Re: [ccp4bb] Patterson Map missing a peak?

[Nicholas M Glykos]

Hi Engin,

Two thoughts:

 * Is the Patterson map consistent ? (with different resolution ranges, 
exclusions, ...). You could possibly give 'GraphEnt' a try [assuming it 
still works with current generation mtz files].

 * The number of heavy atoms may be much larger and may deviate from 
the known NCS (and, so, what you interpret as a self vector may not be a 
self vector at all).

My twopence,
Nicholas



On Sun, 13 Sep 2009, Engin Ozkan wrote:

> Hi everybody,
> 
> I have a little weekend puzzle in my hands. I have (probably) two heavy atom
> sites and pseudo-translation in P2(1) (i.e. an NCS 2-fold parallel to the
> unique crystallographic axis). Doing a little algebra, I would expect two self
> vectors and the pseudo-translation in the Harker section (y=0.5) of the
> Anomolous Difference Patterson map (plus a cross vector at y=0).
> Unfortunately, I am seeing only one of the self vectors and the vector
> corresponding to NCS+CS (pseudo-translation), but not the second self vector,
> which does not make sense to me.  Drawing predicted pattersons confirms my
> expectations but not the real-world patterson map. I have already considered
> one site being weak as a possibility, but then the pseudo translation would
> not be stronger than the only self vector I'm seeing. I would appreciate
> anyone with a fresh brain pointing out what I might be missing here.
> 
> Engin
> 
> Anomalous Difference Patterson:
> CELL   95.4120  132.0710   99.0230   90.  109.0950   90.
> ATOM1   Ano   0.  0.  0.   53.95  0.0 BFAC  20.0
> ATOM2   Ano   0.4784  0.5000  0.06478.63  0.0 BFAC  20.0
> ATOM3   Ano   0.2043  0.5000  0.76317.23  0.0 BFAC  20.0
> ATOM4   Ano   0.1977  0.  0.16893.55  0.0 BFAC  20.0
> ATOM5   Ano   0.4099  0.5000  0.17943.01  0.0 BFAC  20.0
> 
> Native Patterson:
> CELL   95.4120  132.0710   99.0230   90.  109.0950   90.
> ATOM1   Ano   0.  0.  0.   49.32  0.0 BFAC  20.0
> ATOM2   Ano   0.4686  0.5000  0.04658.99  0.0 BFAC  20.0
> ATOM3   Ano   0.5000  0.5000  0.94044.92  0.0 BFAC  20.0
> ATOM4   Ano   0.3074  0.  0.24473.49  0.0 BFAC  20.0
> ATOM5   Ano   0.1803  0.5000  0.77103.44  0.0 BFAC  20.0
> ATOM6   Ano   0.0479  0.  0.90723.35  0.0 BFAC  20.0
> 
> 
> 
> 

-- 


  Dr Nicholas M. Glykos, Department of Molecular Biology
 and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] Using SAXS data for phasing at mediocre resolution.

[James Holton]

There is a program called FSEARCH in the CCP4 Suite that will dock EM 
maps, SAXS envelopes or what have you into a unit cell.


However, I am not aware of any instances where a novel crystal structure 
(~4 A or better and no NCS) was solved this way.  It is not for want of 
trying!  I think the lack of success is not because SAXS envelopes are 
"wrong" or anything like that, but rather because phase extension in a 
crystal starting from ~50A or so is really really hard to do.


That said, I would be delighted if someone could point me to a 
counterexample of my statement.


-James Holton
MAD Scientist

Francis E Reyes wrote:

Hi all

I'm looking for anyone who has had (practical) experience using SAXS 
data to phase 4.2 A crystals.  Please email me.


FR

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

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] Using SAXS data for phasing at mediocre resolution.

[mjvdwoerd]

 Hi Francis,

There is an older paper that mentions this idea: Tsao et al, Acta Cryst B48 
(1992), 75-88. However, when you look at the paper, small-angle scattering data 
is not the only thing that was used. In particular, if my memory serves me 
right, the 60-fold averaging applied to the problem really made all the 
difference in getting the phases right. 
The big difference that works to your advantage is that small-angle scattering 
was not nearly as well developed at the time as it is now. For example, I don't 
think they could get molecular envelopes in 1992. There is sufficient 
information available these days that the test could be done (for appropriate 
systems).

Mark


 


 

-Original Message-
From: Francis E Reyes 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon, Sep 14, 2009 9:47 am
Subject: [ccp4bb] Using SAXS data for phasing at mediocre resolution.









Hi all?
?

I'm looking for anyone who has had (practical) experience using SAXS data to 
phase 4.2 A crystals.  Please email me.?
?

FR?
?

-?

Francis Reyes M.Sc.?

215 UCB?

University of Colorado at Boulder?
?

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D?
?

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D?



 

Re: [ccp4bb] Preparation of seed-stocks without seed-beads

[Ed Pozharski]

You can use the glass cell disruption pestle

http://www.vwrsp.com/catjpg/mp0/mp0440.jpg

to grind them up.  They cost money, of course, and if you plan to buy
something, why not go for seed bead kit?  But if you want something very
cheap, then you'll find this amazing discovery interesting:

"Outer diameter of the bottom of a 0.5 mL "eppendorf" tube is the same
as the inner diameter of a 1.5 mL "eppendorf" tube."

This is known as "eppendorf mortar-pestle phenomenon" :)

On Sat, 2009-09-12 at 13:52 +0530, james09 pruza wrote:
> Dear CCP4bbers,
> 
> Can anyone suggests how to make seed-stocks if one is not having
> seed-beads... Is there any other methods to crush the crystals for the
> same purpose. What if it is simple vortexed. Off-course there wold be
> all sorts of sizes, the intact crystals as well. 
> Please suggest.
> 
> Thanks a lot more for previous help.
> James.
-- 

Re: [ccp4bb] Strange Merohedral Twin result

[Eleanor Dodson]

Neha Kharbanda wrote:

Dear All,

I  submitted my processed.hkl file to the Merohedral Twin server and 
the results are bit strange the curve corresponding to my data 
goes below the perfectly untwinned red line..the complete opposite of 
the theoretically twinned red curve line.


Has anyone seen such a thing before and know why this may be the case?

Thank you

Neha Kharbanda



Do you have any translational NCS - see ctruncate output..
If so it can distort your sitributions a lot
Eleanor

[ccp4bb] Using SAXS data for phasing at mediocre resolution.

[Francis E Reyes]

Hi all

I'm looking for anyone who has had (practical) experience using SAXS  
data to phase 4.2 A crystals.  Please email me.


FR

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

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

[ccp4bb] Strange Merohedral Twin result

[Neha Kharbanda]

Dear All,

I  submitted my processed.hkl file to the Merohedral Twin server and the 
results are bit strange the curve corresponding to my data goes 
below the perfectly untwinned red line..the complete opposite of the 
theoretically twinned red curve line.


Has anyone seen such a thing before and know why this may be the case?

Thank you

Neha Kharbanda

[ccp4bb] Joint Autumn Meeting of the IG and YCG 2009

[Arefeh Seyedarabi]

Joint Autumn Meeting of the IG (Industrial Group) and YCG (Young 
Crystallographers Group), 2009

At The World of Glass, St. Helens

The meeting will be held on Thursday 5th November 2009

Runs from 10.30 till 16.30

With free registration for all YC's

For non-YC members the registration fee is £80

The Agenda will be as follows:

10.00 Registration, Tea & Coffee 
10.30 - 12.30 YC Session 
12.30 - 14.00 Lunch with time to visit the exhibitions and museum with an 
official tour 
14.00 - 16.00 IG Session 
16.00 Discussion, Tea & Coffee 
16.30 Close

The morning session will have speakers from the YCG presenting their work 
and how it can be applied to real world situations/problems. The afternoon 
session will be taken by the IG, with presentations from a spectrum of 
industries to demonstrate the application of crystallography in industry. The 
confirmed speakers (so far) will present the application of crystallography in;

Aerospace 
Semiconductors 
Pharmaceuticals 
Oil 
Glass

Speakers are still required for the morning session. The presentations need to 
be approximately 20 minutes long by any YC about their work. The speakers 
travel expenses will be refunded. A title and abstract must be sent to 
john.kani...@nsg.com by Friday 2nd October 2009.

For any further information please contact mark.farnwo...@nsg.com (IG 
Session) or john.kani...@nsg.com (YC Session), or either for general 
enquires.

[ccp4bb] Low water Bfactors and TLS: a summary

[Alasdair K. Mackenzie]

The problem:
Extremely low Bfactor values for water molecules after TLS refinement
(Bfact. = 2) despite being associated with sidechains with much higher
Bfactors. The problem apparently arises because REFMAC includes the waters
in TLS groups by default.

The solution:
exlude the waters from TLS refinement using the command:
TLSD waters exclude (thanks Roberto Steiner).

observations of a ludite:
I was adding the TLSD command using the "run&view com file", in what i
thought was the logical place (after the REFI-, and ncyc commands), but
interestingly REFMAC appeared to forget about my weight- MATRIX value and
the bond/angles went a bit crazy. when added after the weight command
things look a bit more normal for the bonds/angles, as well as the water
Bfactors. don't know why this should be- maybe it is just Monday messing
with me

Hope this helps,
Al

[ccp4bb] Crystallisation at pH 2.0

[Marta Martínez]

Dear all

Anybody has experience in protein crystallization at pH 2.0? Conditions, 
buffers, temperature...?

Thanks a lot

Marta


Dr. Marta Martínez Júlvez
Departamento de Bioquímica y Biología Molecular y Celular
Facultad de Ciencias
Universidad de Zaragoza
Pedro Cerbuna 12
50009-Zaragoza
Spain

Phone: +34 976 762841/1287
Fax: +34 976 762123

e-mail: mmart...@unizar.es

Re: [ccp4bb] Low Bfactor values for waters after TLS

[Eleanor Dodson]

Yes - I have had a similar problem..
 We need a reply from Garib..
 Eleanor


Alasdair K. Mackenzie wrote:

Greetings CCP4-ers,

I have been running some TLS refinement which does wonders for my R/Rfree
values, but seems to give some spurious Bfactors/ADPs for the waters, e.g.
B= 2.

These low Bfactors appear relatively consistent with the residual protein
B-factors (i.e. the pdb output from REFMAC), but when i use TLS analyse to
apply the TLS contribution to the total B-factors for the model, the low
water B values seem crazy...i apparently have a water with a B-factor
of 2 interacting with a side chain with a B-factor of 60

Has anyone encountered this type of thing before? and does anyone have a
good solution for getting around the problem?

cheers,
Al


  

[ccp4bb] Crystallographer position at Syngenta - permanent post

[jane . wibley]

Dear All,

A permanent post is on offer at Syngenta. Enquiries are welcome but please only 
apply online via the website.





Protein Crystallographer

Jealott's Hill, Bracknell, Berkshire



Syngenta is one of the world's leading companies with more than 24,000 
employees in over 90 countries. As global demand for food and fuel continues to 
rise, we are dedicated to our purpose: 'bringing plant potential to life'. 
Through our world-class science, global reach and commitment to working with 
our customers, we help to increase crop productivity, protect the environment 
and improve health and quality of life. We work in a collaborative and 
inspiring culture where personal contribution is rewarded and growth and 
development are at the heart of our culture. Jealott's Hill International 
Research Centre is the largest research and technology site within the company. 
Further information is available at www.syngenta.com.



Structural biology at Syngenta is at an exciting stage with opportunities to 
work on several projects with the aim of influencing the chemistry design of 
new agrochemicals. We are looking for a PhD or equivalent in structural biology 
with at least 2-3 years postdoctoral experience across the protein 
crystallography pipeline from gene to structure. The successful candidate will 
have demonstrated the ability to work independently with proven experience in 
crystallisation, data collection, and structure determination.



Candidates will need to demonstrate enthusiasm, flexible team working, and a 
tenacious approach to delivering structural solution outputs to projects. 
Excellent communication skills and the ability to translate structural 
knowledge to a meaningful output for multidisciplinary project teams are highly 
desirable qualities for this post.



If you are excited by the prospect of developing your career in a permanent 
post with a world-leading agribusiness, we would like to hear from you. Further 
details of the post and a link to apply on line is available at 
www.syngenta.com by navigating to Careers - Jobs for 
Professionals - UK. Closing date: 2nd October 2009. Informal enquiries can be 
made to Jane Wibley (jane.wib...@syngenta.com) 
tel. 00 44 1344 413957. 


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