions!


Emmanuel

Re: [ccp4bb] How to distinguish microcrystalline, quasicystalline and precipitation?

[Emmanuel Saridakis]

Hi Joy,

Yes, I agree that it is very difficult to distinguish those and it is even more 
difficult to put it in words or in writing: experts have been talking about 
shininess, transparency (rather than brown colour) and birefringence as far as 
I know. All these methods have some grain of truth in them, yet none is as 
simple let alone as accurate as we would like to believe. So, it seems to me 
that the only way to distinguish is what I would call the operational way, 
i.e. to streak seed from that precipitate into a couple of drops set at very 
similar conditions but that are just below the spontaneous nucleation level of 
supersaturation: if something grows along the streak line, the precipitate was 
microcrystalline. However, if it doesn't, that doesn't mean that it was not 
microcrystalline? Dilemma? 

Another interesting question that you are raising is what are quasicrystalline 
or ordered precipitates really worth, in terms of ultimate success near the 
relevant conditions...

Finally, how about these fluorescent pens? I have not had a chance to use one 
of these, but my feeling is that they would only really work on good-sized 
crystals. It would be very interesting to hear members' experiences with these 
on smaller stuff.

Best,

Emmanuel

  - Original Message - 
  From: joybeiyang 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Thursday, June 10, 2010 9:06 AM
  Subject: [ccp4bb] How to distinguish microcrystalline, quasicystalline and 
precipitation?



  Hi everyone, I am preparing a crystallization manual for our group, 
however, I found that it is very difficult to distinguish microcrystalline, 
quasicrystalline and precipitation, especially when the precipitation was 
shiny, like the grit on the beach. Is there a way to distinguish the three? 
   
  Comments and suggestions will be greatly appreciated!


--

  Joy

Re: [ccp4bb] Off-topic: hollow protein crystals

[Emmanuel Saridakis]

Dear Andre,

Yes, hollow crystals are not very uncommon. We have recently also solved a 
structure at very high resolution using long hollow crystals. Initially the 
walls were very thin; we managed to make them thicker (and the hole 
correspondingly smaller) by standard fine-tuning of conditions. I didn't see 
any special effects arising from the hollowness. We just got higher 
resolution as we got more material to fill in some of the hole.

Saridakis E; Giastas P; Efthymiou G; Thoma V; Moulis J-M; Kyritsis P; Mavridis 
I. M
J Biol.Inorg. Chem. 2009;14(5):783-99.

Best,

Emmanuel

  - Original Message - 
  From: Andre Ambrosio 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Wednesday, June 02, 2010 10:07 PM
  Subject: [ccp4bb] Off-topic: hollow protein crystals


  Dear all,

   

  We have recently obtained crystals from a small protein, and interestingly, 
at least for me, they are hollow trigonal rods (please see pictures attached).

  Just out of curiosity, has anybody ever seen such feature for protein 
crystals before?

   

  Regards,

  -Andre.

   

   

   

Re: [ccp4bb] Setting Microbatch trays !!

[Emmanuel Saridakis]

Dear Rashmi,

The original standard for microbatch crystallisation is paraffin oil (from 
Sigma or elsewhere). Drops set under paraffin oil lose almost no water, so it 
works like a well-sealed batch experiment, in other words you need to have your 
conditions right and you do get crystals. Paraffin oil is the only case where 
the reported conditions are the true ones.

Al's oil allows slow water evaporation through the oil, so the drops get slowly 
concentrated, something like a vapour diffusion, except that you don't have a 
well-defined end-point, i.e. a reservoir solution. Douglas Instruments I think 
sell some microbatch plates with a channel around them which can be used as a 
reservoir for such cases. Al's oil may thus give you more hits, since the 
supersaturation of the drops gets progressively higher. Of course, you don't 
know what the true crystallisation conditions are.

Silicone oil allows a great deal of evaporation through it, so it may actually 
give you even more hits but you also may end up with drops drying out before 
having the chance to produce any crystals, unless you use the plates I talked 
about before, in which case it works a lot like a vapour diffusion experiment.

Have a look at Douglas Instruments' web page: there is a lot of relevant info 
in there.

Cheers,

Emmanuel Saridakis


  - Original Message - 
  From: rashmi panigrahi 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Friday, April 23, 2010 5:35 AM
  Subject: [ccp4bb] Setting Microbatch trays !!


  Hi,
  While setting up microbatch trays  (under oil crystallization),
  1.  Has anybody used mineral oil (sigma M8410) and obtained some crystal hits?
  2.  Has anybody used anything other than Al's oil from Hampton, as Parafin 
oil from sigma or silicone oil from sigma and obtained some crystal hits?
  Thanks

  -- 
  rashmi

[ccp4bb] PhD position in protein crystallography

[Emmanuel Saridakis]

PhD position in crystallization and structure solution of natural and 
appropriate variants of the sponge protein silicatein and nanobiotechnology 
applications

 

TOPIC: Research in the field of biomineralization and applications in 
nanobiotechnology. Biomineralization is the formation of minerals by living 
cells and organisms. To understand the processes involved in biomineralization 
(at the cutting edge between inorganic and organic world)and for 
nanobiotechnology applications, the structure determination of natural and 
appropriate variants of silicatein from marine demosponge Suberites domuncula 
is required. The prospective student will carry out European funded research 
(Marie Curie ITN network BIOMINTEC) in two of the partner institutions, NCSR 
Demokritos in Greece and Johannes Gutenberg-Universitaet, Mainz in Germany and 
will operate within a network of institutions highly specialized in 
biomineralisation. The project includes participation in workshops and summer 
schools. Motivation to travel and adapt to a different country and to integrate 
efficiently in a new working team is fundamental.

 

TYPE OF APPOINTMENT-DURATION-STARTING DATE: Full-time contracts in the two 
institutions (overall period 36 months), starting April 2010 at NCSR Demokritos.

 

PROFILE-ELIGIBILITY
Applicants should have a BS or MSc degree in chemistry, biological sciences or 
related sciences and £4 years research experience at the time of hiring. They 
can be nationals of European Union or Associated Countries, other than the 
country of the host organisations (Greece  Germany). Candidates from countries 
outside EU are also eligible. Greek or German citizens who have resided in 
Greece or Germany for less than 12 months in the 3 years prior to the hiring 
dates are also eligible.

 

BENEFITS

The successful candidate as a Marie Curie fellow will enjoy high salary 
(according to the Marie Curie guidelines with social security benefits) and 
additionally a mobility allowance covering family obligations, travel allowance 
and career exploratory allowance. 

 

HOW TO APPLY

Applicants should forward electronically (a) their detailed CV, (b) copies of 
published articles, (c) names, e-mails/phone numbers of two referees to:

 

Dr. I. M. Mavridis

Institute of Physical Chemistry 

National Center for Scientific Research Demokritos

Aghia Paraskevi 1520, Athens -Greece

mavr...@chem.demokritos.gr

[ccp4bb] Post-doctoral opening in macromolecular crystallography, Athens Greece

[Emmanuel Saridakis]

Laboratory of Structural and Supramolecular Chemistry, Institute of Physical 
Chemistry,   National Center for Scientific Research DEMOKRITOS ,Terma 
Patriarhou Gregoriou, Aghia Paraskevi 15310,  Athens-Greece
Opening for a position of Experienced Researcher (4-10 years) in production, 
crystallisation and X-ray crystallography of biological macromolecules

 

TOPIC: TOPCRYST, an academia-industry (IAPP) FP7 Marie Curie project, will use 
Dual Polarimetric Interferometry, pioneered by Farfield Scientific Ltd., to 
probe crystallisation at its earliest, most crucial stages. Transfer of 
knowledge between academia and industry will tackle the problem of detecting 
crystal nucleation phenomena at the very earliest stages of crystallisation and 
holds a number of promises that will be investigated in its course.

The post doctoral, experienced researcher (4-10 years after the bachelor's 
degree) will be mainly occupied with production and/or crystallisation of 
macromolecules (by the method to be developed and by conventional methods), as 
well as with determination of their molecular structures according to the 
needs. Additional activity: the structure-based drug design project, 
specifically on complexes of antibiotics synthesized in-situ with A-site 
ribosomal RNAs (http://lssc.chem.demokritos.gr/).   





TYPE OF APPOINTMENT-DURATION-STARTING DATE: Full-time contract - 24 months - 
Salary, that of an experienced researcher ( 55000/annum gross) according to 
the Marie Curie projects guidelines - Any time up to March 1st  2010.



PROFILE-ELIGIBILITY
Applicants should have a PhD degree, experience in production, crystallisation 
of proteins and X-ray crystallography and 4-10 years research experience at the 
time of hiring. They can be nationals of any country other than the country of 
the host organisation (Greece), preferably citizens of EU Member States or 
Associated Countries, as long as they have not resided or carried out their 
main activity in Greece for more than 12 months in the last 3 years. Candidates 
from countries outside the EU are also eligible. Greek citizens who have 
resided in third countries for at least 3 years in the 4 years prior to this 
hiring date are also eligible.



HOW TO APPLY

Applicants should forward electronically (a) their detailed CV (b) copies of 
published articles, (c) names, e-mails/phone numbers of two referees to:

Dr. Emmanuel Saridakis   or   
Dr Irene Mavridis

esaridakatchem.demokritos.gr 
mavridiatchem.demokritos.gr

Tel. +30-210-6503658  
Tel. +30-210-6503793