[ccp4bb] deadline for beamtime proposals at BM14 -ESRF for 2009 -submit your proposals now!

2008-12-16 Thread Martin A. Walsh
Dear all, deadline for submission of proposals for beamtime at BM14 for
beamtime at ESRF for the first run of 2009 is this Friday, the19th decemeber
2008 -get in your proposals now before the christmas break!. Beamline
proposals can be submitted on-line from the BM14 webpages at
http://www.bm14.ac.uk    

PLEASE remember this call is distinct from ESRF proposal call and allows you
direct access to BM14 -special requests can be forwarded directly to me and
we will do our best to accommodate you.

BEAMLINE FEATURES

**MARMOSIAC 225 CCD detector  (

http://www.mar-usa.com/products/mx_series.htm)

**MD2 Microdiffractometer
(http://www.embl-grenoble.fr/groups/instr/MD2-17.pdf) 

**MiniKappa goniostat (http://www.embl-grenoble.fr/groups/instr/MK2.pdf
-videos available here
-http://www.embl-grenoble.fr/groups/instr/mk2videos.html)

**Robotic Sample changer (

http://journals.iucr.org/d/issues/2006/10/00/gx5085/index.html)

**Easily Tuneable over the 6.5 - 18 keV range with X-ray flux at sample
through 100micron aperture  of ~1.5x10*10 photons/s/200mA beam current at
12.7keV 

**REMOTE ACCESS for data collection 

FULL CALL DETAILS follow:




SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE UK/EMBL MAD
BEAMLINE BM14, ESRF 

Scheduling Period: Jan/Mar 2009

DEADLINE for proposals: 19th December 2008


-

Call for proposals from EMBL member states, EU states and associated states
for Jan/Mar 2009 synchrotron run at ESRF. The bending magnet MAD beamline
BM14 at the ESRF is being operated as a UK Collaborative Research Group(CRG)
beamline in collaboration with the EMBL Grenoble Outstation. Proposals for
beam time can be made via a user-friendly web based application form, both
for monochromatic and multi-wavelength experiments.

Beam time is available to groups from the UK and EMBL, EU and EU associated
member states. Deadline(19th Dec. 2008) for beamtime proposals at BM14/ESRF
for Jan/Mar 2009 

Reimbursement is available for travel and subsistence for groups based in
the UK based and EU member or associate member states (see NeedToKnow Link
in Main menu on Beamline Homepage for details on reimbursement and other
useful information)

Full details of the beamline characteristics, the user program and the
procedure for the submission of electronic proposals can be found at the
beamline homepage http://www.bm14.ac.uk   or by
following the links from  
http://ww.embl-grenoble.fr or   http://www.esrf.eu 


--

Please don't hesistate to contact me if you have any queries

Thanks

Martin

 

 

-

Martin Walsh,

MRC Group Leader and BM14 Responsible

Medical Research Council (MRC) France,

CRG BM14,

c/o ESRF,

6, rue Jules Horowitz,

B.P. 220

38043 Grenoble CEDEX

France

Tel:   +33 4 38.88.19.69

Fax:  +33 4 76.88.23.80

email1:   wa...@esrf.fr

email2:   walshb...@gmail.com

 

 

 



Re: [ccp4bb] About system absence in P4222?

2008-12-16 Thread Eleanor Dodson
Thank you Ian for the example - I hadnt thought of the effect of an NCS 
translation of (x,y,1/2) in higher than 2 fold symmetry..

Eleanor

in Ian Tickle wrote:

Hi Lijun,

I take your point, and you're right I've confused someone else already!  I made 
the NCS exact because a) I was using Eleanor's example (exactly) and was too 
lazy to make it inexact, and b) making it exact makes the point equally well as 
making it inexact (actually IMO better because it makes it very easy to 
distinguish pseudo-absences from accidentally weak reflections) - as long as 
you don't over-interpret the results!

So for anyone who's confused, my apologies, just imagine that the NCS 
translation isn't exact, and consequently the 'absences' won't be exactly zero. 
 The point I was making is that NCS translations do not necessarily produce the 
same systematic absences (or pseudo-absences) as crystallographic translations.

Cheers

-- IAn

  

-Original Message-
From: Lijun Liu [mailto:li...@uoxray.uoregon.edu] 
Sent: 15 December 2008 18:10

To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] About system absence in P4222?

Ian,

Your examples may cause more confusion, especially for those 
beginners with symmetry.
In your P222 and P3 cases, an exact "NCS" (0, 0, 1/2) turns 
to be an exact crystallographic
translation, which reduces the unit cell to a half while the 
reciprocal unit cell gets doubled.  A
half of reflection were absent, including those listed as (0, 
0, 2n+1).  This rule applies generally
to all non-centrosymmetric space groups (P1, P2, P3, P4, and 
P6) with P-lattice when only having
one rotational symmetric element other than P1, and some 
other space groups like P222.


(Pseudo) translational NCS' role in systematic 
absences(weakness) is complicated.  However,

to do the math with
--

		Plug the coordinates (x,y,z) and x+tx, Y+ty, 
z+tz) into the 
		


SF equation.

--
is exactly the only way to test it.

Lijun


On Dec 15, 2008, at 5:04 AM, Ian Tickle wrote:



	But that only means that the SF contribution from that 
pair of molecules in the unit cell is zero for (00l) l=odd 
reflections.  Depending on the crystallographic symmetry 
(e.g. if it were 3-fold or higher order) there may be other 
pairs for which the SF contribution is non-zero for all (00l) 
(but zero for the the odd orders in some other line that is 
symmetry-equivalent to (00l)).


	So for example I did a test with 2 mols in the a.u. 
related by an exact (0,0,1/2) NCS translation in P222:


   h   k   l   Fcalc   phicalc
   0   0   10.00180.00
   0   0   2 5120.88180.00
   0   0   30.00180.00
   0   0   4 1273.09  0.00
   0   0   50.01  0.00
   0   0   6  260.21180.00
   0   0   70.00180.00
   0   0   8   39.42180.00
   0   0   90.01  0.00
   0   0  10   43.19  0.00
   0   0  110.00180.00
   0   0  12  118.59180.00
   0   0  130.01  0.00
   0   0  14  120.89180.00
   0   0  150.01  0.00

	(00l) l odd are definitely absent here! - because none 
of the crystallographic 2-folds affect the (0,0,1/2) translation.


	Then I generated 2 mols in the a.u. related by the 
(1/2,0,0) NCS translation in P4 to get the (h00) line (note 
that the 4-fold along c would not affect a c-axis translation):


   1   0   025189.10  0.00
   2   0   0  200.09  0.00
   3   0   014404.46180.00
   4   0   012608.60180.00
   5   0   0 4669.64180.00
   6   0   0  748.81  0.00
   7   0   0 3184.06  0.00
   8   0   0 3858.87  0.00
   9   0   0 2578.38  0.00
  10   0   0  382.61  0.00
  11   0   0  683.43180.00
  12   0   0  444.89180.00
  13   0   0  236.65180.00
  14   0   0  352.46180.00
  15   0   05.62  0.00

	No absences!  The 4-fold generates a pair of molecules 
related by the (0,1/2,0), not the (1/2,0,0) translation.  So 
Eleanor is right only in specific cases, Ronald is right in 
the general case.


	As an aside, while I was verifying this, I think I 
found a problem with the P3 specific SF calculation in SFALL. 
 Here's what I get for 2 mols in the a.u. related by an exact 
(0,0,1/2) NCS translation in P3 using the default P3 specific routine:


   0   0   18.24   -175.63
   0   0   2 7339.05121.46
   0   0   3   27.32125.92
   0   0   4  949.76-10.37
   0   0   5   39.10   -103.39
   0   0   6  461.79   -115.99
   0   0   7 

[ccp4bb] Recruitment in Structural Biology/Biophysics

2008-12-16 Thread Klaus Futterer

Dear All,

The College of Life and Environmental Sciences at the University of  
Birmingham is seeking to recruit a research group leader in  
structural biology or a related discipline. Individuals pursuing the  
study of structure-function relationships in the context of membrane  
transport or transmembrane signalling are particularly welcome to  
apply. Successful applications will be able to demonstrate research  
endeavour at the highest standing and a proven record of teaching at  
all relevant levels.


Further details can be found at http://www.biosciences.bham.ac.uk/ 
NewAppointments/New_Appointments.htm.
Informal enquiries should be directed to Prof. Kevin Chipman, Head of  
School of Biosciences, 0121-414 5422 or j.k.chip...@bham.ac.uk.





-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: k.futte...@bham.ac.uk
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-


[ccp4bb] clapham, or ccp4 6.1.0 release

2008-12-16 Thread Charles Ballard

Dear All

as we continue our journey up the A65 (towards the heart of  
Yorkshire) we are pleased to announce the release of Clapham (or  
6.1.0).  This is available form the usual locations


http://www.ccp4.ac.uk/download/downloadman.php

or

ftp://ftp.ccp4.ac.uk/ccp4/6.1/

Obviously special thanks to the program authors, testers etc.  Go enjoy

New goodies:

   * REFMAC5: updated to version 5.5.0066.  This adds twinned and  
anomalous

 refinement (Garib Murshudov, Raj Pannu, Pavol Skubak).
   * PHASER: updated to 2.1.4. This version covers MR, SAD and  
combined MR and SAD.
   * AFRO: multivariate substructure factor amplitude estimation for  
SAD/MAD

 (Raj Pannu)
   * BALBES: automated molecular replacement (Fei Long, Garib  
Murshudov,

 Alexei Vagin).
   * cBUCCANEER: statistical model building, optimised for experimental
 phasing. (Kevin Cowtan)
   * CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan
 Abrahams)
   * CTRUNCATE: New program for Intensity to Structure Factor  
conversion and

 checking data quality (Norman Stein).
   * IMOSFLM: imported imosflm 1.0.0
   * MrBUMP: Automated molecular replacement, search model retrieval  
and

 search model preparation for molecular replacement.
   * PARROT: automatic density modification and phase improvement  
(Kevin Cowtan)
   * PISA: the standalone version of the Protein Interfaces,  
Surfaces and

 Assemblies server. (Eugene Krissinel) -- optional
   * POINTLESS: Laue and Patterson group determination, v1.2.23.  
(Phil Evans)
   * RAPPER: conformer modelling through sampling residue rotameric  
states.

 (Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty,
  Swanand Gore and Tom Blundell) -- optional
   * cSEQUINS: Statistical protein chain tracing (Kevin Cowtan)
   * XIA2: Automated data reduction system designed to work from raw
 diffraction data and a little metadata, and produce usefully  
reduced
 data in a form suitable for immediately starting phasing and  
structure

 solution.

plus many updates including

   * CRANK: updated to version 1.2.0.  Greatly enhanced (Raj Pannu)
   * MOLREP: updated to version 10.2.12.
   * MOSFLM: updated to version 7.0.4.

Please note that the downloads are large (very large if you include  
the balbes database), so there may be an issue of browsers timing out  
(observed for firefox so far).


Charles Ballard

on behalf of the CCP4 team.


[ccp4bb] superpose structures .ssm or lsq which is better

2008-12-16 Thread junfeng liu

Dear All,
I am overlaying several structures using coot. There are two ways SSM or 
LSQ can be used  in that package.  But I got clearly different  result  
form  the two methods. In my opinion SSM only works on the secondary 
structures and LSQ can works on the whole atoms ,main chain or CA.

So the question is which one is better to overlay structures, LSQ or SSM ?
Thanks a lot!
liu


Re: [ccp4bb] generating omit maps

2008-12-16 Thread Alexei Vagin

SFCHECK (method unknown)



please see CCP4 documentation


[ccp4bb] disulphide refinement

2008-12-16 Thread dziuba
Hi all,

Can anyone tell me how to refine in Refmac a disulphide bond between
symmetry-related molecules?

Thanks in advance,

Karolina


Re: [ccp4bb] clapham, or ccp4 6.1.0 release

2008-12-16 Thread Jie Liu
We really appreciate all the efforts from the great CCP4 team.

But I am sorry,  there are no prebuilt executables for SGI IRIX6.5 now?
There used to be such a bundle for the older versions. It's really a pain
to do all the compilation which never go through smoothly.

Shall we wait for such a bundle or we should start to struggle with the
compilation right now?

Thanks for your attention.

Jie Liu

Charles Ballard wrote:

> Dear All
>
> as we continue our journey up the A65 (towards the heart of
> Yorkshire) we are pleased to announce the release of Clapham (or
> 6.1.0).  This is available form the usual locations
>
> http://www.ccp4.ac.uk/download/downloadman.php
>
> or
>
> ftp://ftp.ccp4.ac.uk/ccp4/6.1/
>
> Obviously special thanks to the program authors, testers etc.  Go enjoy
>
> New goodies:
>
> * REFMAC5: updated to version 5.5.0066.  This adds twinned and
> anomalous
>   refinement (Garib Murshudov, Raj Pannu, Pavol Skubak).
> * PHASER: updated to 2.1.4. This version covers MR, SAD and
> combined MR and SAD.
> * AFRO: multivariate substructure factor amplitude estimation for
> SAD/MAD
>   (Raj Pannu)
> * BALBES: automated molecular replacement (Fei Long, Garib
> Murshudov,
>   Alexei Vagin).
> * cBUCCANEER: statistical model building, optimised for experimental
>   phasing. (Kevin Cowtan)
> * CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan
>   Abrahams)
> * CTRUNCATE: New program for Intensity to Structure Factor
> conversion and
>   checking data quality (Norman Stein).
> * IMOSFLM: imported imosflm 1.0.0
> * MrBUMP: Automated molecular replacement, search model retrieval
> and
>   search model preparation for molecular replacement.
> * PARROT: automatic density modification and phase improvement
> (Kevin Cowtan)
> * PISA: the standalone version of the Protein Interfaces,
> Surfaces and
>   Assemblies server. (Eugene Krissinel) -- optional
> * POINTLESS: Laue and Patterson group determination, v1.2.23.
> (Phil Evans)
> * RAPPER: conformer modelling through sampling residue rotameric
> states.
>   (Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty,
>Swanand Gore and Tom Blundell) -- optional
> * cSEQUINS: Statistical protein chain tracing (Kevin Cowtan)
> * XIA2: Automated data reduction system designed to work from raw
>   diffraction data and a little metadata, and produce usefully
> reduced
>   data in a form suitable for immediately starting phasing and
> structure
>   solution.
>
> plus many updates including
>
> * CRANK: updated to version 1.2.0.  Greatly enhanced (Raj Pannu)
> * MOLREP: updated to version 10.2.12.
> * MOSFLM: updated to version 7.0.4.
>
> Please note that the downloads are large (very large if you include
> the balbes database), so there may be an issue of browsers timing out
> (observed for firefox so far).
>
> Charles Ballard
>
> on behalf of the CCP4 team.


[ccp4bb] RMSD's authority

2008-12-16 Thread Simon Kolstoe

Dear ccp4bb,

Can anyone point me to a table/paper that gives "acceptable" RMSD's  
for bond lengths and angles against resolution? We have had two  
different referees for a paper contradict each other and I am not sure  
what to use as a good authority for this.


Thanks,

Simon


Re: [ccp4bb] RMSD's authority

2008-12-16 Thread Bernhard Rupp
bond angle an length rmsd is a completely context sensitive data item.

It can be zero (for torsion angle refinement with fixed bonds and angles)
up to the same rmsd values observed for small molecule targets.

Anything in between is fair game, with the general tendency to become larger
with more relaxed restraints (i.e. more data).

So it depends on your refinement protocol and restraint settings.

Asking for certain hard rmsd values that match all refinements is old
school,
despite what some references might tell. Ian will probably expand more
about the relation to maximum log free likelihood. Best check his Acta D 
papers on that subject.

BR 
 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Simon
Kolstoe
Sent: Tuesday, December 16, 2008 9:51 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] RMSD's authority

Dear ccp4bb,

Can anyone point me to a table/paper that gives "acceptable" RMSD's  
for bond lengths and angles against resolution? We have had two  
different referees for a paper contradict each other and I am not sure  
what to use as a good authority for this.

Thanks,

Simon


[ccp4bb] Young Crystallographers Group

2008-12-16 Thread Arefeh Seyedarabi
Young Crystallographers Group

Committee position vacancy

The Young Crystallographers Group founded in 2004 is devoted in bringing
together the
younger and the future generation of crystallographers who are undertaking
either their
PhD or Postdoctoral research in any of the biological, chemical, physical or
industrial
fields. The activities and the environment created by the group encourages
the younger
crystallographers to be more confident and enthusiastic to present, discuss,
and exchange
ideas with their peers and the more senior crystallographers, thus opening
the door to
better understanding and the formation of a solid bridge between the younger
crystallographers and the experts in crystallography. The Young
Crystallographers Group
has a committee composed of members who work to achieve the aim of the group
and are
currently looking for a young and enthusiastic individual to fill a vacancy
on their
committee, representing the Biological Structural Group. If you are
interested in taking
up this committee position and would like to contribute to the positive
efforts of the
Young Crystallographers Group, please contact me on a.seyedar...@qmul.ac.uk.


Re: [ccp4bb] RMSD's authority

2008-12-16 Thread Ian Tickle
Hi Simon

I think I can say without fear of contradiction that this is still a
subject under debate, so I'm not at all surprised that the referees
can't agree between themselves!  I think there are actually two answers
to your question: (1) what is the formally correct answer, and (2) what
is the answer that should be acceptable to a referee who is open to
reasoned argument. In many ways it's easier to give answer (2), since
answer (1) is not yet settled in a way that is easily usable.

The first thing I should point out is that you definitely won't find a
table/paper that gives acceptable RMSDs for bond lengths and angles
against resolution, so don't bother looking for one, sorry!  If you want
the 'CCP4 community view' on this I think I can speak for the majority
and say that a reasonable compromise is to take the median value of
RMSD(bonds) (originally suggested by Clemens Vonrhein I think - as least
that's the value I use if I have to choose one) to use as a target in
refinement at 'typical' resolutions (say between 2.5 and 1.5 Ang).  I
think it is generally accepted now that the RMS Z-score
(Z=deviation/SD)is a more statistically meaningful value to quote
(printed by the latest versions of Refmac), so since the range of
RMSZ(bonds) values is by definition 0 to 1, the median is 0.5, which
corresponds to a RMSD(bonds) of about 0.012 Ang.  For bond angles the
corresponding values are RMSZ(angles) ~ 0.75, RMSD(angles) ~ 1.5 deg.

Having said that, my view (as set forth in Acta Cryst., 2007, D63,
1274-81) is that the correct target for optimisation of weights is not
RMSZ/RMSD(bonds) at all but Rfree (as originally suggested by Brunger),
or better the log(free likelihood) (suggested by Bricogne).  If you do
that (properly) the evidence is that do you get resolution-dependent
values of RMSD/RMSZ, i.e. lower values at lower resolution, and higher
values at higher resolution than the 'typical' resolution range
indicated above.  For example CNS/CNX and phenix.refine (I believe,
though I can't vouch for it as I don't use it), which do implement
weight optimisation 'properly' using Rfree as the target, often gives
RMSD(bonds) ~ 0.006 (RMSZ ~ 0.25) for resolutions around 2.5 Ang or
lower.  Also Shel-X seems to give sensible resolution-dependent
RMSD/RMSZ(bonds) values (though not for angles, since it doesn't
parameterise the uncertainties using the Engh & Huber values).

Sorry if this doesn't give the definitive answer you were looking for,
but I hope it helps to convince the wayward referee!

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk 
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Simon Kolstoe
> Sent: 16 December 2008 17:51
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: RMSD's authority
> 
> Dear ccp4bb,
> 
> Can anyone point me to a table/paper that gives "acceptable" RMSD's  
> for bond lengths and angles against resolution? We have had two  
> different referees for a paper contradict each other and I am 
> not sure  
> what to use as a good authority for this.
> 
> Thanks,
> 
> Simon
> 
> 


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[ccp4bb] Young Crystallographers Group

2008-12-16 Thread Arefeh Seyedarabi
Apologies for the misunderstanding. The Young Crystallographers Group is a
British Group and we are looking for a candidate in Britain to fill the
committee position vacancy.

Many thanks,

Arefeh Seyedarabi

Biological structural Group committee member (Young Crystallographers Group)


[ccp4bb] O/T: microscopes

2008-12-16 Thread Clint Spiegel
Hi,

I am looking to buy a modestly-priced zoom scope for x-ray
crystallographic purposes ($2-3000).  Does anyone have suggestions about
what/where to possibly find this?  I currently have a cheap one that goes
from 7.5-50X, but I'd like something with a little more magnification, a
better light source and better optics.

Thanks,
Clint


Clint Spiegel
Assistant Professor, Chemistry
Western Washington University
516 High Street
Bellingham, WA 98225-9150.


Re: [ccp4bb] O/T: microscopes

2008-12-16 Thread Jim Fairman
Clint,

We have a Leica MZ125 scope with a Leica KL1500 LCD lightsource.  It has
adjustable zoom from 8x to 160x with the 16x occular lenses but can do up to
640x with a different occular.  We also opted for the optional optical
micrometer and polarizing lenses for looking at birefringence.
Additionally, they sell an attachment for hooking up a digital camera to
take pictures of your crystals.

This scope went for about 8k or so a year ago which is a little more than
you're looking to spend but the optics are great and it beats out any scope
I've used thus far even though I've only been doing crystallography for 4
years.

Cheers, Jim

On Tue, Dec 16, 2008 at 2:00 PM, Clint Spiegel wrote:

> Hi,
>
> I am looking to buy a modestly-priced zoom scope for x-ray
> crystallographic purposes ($2-3000).  Does anyone have suggestions about
> what/where to possibly find this?  I currently have a cheap one that goes
> from 7.5-50X, but I'd like something with a little more magnification, a
> better light source and better optics.
>
> Thanks,
> Clint
>
>
> Clint Spiegel
> Assistant Professor, Chemistry
> Western Washington University
> 516 High Street
> Bellingham, WA 98225-9150.
>



-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu


Re: [ccp4bb] generating omit maps

2008-12-16 Thread Jiamu Du
sfcheck -f data.mtz -m model.pdb -omit 2 -map


On Tue, Dec 16, 2008 at 6:29 PM, Alexei Vagin wrote:

> SFCHECK (method unknown)
>>
>>
> please see CCP4 documentation
>



-- 
Jiamu Du, Ph.D.
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
320 Yue-Yang Road
Shanghai 200031
P. R. China
Tel: +86-21-5492-1117
E-mail: jiam...@gmail.com