Re: [ccp4bb] test

[Jeffrey B Bonanno]

All,  seems to be working, thanks for response Kim Van Vliet.

Nukri Sanishvili, I think the issue was that the echo message has my own name 
and email address in it and so it was filtered here.

best, Jeff

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jeffrey B 
Bonanno
Sent: Tuesday, November 26, 2019 11:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] test

just running a test, haven't been receiving my own messages...

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einstein.yu.edu





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Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[Clemens Grimm]

Checking Cryo-Conditions under the microscope can actually be very  
useful. Even if you have access to a X-ray beam, simple pre-tests can  
be very informative.


This can be done as follows:

A 24well plate cover is placed on a stereo microscope open side down,  
a second one on top of it the other way around. Carefully pour lN2  
into it (might make a crackling noise, however the plastic should  
stand it). A 1 mm loop is placed on top of a 'crystal wand' tool,  
dipped first into the cryo buffer under investigation and then quickly  
into the lN2 on the microscope. Hold the loop right under the lN2  
surface and focus. Vitrification of the shock-cooled buffer can now be  
assesed.
I usually check  a series with increasing concentrations of  
cryo-protectant to determine the critical point for successful  
vitrification. To the final buffer I then add a certain safety margin  
to avoid unpleasant surprises during the synchrotron trip, if an X-ray  
test is not possible.


Clemens


Zitat von Karthik S biokart...@gmail.com:


I have not heard of anyone checking for suitable cryo in that fashion how
fast can you do it before it is affected by room temp and how would you know
about the ice rings, but when you have crystal(s) and not crystal you can
freeze different ones in several different cryos (sugars, glycerol etc) and
take them with you to the trip. good luck!
--
Karthik

Graduate Student-Biophysics
University of Michigan
Ann Arbor, MI 48109
karth...@umich.edu
734-763-3384

On Tue, Sep 22, 2009 at 4:24 AM, Claudia Scotti
claudiasco...@hotmail.comwrote:



Dear List,

Sorry for the probably silly question.

Any suggestions to test cryoconditions without X-rays or cryostream?

I'd need to freeze crystals before going to ESRF and I'm a bit anxious. Is
it enough to try to freeze the cryoconditions in liquid nitrogen checking
under the microscope (or by eye) or is this still risky?

Thanks,

Claudia



Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia
Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039
0382 986335/8/1 Facs 0039 0382 303673



--
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Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[James Holton]

You can put your dogbowl dewar under the microscope and focus it on 
the surface of the liquid nitrogen.  This works very well once you have 
got the lighting right.  You want to shine the light on the bottom of 
the dewar so that it acts as a backlight for your loop.  You can hold 
the loop just above the surface of the liquid and it will still be very 
cold, but much easier to see.


However, as has been mentioned there is no substitute for diffraction.  
Transparency of the drop is neither necessary nor sufficient for good 
crystal diffraction.  Salty cryos do cool as amorphous solids, but often 
have a mottled surface that is not optically clear, and 
nano-crystalline cubic ice is optically clear, but still gives sharp ice 
rings. 

That said, some protein crystals diffract better in cubic ice than they 
do in amorphous ice.  The trick to the whole thing is avoiding strain in 
the protein crystal lattice because if it strains as it cools then none 
of your unit cells will be exactly the same size, and high-order Fourier 
terms vanish.  It is easy to imagine how strain could build up if your 
solvent channels contract differently than the protein lattice.  The 
problem is that there is no way to know ahead of time how your protein 
crystal lattice will interact with a particular cryo, so you have to 
screen.  I recommend taking a large VARIETY of cryo conditions to the 
beamline for your first trip (don't just freeze everything in 
glycerol).  Mixed cryos are easier to glassify than single-component 
cryos (the confusion effect).  Don't forget oil, it works about half 
the time (in my experience), and mind the level of liquid nitrogen in 
the dewar or your cooling rate will not be reproducible (Warkentin et 
al., JACr 2006).  Or, better yet, if at all possible take uncooled 
crystals to the beam and learn as you go.  Protein crystals are a lot 
like children, they are all special and unique and expect to be treated 
that way, even after they are fully grown.


-James Holton
MAD Scientist


Claudia Scotti wrote:
 
Dear List,
 
Sorry for the probably silly question.
 
Any suggestions to test cryoconditions without X-rays or cryostream?
 
I'd need to freeze crystals before going to ESRF and I'm a bit 
anxious. Is it enough to try to freeze the cryoconditions in liquid 
nitrogen checking under the microscope (or by eye) or is this still risky?
 
Thanks,
 
Claudia
 



Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di 
Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia 
Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673





With Windows Live, you can organize, edit, and share your photos. 
http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[Karthik S]

I have not heard of anyone checking for suitable cryo in that fashion how
fast can you do it before it is affected by room temp and how would you know
about the ice rings, but when you have crystal(s) and not crystal you can
freeze different ones in several different cryos (sugars, glycerol etc) and
take them with you to the trip. good luck!
--
Karthik

Graduate Student-Biophysics
University of Michigan
Ann Arbor, MI 48109
karth...@umich.edu
734-763-3384

On Tue, Sep 22, 2009 at 4:24 AM, Claudia Scotti
claudiasco...@hotmail.comwrote:


 Dear List,

 Sorry for the probably silly question.

 Any suggestions to test cryoconditions without X-rays or cryostream?

 I'd need to freeze crystals before going to ESRF and I'm a bit anxious. Is
 it enough to try to freeze the cryoconditions in liquid nitrogen checking
 under the microscope (or by eye) or is this still risky?

 Thanks,

 Claudia



 Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia
 Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039
 0382 986335/8/1 Facs 0039 0382 303673



 --
 With Windows Live, you can organize, edit, and share your 
 photos.http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[mesters]

Dear Claudia,

please be so kind and tell us all what is / are the crystallization 
condition(s)? It would help to us to answer your question!


- J. -



Claudia Scotti wrote:
 
Dear List,
 
Sorry for the probably silly question.
 
Any suggestions to test cryoconditions without X-rays or cryostream?
 
I'd need to freeze crystals before going to ESRF and I'm a bit 
anxious. Is it enough to try to freeze the cryoconditions in liquid 
nitrogen checking under the microscope (or by eye) or is this still risky?
 
Thanks,
 
Claudia
 



Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di 
Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia 
Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673





With Windows Live, you can organize, edit, and share your photos. 
http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx



--
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Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
Institut für Biochemie, Universität zu Lübeck
Zentrum für Medizinische Struktur- und Zellbiologie
Ratzeburger Allee 160, D-23538 Lübeck
Tel: +49-451-5004065, Fax: +49-451-5004068
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.selfish-brain.org
Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me  (Macbeth)
--

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[Frank von Delft]

Hi Claudia

By eye is not a bad approximation.  The trick I learnt at the JCSG (I 
forget the originator, sorry) is to suck up some solution in a P2 
pipette tip (the clear ones), dip it in lN2, and then hold it just above 
the lN2 (where it's still cold) to check for clearness or not.


Is a good predictor especially if your loops are very small (volume is a 
big factor in whether you can achieve vitrification or not).


Cheers
phx



On Tue, Sep 22, 2009 at 4:24 AM, Claudia Scotti 
claudiasco...@hotmail.com mailto:claudiasco...@hotmail.com wrote:


 
Dear List,
 
Sorry for the probably silly question.
 
Any suggestions to test cryoconditions without X-rays or cryostream?
 
I'd need to freeze crystals before going to ESRF and I'm a bit

anxious. Is it enough to try to freeze the cryoconditions in
liquid nitrogen checking under the microscope (or by eye) or is
this still risky?
 
Thanks,
 
Claudia
 



Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di
Patologia Generale Universita' di Pavia Piazza Botta, 10 27100
Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673




With Windows Live, you can organize, edit, and share your photos.

http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[Arthur Glasfeld]

It might be risky (and silly), but I have done this successfully.  I  
just put a small dewar of liquid N2 under the scope, focussed  
directly above the surface and looked to see if cryo solutions froze  
clear or not.  The ones that did worked out when we got to the  
beamline (we'd verified that the crystals survived the treatment in  
the solutions by eye as well).  Only tried it that once, so I have no  
idea how reliable it is.


Good luck,

Arthur Glasfeld
Department of Chemistry
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202
USA


On Sep 22, 2009, at 1:24 AM, Claudia Scotti wrote:



Dear List,

Sorry for the probably silly question.

Any suggestions to test cryoconditions without X-rays or cryostream?

I'd need to freeze crystals before going to ESRF and I'm a bit  
anxious. Is it enough to try to freeze the cryoconditions in liquid  
nitrogen checking under the microscope (or by eye) or is this still  
risky?


Thanks,

Claudia



Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di  
Patologia Generale Universita' di Pavia Piazza Botta, 10 27100  
Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673




With Windows Live, you can organize, edit, and share your photos.

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[Paul Leonard]

Hi Claudia

It really is best to test the cryo condition in an X-ray beam.

However, if you don't have access to X-rays in house you could look at the
hampton crystallization screen conditions (or another supplier).  Find a
condition with a similar amount and type of precipitant as you have in
your crystallisation condition and look up how much glycerol they added as
cryoprotectant.  Then try making up your own crystallisation condition
with the amount of glycerol they recommend and freeze your crystals in
that solution.

Also try crystal soaks of varying lengths of time (30 seconds - 5 min) in
the cryo condition as well as trying to soak some crystals where you
gradually increase the %glycerol in the crystal soak prior to freezing (in
2% glycerol steps for example).

see
http://hamptonresearch.com/product_detail.aspx?cid=1sid=20pid=3

Good luck.

Paul



 Dear List,



 Sorry for the probably silly question.



 Any suggestions to test cryoconditions without X-rays or cryostream?



 I'd need to freeze crystals before going to ESRF and I'm a bit anxious. Is
 it enough to try to freeze the cryoconditions in liquid nitrogen checking
 under the microscope (or by eye) or is this still risky?



 Thanks,



 Claudia





 Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia
 Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel.
 0039 0382 986335/8/1 Facs 0039 0382 303673



 _
 With Windows Live, you can organize, edit, and share your photos.
 http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx


Department of Biochemistry
UMDNJ-Robert Wood Johnson Medical School
Center for Advanced Biotechnology and Medicine
679 Hoes Lane
Piscataway, New Jersey 08854-5627

Phone: (732) 235-4206
Email: leon...@cabm.rutgers.edu

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

[Jürgen Bosch]

I think I posted this link maybe two years ago:
http://idb.exst.jaxa.jp/db_data/protein/search-e.php?

Jürgen

On Sep 22, 2009, at 12:48 PM, Elspeth Garman wrote:


or see concentrations given in:
McFerrin and Snell
J.Appl.Cryst (2002) 35, 538
and
Mitchell and Garman,
J.Appl.Cryst. (1996) 29, 584
Good luck
EFG



Paul Leonard wrote:

Hi Claudia

It really is best to test the cryo condition in an X-ray beam.

However, if you don't have access to X-rays in house you could look  
at the
hampton crystallization screen conditions (or another supplier).   
Find a
condition with a similar amount and type of precipitant as you have  
in
your crystallisation condition and look up how much glycerol they  
added as
cryoprotectant.  Then try making up your own crystallisation  
condition
with the amount of glycerol they recommend and freeze your crystals  
in

that solution.

Also try crystal soaks of varying lengths of time (30 seconds - 5  
min) in

the cryo condition as well as trying to soak some crystals where you
gradually increase the %glycerol in the crystal soak prior to  
freezing (in

2% glycerol steps for example).

see
http://hamptonresearch.com/product_detail.aspx?cid=1sid=20pid=3

Good luck.

Paul



Dear List,



Sorry for the probably silly question.



Any suggestions to test cryoconditions without X-rays or cryostream?



I'd need to freeze crystals before going to ESRF and I'm a bit  
anxious. Is
it enough to try to freeze the cryoconditions in liquid nitrogen  
checking

under the microscope (or by eye) or is this still risky?



Thanks,



Claudia





Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di  
Patologia
Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia  
Tel.

0039 0382 986335/8/1 Facs 0039 0382 303673



_
With Windows Live, you can organize, edit, and share your photos.
http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx




Department of Biochemistry
UMDNJ-Robert Wood Johnson Medical School
Center for Advanced Biotechnology and Medicine
679 Hoes Lane
Piscataway, New Jersey 08854-5627

Phone: (732) 235-4206
Email: leon...@cabm.rutgers.edu



--
**NOTE NEW E-MAIL ADDRESS AND PHONE NUMBER

 Elspeth F. Garman,
 President, British Crystallographic Association
 Professor of Molecular Biophysics, University of Oxford
 Visiting Professor in Chemistry, University of Durham
 Postal address:
 Laboratory of Molecular Biophysics,
 Department of Biochemistry,
 University of Oxford,  Tel: (44)-1865-613297
 South Parks Road,  FAX: (44)-1865-613201
 OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.uk
http://www.biop.ox.ac.uk/www/garman/gindex.html
-


-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

Re: [ccp4bb] test data sets part II...

[Mark J. van Raaij]

Dear All,

with regards to diffraction images storage (see also Androulakis et  
al., Acta Cryst. (2008). D64, 810–814: Federated repositories of X- 
ray diffraction images), I am all for it - one to be able to catch  
fraud, but more importantly so structures can be improved in the  
future and better data processing programs can be developed.


However, I would welcome a central repository or at least a central  
organisation of local nodes, because I can see no local solution where  
I am (probably other small macromolecular crystallography groups would  
have the same problem). In fact, if someone would agree to host our  
data I would be happy to upload datasets. For some datasets it would  
even be useful if I could send the digital tapes, we don't have a  
reader for them anymore and in that way we ourselves can have access  
to our own data...


Greetings,

Mark

Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/







On 24 Sep 2008, at 02:43, Ashley Buckle wrote:


We put our raw data, plus metadata here: http://www.tardis.edu.au
JCSG also make data available, but I think its just an archive, with  
little or no annotation

cheers
Ashley

On 24/09/2008, at 7:02 AM, afyfe wrote:


Dear Tommi,
I'm not sure whether 'test data sets part I'  relates to the query   
I mailed the other day but,  in light of the  recent posts  
regarding  fundamental literature, your suggestion seems an  
excellent one.


Perhaps I'm not looking in the right places, but finding examples  
of image sets exhibiting e.g., radiation damage, crystal slippage,  
autoindexing failures or any of the aberrations shown in Phil  
Evans' excellent scala tutorial seems  difficult. Likewise for  
examples of good and bad final-refinement maps. Making primary/ 
intermediate data available would benefit both students and  
algorithm comparison/validation (e.g.  measuring performance on  
standard data sets is routine in data-visualization/image- 
processing papers).


Tommi Kajander wrote:

Also, i think that would be nice if this type of info could be put  
on  the web, part of the wiki for instance..
if there is some consensus to what works + the typical proteins  
easily  available.


Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
[EMAIL PROTECTED]




--
Alastair Fyfe
Graduate Student
Biomolecular Engineering Dept.
University of California, Santa Cruz




Associate Professor Ashley M Buckle
NHMRC Senior Research Fellow
The Department of Biochemistry and Molecular Biology
School of Biomedical Sciences, Faculty of Medicine 
Victorian Bioinformatics Consortium (VBC)
Monash University, Clayton, Vic 3800
Australia

http://www.med.monash.edu.au/biochem/staff/abuckle.html
iChat/AIM: blindcaptaincat
skype: ashley.buckle
Tel: (613) 9902 0269 (office)
Tel: (613) 9905 1653 (lab)

Fax : (613) 9905 4699

Re: [ccp4bb] test data sets part II...

[Kay Diederichs]

I have put some data sets, and data reductions including 
crystallographic calculations, into XDSwiki: check out 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Quality_Control
This is work in progress, so expect additions/changes! And the best is: 
anyone may contribute ...


HTH,

Kay


smime.p7s
Description: S/MIME Cryptographic Signature

Re: [ccp4bb] test data sets part II...

[Uwe Mueller]

EMBL-Hamburg and BESSY have put a number of interesting data-sets 
including tutorial materials for data processing and phase determination 
made available recently.


You can download the data from both locations:
http://www.mx.bessy.de/xray_tutorial.shtml
http://webapps.embl-hamburg.de/Xray_Tutorial/


Uwe

--
___
Dr. Uwe Mueller
AG Makromolekulare Kristallographie   
BESSY GmbH   
Albert-Einstein-Straße 15   
D-12489 Berlin 
Phone: +49-(0)30-6392 4974   
Fax  : +49-(0)30-6392 4975   
email: [EMAIL PROTECTED]   
url  : http://www.mx.bessy.de 

Re: [ccp4bb] test data sets part II...

[afyfe]

Dear Tommi,
I'm not sure whether 'test data sets part I'  relates to the query  I 
mailed the other day but,  in light of the  recent posts regarding  
fundamental literature, your suggestion seems an excellent one.


Perhaps I'm not looking in the right places, but finding examples of 
image sets exhibiting e.g., radiation damage, crystal slippage, 
autoindexing failures or any of the aberrations shown in Phil Evans' 
excellent scala tutorial seems  difficult. Likewise for examples of good 
and bad final-refinement maps. Making primary/intermediate data 
available would benefit both students and algorithm 
comparison/validation (e.g.  measuring performance on standard data sets 
is routine in data-visualization/image-processing papers).


Tommi Kajander wrote:

Also, i think that would be nice if this type of info could be put on  
the web, part of the wiki for instance..
if there is some consensus to what works + the typical proteins 
easily  available.


Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
[EMAIL PROTECTED]




--
Alastair Fyfe
Graduate Student
Biomolecular Engineering Dept.
University of California, Santa Cruz