Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.

[Zhijie Li]

Hi,

If those are spams, then Kevin must be the most successful spammer I have 
ever encountered, as I have actually read all his posts and linked web 
pages.


About the twitter idea, I am not sure if I would ever become a twitter user 
in the near future. Compared to following tens of authors, I think a quick 
glance at the CCP4BB would remain a much more efficient means for learning 
about new things. There is also a filtering function in my email client 
program - certainly beats twitter/FB/groups IMHO.


Zhijie



--
From: "Bryan Lepore" 
Sent: Friday, March 30, 2012 3:04 PM
To: 
Subject: Re: [ccp4bb] a small trick for protein and organic compound 
cocrystallization.



On Fri, Mar 30, 2012 at 4:02 AM, Kevin Jin  wrote:

Here is way I have used for [...]


I hate to be a curmudgeon, but can a list member please explain why
this is not specifically blogspam or spam - or whatever it is exactly?


-Bryan 

[ccp4bb] Reminder - Gordon Research Conference on Diffraction Methods

[Ana Gonzalez]

We would like to remind you of the biannual Gordon Conference on Diffraction
Methods in Structural Biology, which will be held at Bates College in 
Lewiston, Maine from July 15-20. We are closer to the application 
deadline now (June 17th), and places will be filling up pretty fast!


We have assembled by now an advanced draft of the final program, covering 
all established but also new and exciting methodological aspects of 
structural biology: the latest news on diffraction methods is combined 
with sessions on  complementary methods and with  examples of successful 
application of methods to challenging cases. A whole session on the last 
day is dedicated  to presentations selected from the posters sessions. 
The speakers for this session will be selected during the meeting and all 
poster presenters will have a chance to speak about their work.


The free afternoons providing ample opportunities for informal 
discussions, and outdoors activities, including the traditional football 
(aka soccer) game and the Great Outdoors outing to Auburn Lake and hiking 
in the Thorncrag park - or just relaxing.


The Gordon Research Conference offers fellowships for underrepresented
minority members attending a conference for the first time. See:
http://www.grc.org/diversity.aspx

Very limited  funding on a first come first served basis is also available
for international minority graduate students or post docs, scientists
working in Eastern European or Former Soviet Union countries and research
active scientists from "Predominantly Undergraduate Institutions" (NSF
definition ). Eligible applicants should contact directly the conference
chair.

We hope to see you there !

Ana Gonzalez (Chair) & Tassos Perrakis (Vice-Chair)

Program:

SUNDAY
*Evening Session: Highlights in structure solution
Discussion Leader: Andrew Leslie
Speakers: Andrea Mussacchio, William Weis

MONDAY
Morning Session: Getting the Best Out of Your Data I
Discussion Leader: James Holton
Speakers: Antony Kossiakoff, Aina Cohen, Elspeth Garman, Gerard
Poster Session I
Evening session: Runway-fit Models
Discussion Leader: Jane Richardson
Speakers: Robbie Joosten, Gerard Kleywegt, Zbigniew Dauter

TUESDAY
Morning Session: Complementary Methods
Discussion Leader: Edward Snell
Speakers: Axel Brunger, John Tainer, Arwen Pearson, Piet Gros
Poster Session I
Evening Session: Driving Methods Development: Challenging Cases
Discussion Leader: Anastassis Perrakis
Speakers: Partho Ghosh, Jonathan Grimes, Maike Bublitz

WEDNESDAY
Morning Session: Getting the Best Out of Your Data II
Discussion Leader: Airlie McCoy
Speakers: Kay Diederichs, Dominika Borek, Frank DiMaio, Jeffrey J. Headd
Poster Session II
Business Meeting
Evening Session: Towards Ultimate Sources
Discussion Leader: Janet Smith
Speakers: Thomas Schneider, Vivian Stojanoff, Sol Gruner

THURSDAY
Morning Session: Talks Selected from Posters
Discussion Leader: Paul Adams (Lawrence Berkeley Laboratory)
Speakers: To be announced at the meeting
Poster Session II
Evening session: Structural Biology at XFELs
Discussion Leader: John C. H. Spence
Speakers: Sébastien Boutet, Thomas White, Tomas Ekeberg

Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.

[James Stroud]

On Mar 30, 2012, at 1:04 PM, Bryan Lepore wrote:
> On Fri, Mar 30, 2012 at 4:02 AM, Kevin Jin  wrote:
>> Here is way I have used for [...]
> 
> I hate to be a curmudgeon, but can a list member please explain why
> this is not specifically blogspam or spam - or whatever it is exactly?


It's not really "spam", but there are better channels to communicate these type 
of updates. Twitter is probably the best known channel. People get to subscribe 
and authors can push their contributions to willful and interested subscribers. 
The author posts a summary of what's behind the link and then posts the link, 
just as Jin is doing with his ad-hoc feed here.

For example, a few days ago I created the @amyloids twitter feed 
(https://twitter.com/#!/amyloids) that features recent publications I have read 
and that I also think are of interest to amyloid researchers.

Instead of being to critical, let's just direct authors to use the proper 
channels. Social media has moved fast in recent years, and we should be 
understanding as the scientific community plays catch-up.

If Jin created a twitter feed for tips, it would probably get some subscribers 
from this board--as long as we don't begrudge the Jin an opportunity to send 
out an advertisement for the feed itself.

James

Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.

[Bryan Lepore]

On Fri, Mar 30, 2012 at 3:26 PM, Jacob Keller
 wrote:
> What's the harm?

have you seen usenet/Google groups?

-Bryan

Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.

[Jacob Keller]

What's the harm? Seems relevant to crystallographers, and not for
self-promotion, but just to help, share an interesting tip. Perhaps you can
think of it as a response to an un-asked but plausible question, i.e., "how
can I treat my coverslips to make them more receptive to organic
solvent-containing drops?

Jacob

ps I bet you don't really hate to be a curmudgeon--there is a certain
pleasure in it!

-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.

[Bryan Lepore]

On Fri, Mar 30, 2012 at 4:02 AM, Kevin Jin  wrote:
> Here is way I have used for [...]

I hate to be a curmudgeon, but can a list member please explain why
this is not specifically blogspam or spam - or whatever it is exactly?


-Bryan

Re: [ccp4bb] an ambiguous result of molecular replacement

[Leonid Sazanov]

Hi, we had the same case in apparent C2221, with many similarly shifted Phaser 
solutions with high scores. The reason was that crystals were actually nearly 
perfectly twinned in P21, so indexing and processing indicated C2221. Once data 
was re-processed in P21, Phaser could easily find two distinct solutions - one 
for each of twin domains, with LLG scores roughly reflecting twin ratios. 
Similar case is discussed in detail here:
http://www.ncbi.nlm.nih.gov/pubmed/15039553

Re: [ccp4bb] need help for crystallization

[Kevin Jin]

My pleasure !
Since this may be help for other people, I  also cc it to CCP4BBS.

According to your email, I guess the buffer is phosphate buffer at pH
7.4.  You can do a quick buffer exchange before crystallization.

Since PO4 is a competitor in this case, I will also avoid PO4 and
Cocodylate buffer from screen kits.

Here is what you can do,
1. concentrate your protein using an amicro centrocon with 3KD cutoff.
2. Measure how much buffer has been spin down, then add equal amount
of Tris with same pH back to the top.
3. Then, spin down again.
4. Repeat several times, 5 times may be good enough.
5. Most of Phosphate buffer should be removed.

That's what I used before.

Let me know if it works.

Best,

Kevin Jin





On Fri, Mar 30, 2012 at 9:40 AM, Afshan Begum  wrote:
>
>  Dear Kevin
>
> I have seen your website and come to you to discuss my problem actually i
> want to co-crystallized my enzyme with inhibitor but problem is that the
> phosphate ion come to the active site and occupied the cavity and my
> inhibitor not bind to the active center i purchase this enzyme from a
> commercial source and they purify  with phosphate buffer that's why also
> phosphate is occupied the cavity how can i get ride of it from the active
> center could you kindly help me regarding this i would be really thankful to
> you.
>
>
> Best Regards
>
> AFSHAN
> ===
> Dr. Afshan Begum
> University of Hamburg
> Institute of Biochemistry and Molecularbiology
> Laboratory for Structural Biology of Infection and Imflammation
> c/o DESY, Build. 22a
> Notkestr. 85
> 22603 Hamburg
> Germany
> Home phone: +49 40 22888618
> Fax:      +49 40 8998-4747
> E-mail: afshan...@yahoo.com
>



-- 
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/

[ccp4bb] Announcement: EMBO Global Exchange Lecture Course: Structural and biophysical methods for biological macromolecules in solution

[Clement Blanchet]

Structural and biophysical methods for biological macromolecules in solution
EMBO Global Exchange Lecture Course
29 November?6 December 2012 Hyderabad, India

http://events.embo.org/12-macromolecule/index.html

The main objective of the Course is to teach the young PhD students  
and postdocs
from all areas of biology the methods applicable to study biological  
macromolecules in solution. We aim at a comprehensive coverage of the  
field including the major structural and biophysical techniques  
employed for the characterization of high and low resolution structure  
and structural transitions, macromolecular complex formation, protein  
folding and stability, protein-protein and protein-ligand interactions  
and enzymatic mechanisms. The Course will include lectures on  
small-angle X-ray and neutron scattering (SAXS/SANS), nuclear magnetic  
resonance (NMR), static and dynamic light scattering (SLS/DLS),  
analytical ultracentrifugation (AUC), surface plasmon resonance (SPR),  
differential and isothermal calorimetry (DSC/ITC) and spectroscopic  
approaches. Bioinformatic tools to analyze protein-protein  
interactions will also be considered, and the joint use of the  
solution characterization methods with the major non-solution  
structural techniques,
macromolecular crystallography (MX), electron microscopy (EM), mass  
spectrometry (MS) and with the in situ methods will be covered.  
Special attention will be paid to interdisciplinary approaches, where  
the synergistic use of complementary techniques leads to a  
comprehensive description of macromolecular systems.


From the Indian side, the Course will be co-organized by  the Centre  
for Cellular and Molecular Biology (CCMB), Hyderabad, and the Tata  
Institute of Fundamental Research (TIFR), Mumbai. The course will be  
held at CCMB in Hyderabad immediately following an International  
meeting on biology (25-27 November 2012), commemorating 25 years of  
moving into the current CCMB R&D complex.



A maximum of 40 participants will be selected to attend the course.
No registration fee will be requested from the academic participants.
Applicants from industry are expected to pay a 1000 Euro fee.

The Course is oriented towards applicants active in structural biology,
mostly late Ph.D. students and early post-docs but more senior scientists,
depending on circumstances, could also participate.
Students working in India or Indian students working abroad will be
given preference but all applications are welcome at

http://events.embo.org/12-macromolecule/application.html

Application deadline for the Course: September, 17th, 2012

Re: [ccp4bb] about heavy atom derivatization

[Francis E Reyes]

To add to Ed's comments: 


Find someone in the immediate department/area to walk you through your first 
structure. 


But to answer your question:

What about the MR didn't work? 

Use your MR model to find your heavy atoms. They can be found using anomalous 
data  difference fouriers (or even better log likelihood gradient maps) using 
data  as low as 6-8A, and, in my case, using a model that was about 50% (mass) 
of the ASU with the placement of that 50% to be about 80-90% correct. 


F

On Mar 30, 2012, at 7:34 AM, Shanti Pal Gangwar wrote:

> Dear all
> 
> I am beginner in crystallography.We have collected a native data of a given 
> protein at 2.2A resolution but are unable t solve by MR
>  therefore we collected Hg, and Pt derivative after  soaking the crystals. I 
> don't know how to process this heavy atom derivative data 
> and find the anomalous signal if heavy atom is there?
> 
> thanks in advance for help and suggestions..
> 
> 
> 
> 
> 
> regards
> 
> Shanti Pal Gangwar
> 
> 
> 
> 



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] about heavy atom derivatization

[Ed Pozharski]

http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mir.html

seems relevant

On Fri, 2012-03-30 at 19:04 +0530, Shanti Pal Gangwar wrote:
> Dear all
> 
> I am beginner in crystallography.We have collected a native data of a
> given protein at 2.2A resolution but are unable t solve by MR
>  therefore we collected Hg, and Pt derivative after  soaking the
> crystals. I don't know how to process this heavy atom derivative data 
> and find the anomalous signal if heavy atom is there?
> 
> thanks in advance for help and suggestions..
> 
> 
> 
> 
> 
> regards
> 
> Shanti Pal Gangwar
> 
> 
> 
> 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /

[ccp4bb] about heavy atom derivatization

[Shanti Pal Gangwar]

Dear all

I am beginner in crystallography.We have collected a native data of a given
protein at 2.2A resolution but are unable t solve by MR
 therefore we collected Hg, and Pt derivative after  soaking the crystals.
I don't know how to process this heavy atom derivative data
and find the anomalous signal if heavy atom is there?

thanks in advance for help and suggestions..





regards

Shanti Pal Gangwar

Re: [ccp4bb] processing data with ice ring

[Loes Kroon-Batenburg]

Dear Shanti,

You may want to try EVAL (www.crystal.chem.uu.nl/distr/eval). It provides 
options to exclude regions affected with ice diffraction, or practically any 
region you'd like. In our experience data treated in this way have a lower 
Rmerge. However, the difference with respect to refinement statistics is not all 
that large, because ice-affected reflections are mostly rejected in the scaling 
step if you have sufficient redundancy. Ice scattering is rarely constant over 
theta-rings.


Regards,
Loes.


On 03/30/12 06:30, Shanti Pal Gangwar wrote:

Hello all,

I have a query regrading processing of data.  I have  good diffraction data that
has ice rings. Is it possible to mask the regions of the ice rings during 
processing?
I have been using Mosflm to process data.
Is this feature available with this program?

Suggestions and advice would be greatly appreciated.


Thanks





regards

SHANTI PAL








--
__

Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands

E-mail : l.m.j.kroon-batenb...@uu.nl
phone  : +31-30-2532865
fax: +31-30-2533940
__

Re: [ccp4bb] processing data with ice ring

[Harry Powell]

Hi

Actually, it's *much* easier than this in iMosflm (though Sita's  
suggestion is already pretty easy). There's no need to open the  
"Processing Options" menu in this case.


On each of the indexing,  the refinement and integration panes, there  
is a small button on the top row of widgets with what looks like a  
snow flake - click on this to activate ice ring exclusion for  
processing the data.


As Sita says, you will lose some information about genuine non-ice  
spots on (or very near to) the ice rings, but this is generally more  
than compensated for by the improved processing of the spots you  
actually do integrate.



On 30 Mar 2012, at 05:53, Sita Ram Meena wrote:


Hi Shanti

Mosflm has a default option in the "processing options" menu.

when you runs imosflm  go to the setting and than processing option.

setting => processing options.
This has five tabs 1. Spot finding, 2. indexing, 3. Processing 4.  
Advance Processing, 5. Advance integration.


initial three (1, 2, 3) tab has has ice ring exclusion options ,  
you just need to check them that's it.


1. In the Spot finding => Automatic ice and Powder ring exclusion.
2. In Indexing => Exclude any spot rings.
3. Processing => Do not process spots near ice rings.

This will exclude your ice ring but you may loose some information  
from your data.


Good luck

On Fri, Mar 30, 2012 at 10:00 AM, Shanti Pal Gangwar  
 wrote:

Hello all,

I have a query regrading processing of data.  I have  good  
diffraction data that
has ice rings. Is it possible to mask the regions of the ice rings  
during processing?

I have been using Mosflm to process data.
Is this feature available with this program?

Suggestions and advice would be greatly appreciated.

Thanks





regards

SHANTI PAL








--
Sita Ram


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH

Re: [ccp4bb] an ambiguous result of molecular replacement

[Randy Read]

Hi,

Do you mean that the second molecule is always overlapped with the first, by 
saying that it shifts several Angstrom along the x axis?  If there were a 
larger translation, then what you're seeing would be consistent with 
translational NCS (tNCS), but the translation should be large enough to shift 
the second copy off the first!

If you did have tNCS, then the version of Phaser currently distributed with 
CCP4 would have trouble dealing with it.  We have a new version that accounts 
well for the statistical effects of tNCS.  It's available in current releases 
of Phenix and will soon be available with the upcoming CCP4 release.  
Alternatively, the version of Molrep in the current CCP4 has its own treatment 
for tNCS.

However, if it's really a small vector, then it's more likely that something 
else is going on.  You could have some kind of lattice translocation disorder.  
The crystal could be twinned so the real symmetry could be lower, or even some 
combination of the above.

Good luck sorting it out!

Best wishes,

Randy Read

On 30 Mar 2012, at 05:22, Zhiyi Wei wrote:

> Dear all,
> 
> I got a weird solution from Phaser. The background is that, space
> group C2221, resolution ~4A, in complex with a peptide, and having a
> apo form structure as the search model. Phaser gave two rotation
> function peaks with Z > 7. But when searching translation function
> peaks, Phaser gave many high Z score peaks listed below rather than a
> single solution. These peaks share same fraction Y&Z but with
> different X. Most of them pasted the packing validation. The when
> searching the second copy, each solutions have a single translation
> peak that showed very high Z score (> 20). I check some of these
> solutions in Coot, and found that the two copies of each solution has
> the same relative orientation and each solution shifts several
> angerstroms in X axis. I also tried C222 and did not get better result
> than C2221. Any comments or suggestion? Thanks a lot!
> 
> Best,
> Zhiyi
> 
>   # (#)   Frac X Frac Y Frac Z   LLG   Z-score Split #Groupraw/top
>   1 1  0.155  0.436  0.287 +219.80   11.17 0  1 272.58/272.58
>   2 2  0.350  0.436  0.287 +211.92   10.5324  1 267.42/267.42
>   3 3  0.542  0.436  0.287 +211.31   10.4844  1 266.05/266.05
>   4 5  0.579  0.436  0.287 +209.66   10.3440  2 260.14/260.14
>   5 12 0.267  0.436  0.287 +209.11   10.3014  2 256.53/256.53
>   6 4  0.224  0.435  0.288 +208.41   10.24 8  2 261.39/261.39
>   7 11 0.485  0.436  0.287 +208.28   10.2340  2 256.95/257.13
>   8 7  0.191  0.435  0.287 +205.189.97 4  2 258.95/258.95
>   9 15 0.400  0.436  0.287 +201.909.7030  2 254.20/254.20
>   109  0.297  0.437  0.287 +201.799.6917  1 257.75/257.75
>   1116 0.449  0.436  0.287 +198.779.4536  1 252.80/252.80
>   1217 0.129  0.437  0.287 +195.669.19 3  1 252.41/252.41
>   1320 0.377  0.436  0.287 +194.959.1327  1 246.37/246.37
>   1421 0.422  0.436  0.287 +190.728.7833  1 245.42/245.42
>   1519 0.521  0.437  0.287 +190.228.7445  1 246.46/246.46

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

[ccp4bb] a small trick for protein and organic compound cocrystallization.

[Kevin Jin]

Dear All,

Here is way I have used for protein and hydrophobic organic compound
cocrystallization. Via this method, less amount of DMSO will be used
to aviod protein ppt.

I hope you can use for your research.

http://www.jinkai.org/Xtal.html

Regards,

-- 
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/

[ccp4bb] 24/25 May 2012 IGBMC symposium on “Future Challenges in Integrative Structural Biology”

[Bruno KLAHOLZ]

Dear all,

kind reminder for the Instruct/FRISBI symposium at the IGBMC on 24/25 of May on 
“Future Challenges in Integrative Structural Biology” since the deadline (april 
9th 2012) is approaching. Seehttp://fcisb2012.u-strasbg.fr for 
registration.



The conference includes presentations by:


Rolf Boelens, Utrecht University, The Netherlands.
Macromolecular Structure and Dynamics of Gene Regulation and DNA Repair.

Nathalie Garin, Leica Microsystems, Switzerland.
Super-resolution microscopy: new horizons for life scientists.

Robert M. Glaeser, University of California, Berkeley, USA.
Single-particle Cryo-EM: Closing The Gap With What Physics Allows.

Jack Johnson, Scripps Research Institute, San Diego, USA.
Macromolecular Dynamics with CryoEM: Maximum Likelihood Approach.

Abraham J. Koster, Leiden University, The Netherlands.
Zooming in on Cellular Architecture with Cryo Correlative Electron Microscopy.

Rasmus Schröder, University of Heidelberg, Germany.
Latest News on Phase Plate Developments for High-Contrast Imaging of Biological 
Samples.

David Stuart, University of Oxford, United Kingdom.

Some emerging X-ray diffraction techniques for the analysis of complexes, 
exemplified by viruses.



Best regards,



Bruno Klaholz




De : CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] De la 
part de Bruno KLAHOLZ
Envoyé : Thursday, March 01, 2012 7:26 AM
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] 24/25 May 2012 IGBMC symposium on “Future Challenges in 
Integrative Structural Biology”


Dear all,

registration is now open for our IGBMC symposium on “Future Challenges in 
Integrative Structural Biology”.



24/25 May 2012, Strasbourg, France



Seehttp://fcisb2012.u-strasbg.fr for registration and a detailed 
description of the meeting.



Application deadline is April 9th 2012, but registration is limited to about 
100 people and will be processed on a first-comes-first basis.



Best regards,



Bruno Klaholz






###
Dr. Bruno P. Klaholz
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 964
1, rue Laurent Fries
BP 10142
67404 ILLKIRCH CEDEX
FRANCE
Tel. from abroad: 0033.388.65.57.55
Tel. inside France: 03.88.65.57.55
Fax from abroad: 0033.388.65.32.76
Fax inside France: 03.88.65.32.76
e-mail: klah...@igbmc.fr
websites:
http://www.igbmc.fr/
http://igbmc.fr/Klaholz