Re: [ccp4bb] largest protein crystal ever grown?

[Tobias Beck]

Dear all, dear John,

Thanks for the replies and references! I like the ice cream tub setup.

Best wishes, Tobias.


On Thu, Oct 24, 2013 at 10:05 PM, Jrh  wrote:

> Dear Tobias,
> There is also this one :- http://dx.doi.org/10.1107/S0021889801007245
> In this study we had to use a smaller crystal than the largest ones
> available of 125mm3. They were a lovely rhombic dodecahedral crystal habit.
> Nb we only published details of the size of the one used. These crystals
> were grown by Joseph Gilboa at The Weizmann Institute, who we miss dearly.
> See the appreciation of Joseph by Felix Frolow and myself  at
> http://dx.doi.org/10.1107/S0021889810006941
> Yours sincerely,
> John
>
> Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
> Chair School of Chemistry, University of Manchester, Athena Swan Team.
> http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
>
>
>
> On 24 Oct 2013, at 16:33, Tobias Beck  wrote:
>
> Dear all,
>
> I was just wondering if anyone has some information or references about
> the dimensions of the largest protein crystal ever grown? I am aware that
> for neutron protein crystallography one usually needs crystals with mm
> dimensions. I have found some information on crystallization under
> micro-gravity and how this can enlarge the crystal size. However, I would
> rather be interested in the dimensions for crystals obtained from a regular
> lab setup.
>
> Thanks, Tobias.
>
> --
> ___
>
> Dr. Tobias Beck
> ETH Zurich
> Laboratory of Organic Chemistry
> Wolfgang-Pauli-Str. 10, HCI F 322
> 8093 Zurich, Switzerland
> phone:   +41 44 632 68 65
> fax:+41 44 632 14 86
> web:  http://www.protein.ethz.ch/people/tobias
> ___
>
>


-- 
___

Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Wolfgang-Pauli-Str. 10, HCI F 322
8093 Zurich, Switzerland
phone:   +41 44 632 68 65
fax:+41 44 632 14 86
web:  http://www.protein.ethz.ch/people/tobias
___

Re: [ccp4bb] Electron density server

[Clement Angkawidjaja]

Dear Rojan,

Get the mmCIF, then use CIF2MTZ from CCP4.

Cheers,
Clement

On 10/25/13 3:07 PM, Rojan Shrestha wrote:


Hello,

Is EDS (electron density server) dead? In the absence of EDS, how can 
be mtz file directly downloaded?


Regards,

Rojan

[ccp4bb] Electron density server

[Rojan Shrestha]

Hello,

 

Is EDS (electron density server) dead? In the absence of EDS, how can be mtz
file directly downloaded?

 

Regards,

 

Rojan

[ccp4bb] strange unit cell

[유상헌]

Hi everyone,

 

Recently I’ve got a protein crystal and I did indexing and scaling with a
cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a
Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry
space groups and I successfully solved the structure with a space group P21
(Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit
cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m
confused with this fact that a, b, and c of the unit cell are almost same,
and in addition, the beta angle is too close to 90. I didn’t do refinement
with a twin option. So, is the space group correct? Is there anyone who
know this case?

 

Thanks,

 

Sangheon Yu

Rm. 1053 Bldg. 200

School of Agricultural Biotechnology

College of Agriculture & Life Sciences

Seoul National University

Seoul 151-921, KOREA 

 

 

Re: [ccp4bb] largest protein crystal ever grown?

[Jrh]

Dear Tobias,
There is also this one :- http://dx.doi.org/10.1107/S0021889801007245
In this study we had to use a smaller crystal than the largest ones available 
of 125mm3. They were a lovely rhombic dodecahedral crystal habit. Nb we only 
published details of the size of the one used. These crystals were grown by 
Joseph Gilboa at The Weizmann Institute, who we miss dearly. See the 
appreciation of Joseph by Felix Frolow and myself  at 
http://dx.doi.org/10.1107/S0021889810006941
Yours sincerely,
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 24 Oct 2013, at 16:33, Tobias Beck  wrote:

> Dear all,
> 
> I was just wondering if anyone has some information or references about the 
> dimensions of the largest protein crystal ever grown? I am aware that for 
> neutron protein crystallography one usually needs crystals with mm 
> dimensions. I have found some information on crystallization under 
> micro-gravity and how this can enlarge the crystal size. However, I would 
> rather be interested in the dimensions for crystals obtained from a regular 
> lab setup.
> 
> Thanks, Tobias. 
> 
> -- 
> ___
> 
> Dr. Tobias Beck
> ETH Zurich
> Laboratory of Organic Chemistry
> Wolfgang-Pauli-Str. 10, HCI F 322
> 8093 Zurich, Switzerland
> phone:   +41 44 632 68 65
> fax:+41 44 632 14 86
> web:  http://www.protein.ethz.ch/people/tobias
> ___

Re: [ccp4bb] largest protein crystal ever grown?

[Derek Logan]

Hi,

Last spring I visited the Protein Crystallography Station at Los Alamos. On a 
shelf, in a capillary in a serious exhibition-quality glass dome, was a crystal 
of myoglobin some 50 mm**3, if I remember correctly. I was told it had been 
made by Benno Schoenborn some decades earlier and had been exposed to most of 
the neutron sources in the world (radiation damage - forget about it!) Paul 
Langan or Zoë Fisher can correct me if I've exaggerated the size or age.

Anyway, as I already lost the record several times over for having seen the 
biggest protein crystal ever, I can share with you the surprise and delight of 
having to centre the crystals using a telescope mounted on a tripod on the 
other side of the room. Apparently the magnification on the microscope on the 
diffractometer (visible in this photo, and maybe the giant crystal too? 
http://www.lanl.gov/_assets/php/flickrImage.php?photo_id=5033219363&secret=291f519124)
 was too high, so any "neutron-size" crystals would filled the whole field of 
view even if they were not well-centered.

FWIW, my crystals (somewhat optimistically 0.4 mm**3) didn't diffract neutrons 
even after a 24h exposure :-)

Derek

Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  www.cmps.lu.se
Centre for Molecular Protein Science   www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden

On 24 Oct 2013, at 18:35, Victor Lamzin  wrote:

> Also following on from John's comment - back to the times of my PhD I was 
> repeatedly growing crystals of bacterial formate dehydrogenase (80 kDa) of a 
> size about 7x1.5x1 mm. I thought that was quite normal and did not even think 
> of making a photo of 'just a protein crystal'.
> 
> Victor

[ccp4bb] Call for proposals at ALBA Synchrotron - Deadline 4 Nov.

[Jordi Juanhuix]

Dear all,

 

The MX beamline at the Alba Synchrotron (Barcelona), BL13-XALOC, is now open
for user proposal applications. Worldwide institutes are eligible for
beamtime, which is awarded upon peer-reviewed proposals. The beamline is
included in the   Biostruct-X funding program
for transnational beam time access within EU. In order to apply, please
register at the Alba User Office Application (http://useroffice.cells.es
  ).

 

Application deadline is November 4, 2013, for the period April-December,
2014.

You can find information about the beamline at 

  http://www.cells.es/Beamlines/XALOC

 

Experimental setup includes: 

*   In-vacuum undulator IVU21, 2-m long in a 3-GeV storage ring.
*   Tuneable energy range 5.5-21 keV, DE/E = 2×10-4 
*   Full beam size 50×7 µm2 (h×v, FWHM) – Larger vertical beam size with
same flux upon request
*   Vertical beam divergence <0.1µrad 
*   Pilatus 6M detector 
*   Microdiffractometer (MD2), with optional Mini-kappa goniometer MK3.
*   Automatic sample changer (CATS), 90 sample storage capacity (SPINE
pin compatibility) 
*   Bruker AXS X-Flash fluorescence detector 
*   Common MX software installed 

 

Best regards,

 

 

Jordi Juanhuix Gibert

Experiments Division, CELLS-ALBA Synchrotron

Carretera BP 1413, de Cerdanyola a Sant Cugat, km 3,3

E-08290 Cerdanyola del Vallès, Barcelona

Tel: (+34) 93 592 43 22

www.cells.es  

 

 

Re: [ccp4bb] largest protein crystal ever grown?

[Victor Lamzin]

Also following on from John's comment - back to the times of my PhD I  
was repeatedly growing crystals of bacterial formate dehydrogenase (80  
kDa) of a size about 7x1.5x1 mm. I thought that was quite normal and  
did not even think of making a photo of 'just a protein crystal'.


Victor

[ccp4bb] Double screen bug in Xquartz, Mac OS 10.9 (Mavericks)

[Carlos Kikuti]

This is just to inform that if you have a second screen plugged to your Mac and 
you want to use Mac OS 10.9, you should consider disabling the “Displays have 
separate Spaces” option, or you won’t be able to work with Coot (the window 
will keep hiding from you). This is not a Coot bug (and probably will appear 
with other Xquartz-based software, too) it’s due to a compatibility issue 
between Xquartz and OS 10.9. More details below:

Extracted from http://xquartz.macosforge.org/trac/ticket/797 :
"
Came across this from the Ars Technica review of Mavericks:

Well, perhaps not all of us. If you prefer the old behavior, uncheck the 
"Displays have separate Spaces" checkbox in the Mission Control preference 
pane. Doing so will also restore the ability to have windows that span more 
than one display.'

This should return your desktop to the way you expect it to behave.

​http://arstechnica.com/apple/2013/10/os-x-10-9/11/

Modificado 7 horas atrás por jeremyhu@…

Yes, that is a valid workaround, but the actual fix is something that requires 
a change in OS X

“

Carlos


Em 24 oct. 2013, à(s) 00:21, Francis Reyes  
escreveu:

> I'm currently using CCP4/COOT (from the official installer) and autoPROC  on 
> Mavericks without any problems. I imagine the rest of the global phasing 
> tools will work nicely. 
> 
> 
> I had issues with fink, you have to use a branch from github as well as 
> manually install and update the Command Line Tools just to get fink working...
> 
> 
> F
> 
> -
> Francis E. Reyes PhD
> 215 UCB
> University of Colorado at Boulder
> On Oct 23, 2013, at 3:16 PM, Carlos Kikuti  wrote:
> 
>> Hi,
>> 
>> Can I profit from Kristin's question and add one: is it too soon to know if 
>> the crystallography software (CCP4, Coot, Autobuster, XDS) will work fine 
>> with Mavericks (Mac OS X 10.9)? 
>> 
>> (I remember a bit of trouble when Lion came off).
>> 
>> Carlos
>> 
>> Em 23 oct. 2013, às 22:10, Kristin Low  escreveu:
>> 
>>> Hi everyone,
>>> 
>>> Sorry for being a bit off topic, but I thought this group would be great 
>>> for advice.
>>> 
>>> I’m looking at upgrading my current laptop to a newer MacBook Pro. I’m torn 
>>> as to whether I need integrated vs discrete graphics for structural 
>>> biology, including molecular modelling, especially since the latest 
>>> advances by Intel in terms of integrated graphics. Right now with the new 
>>> releases, the options are between Intel Iris Pro (5200 series) and Intel 
>>> Iris Pro + Nvidia GT 750M. Thoughts?
>>> 
>>> 
>>> Thanks everyone!
>>> 
>>> Kristin
>>> 
>>> 
>>> -
>>> Kristin Low
>>> Ph.D. Candidate
>>> Queen's University
>>> Department of Biomedical and Molecular Sciences
>>> Botterell Hall, Room 645
>>> Kingston, ON
>>> Canada  K7L 3N6
>>> 
>>> tel: +1-613-533-3019
>>> -
>>> 
>> 
> 
> 
> 
> 
> 
> 
> 

Re: [ccp4bb] largest protein crystal ever grown?

[David Briggs]

Following on from John's comment, when I did my PhD at Birkbeck in the
early 2000s, one of David Moss's other PhD students (John Bond) grew some
gigantic (>1cm edges) crystals of things like HEWL & Myoglobin, which he
then (somewhat perversely) crushed to load into capillaries for powder
diffraction analysis.

IIRC, John fashioned a vapour diffusion setup from a 2l Ice cream tub, and
used a watch glass to support the sitting drop, which was centimetres
across. Truly "bucket crystallography".

Regards,

Dave


David C. Briggs PhD
http://about.me/david_briggs


On 24 October 2013 17:08, Jrh  wrote:

> Dear Tobias,
> Take a look at http://dx.doi.org/10.1107/S0108767389012912
> The ribonuclease crystal I used to measure the speed of sound, using laser
> generated ultrasound, was of volume 129 mm3 ie 7.7x6.2x2.7 mm . David Moss
> of Birkbeck College provided it.
> Best wishes,
> John
>
> Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
> Chair School of Chemistry, University of Manchester, Athena Swan Team.
> http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
>
>
>
> On 24 Oct 2013, at 16:33, Tobias Beck  wrote:
>
> Dear all,
>
> I was just wondering if anyone has some information or references about
> the dimensions of the largest protein crystal ever grown? I am aware that
> for neutron protein crystallography one usually needs crystals with mm
> dimensions. I have found some information on crystallization under
> micro-gravity and how this can enlarge the crystal size. However, I would
> rather be interested in the dimensions for crystals obtained from a regular
> lab setup.
>
> Thanks, Tobias.
>
> --
> ___
>
> Dr. Tobias Beck
> ETH Zurich
> Laboratory of Organic Chemistry
> Wolfgang-Pauli-Str. 10, HCI F 322
> 8093 Zurich, Switzerland
> phone:   +41 44 632 68 65
> fax:+41 44 632 14 86
> web:  http://www.protein.ethz.ch/people/tobias
> ___
>
>

Re: [ccp4bb] largest protein crystal ever grown?

[Jrh]

Dear Tobias,
Take a look at http://dx.doi.org/10.1107/S0108767389012912
The ribonuclease crystal I used to measure the speed of sound, using laser 
generated ultrasound, was of volume 129 mm3 ie 7.7x6.2x2.7 mm . David Moss of 
Birkbeck College provided it. 
Best wishes,
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 24 Oct 2013, at 16:33, Tobias Beck  wrote:

> Dear all,
> 
> I was just wondering if anyone has some information or references about the 
> dimensions of the largest protein crystal ever grown? I am aware that for 
> neutron protein crystallography one usually needs crystals with mm 
> dimensions. I have found some information on crystallization under 
> micro-gravity and how this can enlarge the crystal size. However, I would 
> rather be interested in the dimensions for crystals obtained from a regular 
> lab setup.
> 
> Thanks, Tobias. 
> 
> -- 
> ___
> 
> Dr. Tobias Beck
> ETH Zurich
> Laboratory of Organic Chemistry
> Wolfgang-Pauli-Str. 10, HCI F 322
> 8093 Zurich, Switzerland
> phone:   +41 44 632 68 65
> fax:+41 44 632 14 86
> web:  http://www.protein.ethz.ch/people/tobias
> ___

Re: [ccp4bb] largest protein crystal ever grown?

[Simon . Phillips]

I once grew an oxymyoglobin crystal 1 cm long for neutron diffraction at 
Brookhaven.  I was very proud of it, but when I got to Brookhaven I was told it 
was too big for the beam (!) so I had to use a much smaller one of only 8 mm**3 
(Nature 292:81-82 (1981).  I still have a few left over that look like 5-7 mm 
long (I just held a ruler up to the tube which is still on my office shelf)

Simon E.V. Phillips
Director, Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email: susan.jo...@rc-harwell.ac.uk
Direct email: 
simon.phill...@rc-harwell.ac.uk
Tel:   +44 (0)1235 567701 (direct)
   +44 (0)1235 567700 (sec)
   +44 (0)7884 436011 (mobile)
www:   www.rc-harwell.ac.uk

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tobias 
Beck
Sent: 24 October 2013 16:34
To: ccp4bb
Subject: [ccp4bb] largest protein crystal ever grown?

Dear all,
I was just wondering if anyone has some information or references about the 
dimensions of the largest protein crystal ever grown? I am aware that for 
neutron protein crystallography one usually needs crystals with mm dimensions. 
I have found some information on crystallization under micro-gravity and how 
this can enlarge the crystal size. However, I would rather be interested in the 
dimensions for crystals obtained from a regular lab setup.
Thanks, Tobias.

--
___

Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Wolfgang-Pauli-Str. 10, HCI F 322
8093 Zurich, Switzerland
phone:   +41 44 632 68 65
fax:+41 44 632 14 86
web:  http://www.protein.ethz.ch/people/tobias
___

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[ccp4bb] Faculty Position in Structural Biology - Purdue

[Mesecar, Andrew D]

Dear Colleagues, I want to bring the following position to your attention:

Faculty Position in Structural Biology
Purdue University

The Department of Biological Sciences and the Markey Center for Structural 
Biology at Purdue University invite applications for a tenure-track faculty 
position in Structural Biology. We expect to fill this academic-year 
appointment at the Assistant Professor level, but appointment at the Associate 
level will also be considered.  Applicants must have a Ph.D. or equivalent in 
biology, chemistry, physics or related field and at least 2 years of 
postdoctoral experience in X-ray crystallography, cryo-EM, NMR or other 
relevant field. The successful applicant will be required to establish a strong 
and independent research program in structural biology and to teach at the 
undergraduate and graduate levels. Applicants with research interests in cancer 
biology, drug discovery, energy & signal transduction, infectious disease, 
large macromolecular complexes, membrane-based transport, molecular 
pathogenesis, neurobiology, viruses or viral-host interactions are encouraged 
to apply.

The Markey Center for Structural Biology at Purdue is recognized worldwide for 
its leadership in structural biology of viruses, membrane proteins, receptors, 
signaling proteins and enzymes in addition to methods development in 
crystallography, NMR and electron microscopy.  The Department has over 50 
faculty members conducting research in a wide range of fields including those 
areas listed above, bioinformatics, computational chemistry and biology, 
ecology, evolutionary biology and vision research. The successful candidate 
will have opportunities to interact with colleagues in many departments and 
colleges including Chemistry, Medicinal Chemistry and Molecular Pharmacology, 
Computer Science and Physics, and to join centers such as the Center for Cancer 
Research and the new Center for Drug Discovery.  The successful candidate will 
also have laboratory space in the newly constructed Hockmeyer Hall of 
Structural Biology and will have access to state-of-the-art shared resources 
across Purdue including a Titan Krios cryo-TEM, Bruker Avance-III 800 MHz NMR, 
Rigaku X-ray generators and detectors, and other advanced biophysical 
instrumentation available at the Bindley Bioscience Center and the Birck 
Nanotechnology Center.

Applications must be submitted electronically to 
sea...@bio.purdue.edu as a PDF file that includes 
a detailed curriculum vitae, names and addresses of three referees, a 2 - 3 
page summary of research interests, and a one-page statement on a vision for 
teaching.  Inquiries should be directed to Structural Biology Search Committee, 
Department of Biological Sciences, Purdue University, 915 W. State St., West 
Lafayette, IN 47907-2054.  Review of applications will begin November 1, 2013 
and continue until the position is filled. Further information about the 
Department is available at http://www.bio.purdue.edu/.


Purdue University in an Equal Opportunity/Equal Access/Affirmative Action 
employer fully committed to achieving a diverse workforce.


Andrew D. Mesecar
Walther Professor of Cancer Structural Biology
& Deputy Director, Purdue University Center for Cancer Research
Departments of Biological Sciences and Chemistry
Hockmeyer Hall of Structural Biology
Room 311
240 S. Martin Jischke Drive
West Lafayette, IN 47907-1971
Ear Mail:  765-494-1924
E-Mail: amese...@purdue.edu

Re: [ccp4bb] largest protein crystal ever grown?

[William G. Scott]

I remember seeing an approx (5mm)^3 haemoglobin crystal in the MRC LMB crystal 
growing room, and the nucleosome crystals there were almost as big in their 
longest dimension.

Bill


On Oct 24, 2013, at 8:33 AM, Tobias Beck  wrote:

> Dear all,
> 
> I was just wondering if anyone has some information or references about the 
> dimensions of the largest protein crystal ever grown? I am aware that for 
> neutron protein crystallography one usually needs crystals with mm 
> dimensions. I have found some information on crystallization under 
> micro-gravity and how this can enlarge the crystal size. However, I would 
> rather be interested in the dimensions for crystals obtained from a regular 
> lab setup.
> 
> Thanks, Tobias. 
> 
> -- 
> ___
> 
> Dr. Tobias Beck
> ETH Zurich
> Laboratory of Organic Chemistry
> Wolfgang-Pauli-Str. 10, HCI F 322
> 8093 Zurich, Switzerland
> phone:   +41 44 632 68 65
> fax:+41 44 632 14 86
> web:  http://www.protein.ethz.ch/people/tobias
> ___

Re: [ccp4bb] largest protein crystal ever grown?

[Frank von Delft]

Very recently (last few months), 3x1x1mm monsters for neutrons.  I think 
J. Crystal Growth.


On 24/10/2013 16:33, Tobias Beck wrote:

Dear all,

I was just wondering if anyone has some information or references 
about the dimensions of the largest protein crystal ever grown? I am 
aware that for neutron protein crystallography one usually needs 
crystals with mm dimensions. I have found some information on 
crystallization under micro-gravity and how this can enlarge the 
crystal size. However, I would rather be interested in the dimensions 
for crystals obtained from a regular lab setup.


Thanks, Tobias.

--
___

Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Wolfgang-Pauli-Str. 10, HCI F 322
8093 Zurich, Switzerland
phone:   +41 44 632 68 65
fax:+41 44 632 14 86
web: http://www.protein.ethz.ch/people/tobias
___

[ccp4bb] largest protein crystal ever grown?

[Tobias Beck]

Dear all,

I was just wondering if anyone has some information or references about the
dimensions of the largest protein crystal ever grown? I am aware that for
neutron protein crystallography one usually needs crystals with mm
dimensions. I have found some information on crystallization under
micro-gravity and how this can enlarge the crystal size. However, I would
rather be interested in the dimensions for crystals obtained from a regular
lab setup.

Thanks, Tobias.

-- 
___

Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Wolfgang-Pauli-Str. 10, HCI F 322
8093 Zurich, Switzerland
phone:   +41 44 632 68 65
fax:+41 44 632 14 86
web:  http://www.protein.ethz.ch/people/tobias
___

[ccp4bb] Registration open - EMBO Practical Course on Computational Structural Biology

[Gary Battle]

Dear colleagues,

We are pleased to announce that the 2014 EMBO practical course on 
"Computational Structural Biology - from data to structure to function" 
will be held at EMBL-EBI, 7th - 11th April, 2014.


Now in its 5th consecutive year, this unique and highly popular 
practical course covers computational aspects of protein structure 
determination, validation and analysis, including background in X-ray 
crystallography, Nuclear Magnetic Resonance Spectroscopy, Electron 
Microscopy and Small-angle X-ray scattering and hands-on experience in 
model building from X-ray diffraction data, comparing and integrating 
different types of structural data, and the differences in 
interpretation. Participants will also learn how to critically examine 
and validate data from these techniques.


The course is aimed at PhD students and post-docs working on the 
collection and analysis of protein structure data. The goal is to 
provide them with insight into the protein structure determination 
process, training on how to critically assess the quality of data and 
models, and expertise in the integration and visualisation of data from 
different techniques, thus allowing the analysis of protein structure 
data for functional relationships.


For more information and to apply, please go to:

http://www.ebi.ac.uk/training/course/structural-biology-2014

Application deadline: 31st January 2014

We look forward to receiving your application!
Kind regards,
Gary Battle

On behalf of the organising committee,
Gerard Kleywegt
Victor Lamzin
Christine Orengo
Gert Vriend
Tom Hancocks

--
Gary Battle
Outreach Coordinator
Protein Data Bank in Europe (PDBe)
EMBL-EBI
email: bat...@ebi.ac.uk

http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope

Re: [ccp4bb] Error with iMosflm 1.0.7 of CCP4 6.4.0 kit

[Charles Ballard]

Dear All

the soon to be released update (via the update mechanism)  will address this by 
applying the patch to imosflm.tcl. 

Charles Ballard
CCP4

On 23 Oct 2013, at 23:35, Andreas Förster wrote:

> Hi David,
> 
> I've just renamed the ipmosflm in $CCP4/bin to ipmosflm_new and then defined
> 
> MOSFLM_EXEC as /path/to/ccp4-6.3.0/bin/ipmosflm.
> 
> CCP4 6.3 needs to be installed for this to work.
> 
> 
> Andreas
> 
> 
> 
> On 23/10/2013 5:39, David Schuller wrote:
>> iMosflm developers:
>> 
>> I have installed CCP4 6.4.0, which includes iMosflm 1.0.7 and ipmosflm
>> 7.0.9.
>> This is on Scientific Linux 6.x, 64 bit distribution.
>> 
>> When I run iMosflm either from the command shell or from the ccp4i
>> interface, I get an error just like this:
>> http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27243.html
>> 
>> iMosflm claims it cannot run without mosflm 7.0.9, followed by output
>> indicating that mosflm 7.0.9 runs. (See attached screen capture of error
>> message)
>> Note the linked description is for the previous versions of imosflm amd
>> mosflm, so this error seems to be a repeat.
>> 
>> I downloaded the iMosflm and ipmosflm executables from the iMosflm web
>> site, put ipmosflm in my executable directory, and this seems to fix the
>> problem.
>> 
>> You should get the CCP4 folks to investigate this and propagate a fix.
>> 
>> Cheers,
>> 
> 
> -- 
>  Andreas Förster
> Crystallization and Xray Facility Manager
>   Centre for Structural Biology
>  Imperial College London

--
Scanned by iCritical.

Re: [ccp4bb] The binding between disordered and ordered proteins

[Carlos Kikuti]

Hmmm… is it really (physiological-like) "binding", or your protein A is 
aggregating/precipitating on the "partner"? Do you have a good negative control 
(a similar protein to which protein A should not bind)? Also, as a general 
rule, be careful about your detection method for the pull-down, don't get too 
sensitive or you'll start seeing hair on eggs -- maybe that's not the case, 
since you say "strong interaction".

Carlos


 
Em 22 oct. 2013, às 04:39, Clement Angkawidjaja 
 escreveu:

> Dear Dee,
> 
> Some proteins with chaperone-like activity (perhaps your B?) can only bind to 
> partially folded proteins.
> Probably A folds to a molten globule structure after 1-2 days. You can check 
> by spectroscopic techniques (ANS or Trp fluorescence, CD).  
> Hope that helps.
> 
> Cheers,
> Clement
> 
> On 10/22/13 11:10 AM, Xiaodi Yu wrote:
>> Dear All:
>> 
>> I have a general question about protein- protein interactions. I have two 
>> proteins, A and B. A is a disordered protein while B is a well folded 
>> protein. The binding between A and B has been approved by GST-pull down 
>> assay previously. The strange thing is I cannot get them bind if protein A 
>> were just freshly prepared. However, if I kept these two proteins separately 
>> for one or two days at 4 degree and then did the GST-pull down assay again, 
>> I can observe very strong interaction between A and B. 
>> 
>> Protein A doesn't contain any cys residue. I have already test certain 
>> chemicals which might affect the interactions, for example, DTT and EDTA. 
>> These chemicals seems to have no effect on the binding. 
>> 
>> Although A is a disordered protein, does it need such long time to find its 
>> proper conformation?
>> 
>> Do any people have similar experience? Any suggestions are greatly 
>> appreciated.
>> 
>> Thanks,
>> 
>> Dee
>