[ccp4bb] Release of ARP/wARP 8.0 patch 1

[Victor Lamzin]

Dear Colleagues,

We are happy to announce an update (patch 1) to ARP/wARP 8.0 (released 
in October 2018). Updated package can be downloaded from the ARP/wARP 
homepage (www.arp-warp.org or www.embl-hamburg.de/ARP). A joint 
ARP/wARP-CCP4 distribution of the ARP/wARP 8.0 patch 1 will shortly be 
announced by the CCP4 core team.


News in ARP/wARP 8.0 patch 1:

Protein model building:
- Large structures up to 50,000 residues can now be handled; within this 
limit the number of NCS-related copies can be up to 1000
- Both main-chain and side-chain building steps are now considerably 
faster for large structures

- Output file names are customisable

Ligand building:
- Ligand validation using LigEnergy is added to all ligand-building 
protocols


Webservice:
- Additional plots and a viewer are added

Other changes:
- Various bugs fixed in protein model building (both for MX and 
cryo-EM), ligand building and webservice

- Example files have been updated

Victor and the ARP/wARP developers



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[ccp4bb] Postdoctoral position at EMBL in Hamburg

[Victor Lamzin]

Dear Colleagues,

We are looking for a highly motivated Postdoctoral researcher to join 
our efforts in structure-based search of new drug leads. If you have 
experience in macromolecular crystallography, sample preparation and 
scientific programming, and interested in this position, please refer to 
the job description and application instructions at:


https://www.embl-hamburg.de/jobs/searchjobs/index.php?ref=HH_00144

The closing date for applications is 12th August 2018.

With best regards,
Victor Lamzin




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Re: [ccp4bb] "Atomic resolution"

[Victor Lamzin]

Dear Jacob,

The resolution in reciprocal and real space was addressed by R. W. James 
in his paper 'False Detail in Three-Dimensional Fourier Representations 
of Crystal Structures' piblished in Acta Cryst. (1948). 1, 132-134. 
James showed that atomic density shape in the presence of series 
terminations is described by the Bessel function of zero order:


3*[sin(m) - m*cos(m)]/m^3
where m=2*Pi*r/dmin

This function is equal to 1 at the atomic centre (r=0) and decreases as 
r increases, then it oscillates. The function reduces to 0.5 for 
r/dmin=0.4. Therefore, the two equal atoms to be separated (in a sense 
of having a density in between lower than at their centres) the distance 
between them should be equal (or higher) than 2*dmin*0.4


Main chain C and O atoms separated by 1.23 A should be resolved if dmin 
is better than 1.55 A.


Two carbon sp3 atoms (distance 1.53 A) should be resolved if dmin is 
better than 1.9 A.


Indeed, as Thomas wrote, 1.5 A is about right.

The above is correct in the absence of atomic displacement parameters 
(Bfactor=0), for example for the normalised (sharpened) structure factor 
amplitudes. And, of course, for the complete and error-free diffraction 
data.


Victor



On 11/01/2018 21:07, Keller, Jacob wrote:


The reason behind this query is that I want to illustrate the power of 
prior knowledge in data analysis. I want to say something like “even 
though atoms cannot be directly observed at worse than X resolution, 
which represents Y% of the PDB, all of these data sets have been fit 
correctly with atomic models. This is due entirely to the power of the 
excellent priors which exist in crystallography.”


JPK

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the 
recipient specified in message only. It is strictly forbidden to share 
any part of this message with any third party, without a written 
consent of the sender. If you received this message by mistake, please 
reply to this message and follow with its deletion, so that we can 
ensure such a mistake does not occur in the future.


*From:* Thomas Edwards [mailto:t.a.edwa...@leeds.ac.uk]
*Sent:* Thursday, January 11, 2018 2:59 PM
*To:* Keller, Jacob 
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] "Atomic resolution"

Dear Jacob,

Ah... this old chestnut!

Current EM people say that they are at atomic resolution because they 
are building atomic models (naive??).


I have been criticised in the past for using the term with say 2.2A 
diffraction data. By co-authors and reviewers alike. When I was young 
and naive.


My (current) definition would be yours - visible with data.

I think 1.5A is about right for X-ray. Maybe higher res?

I’m sure there are lots of rigorous ways to think. I probably haven’t 
taken that route. However, I think it is a semantic problem that might 
benefit from some disambiguation rather than rigour.


It depends why you are asking the question...

Sorry..!

*/Ed is: Out and about.../*

*/Sent from iPhone6sPlus./*


On 11 Jan 2018, at 19:31, Keller, Jacob > wrote:


Dear Crystallographers,

Has there been a consensus as to what is meant by “atomic
resolution?” Seems like the term is taken by various practitioners
to mean different things.

A related question: at what resolution are atoms “visible” using
only the data? I have an empirical feeling that this would be
around 1.5 Ang Bragg spacings, but on the other hand, one can
contour up most maps and see individual atom peaks. I would be
interested to hear a more rigorous way to think about this.

All the best,

Jacob Keller

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

(571)209-4000 x3159

+

The content of this email is confidential and intended for the
recipient specified in message only. It is strictly forbidden to
share any part of this message with any third party, without a
written consent of the sender. If you received this message by
mistake, please reply to this message and follow with its
deletion, so that we can ensure such a mistake does not occur in
the future.

Re: [ccp4bb] DipCheck Webservice

[Victor Lamzin]

Dear Ameya,

DipCheck uses a novel 3-dimensional parameter space for validation of 
the backbone geometry, and we hope that it can be more informative than 
some of the existing validation approaches. We also hope that DipCheck 
can be a good validation tool as its inverse task does not seem to be 
solvable - in other words the DipCheck parameter space cannot be used to 
better 'geometrise' a protein model. We are discussing with the PDB 
colleagues a possibility for DipCheck to join the PDB validation tools.


With best regards,
Victor


On 04/09/2017 16:53, ameya benz wrote:

Dear Victor,

I used the server. However I found that the % of residues in 
disallowed region given by your server and PDB validation server 
differs. What could be the probable reason?


regards,
Ameya

On Mon, Sep 4, 2017 at 8:12 PM, Victor Lamzin <vic...@embl-hamburg.de 
<mailto:vic...@embl-hamburg.de>> wrote:



Dear Colleagues,

We announce the DipCheck Webservice for validation of backbone
geometry in protein structures as described in:
https://doi.org/10.1107/S2052252517008466
<https://doi.org/10.1107/S2052252517008466>

The Webservice is available at:
http://cluster.embl-hamburg.de/dipcheck
<http://cluster.embl-hamburg.de/dipcheck>

Joana Pereira, Umut Oezugurel, Philipp Heuser and Victor Lamzin

[ccp4bb] DipCheck Webservice

[Victor Lamzin]

Dear Colleagues,

We announce the DipCheck Webservice for validation of backbone geometry 
in protein structures as described in:

https://doi.org/10.1107/S2052252517008466

The Webservice is available at:
http://cluster.embl-hamburg.de/dipcheck

Joana Pereira, Umut Oezugurel, Philipp Heuser and Victor Lamzin

Re: [ccp4bb] "reset" a structure before re-refinement

[Victor Lamzin]

Dear Graeme,
You can also type the following on a command line, optional commands are 
given in square parentheses.

Victor

$warpbin/arp_warp
mode shakemodel allatoms
files ccp4 xyzin FILENAME.pdb xyzout FILENAME.pdb
symmetry SPACEGROUP
shakemodel   [ bexclude B1 ] [ breset B1 B2 ] [ randomise X ] [ shift X 
Y Z ]

end


On 17/08/2017 17:17, Graeme Winter wrote:

Dear All,

Is there a protocol out there to gently perturb atomic positions so that re-running 
refinement can essentially put them back without bias from the original refinement? In 
particular, if trying to perform the Karplus and Diederichs paired refinement protocol, I 
do not want to run the lower resolution refinements with the "memory" of the 
weak high resolution data present... and only have the refined structure to work from...

Am using refmac5, but any pdb randomizer would hit the spot

Many thanks Graeme

[ccp4bb] ARP/wARP webservice

[Victor Lamzin]

Dear Colleagues,

We are happy to announce a redesigned and extended webservice for remote 
ARP/wARP execution. In addition to the crystallographic protein chain 
tracing, many other functionalities of ARP/wARP are now also available 
online. These include:


- classic protein model building starting from phases or from existing model
- secondary structure building
- nucleotide building
- solvent modelling
- ligand modelling and identification

The webservice offers a registration with an email address, which 
provides more options to the users. For example, all jobs a user has 
previously submitted are now in one place, can be easily evaluated, 
compared or run again with different parameters.


The link for the new ARP/wARP webservice is 
https://arpwarp.embl-hamburg.de. The former link 
http://cluster.embl-hamburg.de/ARPwARP/remote-http.html continues to 
function too. The webservice is using the current ARP/wARP version 
7.6.1, which has been jointly released with the CCP4 software.


The website contains links to related webservices: Auto-Rickshaw for 
structure solution, ViCi for ligand scaffold hopping and DipCheck for 
protein model validation.


Your feedback, comments and suggestions are welcome.

Happy model building!
The ARP/wARP team at EMBL Hamburg

Re: [ccp4bb] NAD dihedral for C2N-C3N-C7N-N7N

[Victor Lamzin]

There are theories that the NAD carboxamide group in an enzyme active 
site should be out of the nicotine plane by 20-30 degrees, to help 
develop a partial positive charge on the C4 atom. This also helps 
distorting the planarity of the nicotine ring to ease the catalytic 
transformation of NAD to NADH. A while ago we published a paper on a 
related topic, the enzymatic activation of NADH: Meijers et al 
https://www.ncbi.nlm.nih.gov/pubmed/11134046


Victor Lamzin


On 19/05/2017 00:44, Dale Tronrud wrote:

I have looked over a number of high resolution models with NAD+ and
NADH in the PDB as well as small molecule structures.  I also have some
familiarity with similar chemistry in the decorations on the edge of
bacteriochlorophyll-a molecules.  The CONH2 group does flip over when
the hydrogen bonding environment calls for it.  It is very hard to tell
the difference between the oxygen atom and the nitrogen atom from the
appearance of the electron density so you always have to check the
hydrogen bonding environment when building an NAD? model.

I have seen one case where a Ser -> Ala mutation in the protein
caused the group to flip with interesting consequences on the far side
of the co-factor.  My go-to QM person tells me that flipping this group
will change the energies of the molecular orbitals and therefor the
redox potential of the NAD? molecule so this conformational change may
be important to the action of your catalysis.

I have also seen a number of NAD? models in the PDB where this group
is clearly misorientated.

As you note, the torsion angle should be close to zero or 180.
However it is unlikely to have exactly those values because there are
non-bonded clashes when everything is in one plane.  Some restraint
libraries inappropriately restrain this group to be co-planar with the
six-membered ring.  As always, check you CIF!

Dale Tronrud


On 5/17/2017 12:46 PM, Jorge Iulek wrote:

Dear all,

 I came across some difficulty to refine a NAD molecule in a
structure, specially its amide of the nicotinamide moiety.
 A (very) brief search in deposited structures seems to point that
not so ever the C2N-C3N-C7N-N7N dihedral is close to either 0 or 180
degrees, but in most cases it is to one of these, with a preference
towards 0 degrees. Another search in the literature, and I could not
find any study on either NAD or even the nicotinamide alone to calculate
the energy barrier to rotate around this bond (in vacuum, eg).
 My data quality and resolution do not put much confidence on
B-factor differences, but they seem to indicate that the cited dihedral
angle should be close to 180 degrees, id est, O7N is "closer" to C2N
(and, consequently, to N1N) than N7N is. In fact, I have a glutamine
nearby whose terminal amide is interacting with the nicotinamide amide,
so my idea is to make one's nitrogen to interact with other's oxygen.
Concerning b-factor differences for this glutamine, they favor its NE2
to point to nicotinamide amide, what would imply that the
C2N-C3N-C7N-N7N dihedral to would be close to 180 degrees rather than 0
degree.
 Is there any wide study on NAD nicotinamide amide conformation?
Specially, bound to protein structures?
 Thanks,

Jorge

Re: [ccp4bb] on NCS restraint

[Victor Lamzin]

  
  

  Hi all,
  
  We have carried out a large-scale test of the use of Refmac's
  NCS-restraints during model building with ARP/wARP. We have found
  advantageous to have such restraints turned on with data
  resolution extending to as high as 1.5 A.
  
  Victor
  
  
  
  On 21/04/2015 14:46, Sheriff, Steven wrote:


  
  
  
  
All:
 
I strongly disagree with Reza’s suggestion that
one should abandon NCS at better than 2.5 Å resolution (or
even Herman’s suggestion at better than 2.0 Å resolution).
Either of these may be true in any particular case, BUT one
should do the experiment – Run parallel refinements from the
same starting model with and without NCS restraints and
compare R-free, the gap between R-free and R-work, and
particular places where one knows or suspects that the local
geometry is different, before deciding to abandon NCS
restraints. This was certainly true in the bad old days when
“loose” (as opposed to strict) NCS restraints were used and
“bound” each chain more-or-less to a single chain’s
geometry, even though one was refining all extant chains.
Using so-called “loose” NCS restraints, I once had a loop
pulled out of electron density during refinement and the tip
moved ~6 Å!
 
However, for the last 5 years or so, BUSTER,
which I use, and REFMAC (and presumably PHENIX) have used
LSSR (local secondary structure restraints) where the
maximum “pull” to uniformity tops out at a certain value. I
have not rigorously followed my own advice above to run
parallel refinements, but I have yet to find a case where
LSSR-type NCS restraints have “hurt” the refinement down to
at least ~1.5 Å resolution.

 
To give credit where it is due, Oliver Smart, who
implemented LSSR in BUSTER, attributed the concept to George
Sheldrick.
 
Steven
 
--
Date:    Mon, 20 Apr 2015 10:38:27 +
From:    Reza Khayat rkha...@ccny.cuny.edu
Subject: Re: [ccp4bb] on NCS restraint
 
Hi,
 
The purpose of NCS is to reduce the
  degrees of freedom in order to avoid over refinement -not only
  to expedite refinement. Strict or restrained NCS should be
  applied at lower resolutions (2.7Å) or data completeness.
  Forgo NCS If you have a complete and better than 2.5Å dataset.
  Also, you can define the regions where NCS is applied and thus
  avoid loops/regions where the NCS is violated.
 
Best wishes,
Reza
 
Reza Khayat, PhD
Assistant Professor
City College of New York
160 Convent Ave, MR-1135
New York, NY 10031
(212) 650-6070
rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu
 
--
On Apr 20, 2015, at 4:01 AM, herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com
  wrote:
 
Dear Smith,
 
There used to be something called
  “strict NCS“ which meant that instead of many identical
  subunits, only one “average” subunit was refined, which would
  speed up the refinement significantly, at the expense of
  requiring that all subunits are exactly identical.
 
I do not think that this option is used
  anymore and most refinement programs would require NCS related
  subunits to be similar, but not identical to each other. As
  Robbie Joosten pointed at, this can help a lot, especially
  when you do not have high resolution data. So for data with
  better than 2.0 Å resolution, including NCS restraints would
  probably not make a big difference, but otherwise I would
  switch them on.
 
Best,
Herman
 
--
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
  Im Auftrag von Smith Liu
Gesendet: Freitag, 17. April 2015 06:02
An: 
CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] on NCS restraint
 
Dear Jurgen,
 
My understanding is that NCS restraint
  can significantly enhance the speed of calculation, but
  considering the subunits even with the eactly same sequence
  may not be identical, to have NCS restraint may be not
  necessary or may be not good for the refinement, am I right?
 
Smith
 
At 2015-04-17 09:09:05, "Jurgen 

Re: [ccp4bb] on NCS restraint

[Victor Lamzin]

  
  

  Dear Reza,
  
   have the results been published?
  
  Not all of them. 
  
  The first implementation of NCS-restraints in ARP/wARP's model
  building at a resolution of 2.3 A and lower was published: Wiegels
  T, Lamzin VS. Use of noncrystallographic symmetry for automated
  model building at medium to low resolution. (2012) Acta
  Crystallogr D Biol Crystallogr. 68, 446-453. PMID: 22505265
  
  Subsequent advances and applicability to data up to 1.5 A is still
  to be published; however it is now the default setting of
  ARP/wARP.
  
  Victor
  
  
  
  
  
  On 21/04/2015 15:32, Reza Khayat wrote:


  
  
  
  
  
Hi,
 
I have to agree
with Steven. I was too haste in my reply to the initial
e-mail. As Steven put it, it is best to run multiple
experiments at the same time and identify which produces the
best result.

 
On a follow up
to Victor Lamin’s reply, have the results been published?
 
Best wishes,
Reza
 
 

  Reza Khayat,
  PhD
  Assistant
  Professor
  Department of
  Chemistry
  City College
  of New York
  New York, NY
  10031
  http://www.khayatlab.org/
  212-650-6070

 

  
From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK]
On Behalf Of Victor Lamzin
Sent: Tuesday, April 21, 2015 9:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] on NCS restraint
  

 

  
Hi all,

We have carried out a large-scale test of the use of
Refmac's NCS-restraints during model building with ARP/wARP.
We have found advantageous to have such restraints turned on
with data resolution extending to as high as 1.5 A.

Victor



On 21/04/2015 14:46, Sheriff, Steven wrote:


  All:
   
  I strongly disagree with Reza’s
  suggestion that one should abandon NCS at better than 2.5
  Å resolution (or even Herman’s suggestion at better than
  2.0 Å resolution). Either of these may be true in any
  particular case, BUT one should do the experiment – Run
  parallel refinements from the same starting model with and
  without NCS restraints and compare R-free, the gap between
  R-free and R-work, and particular places where one knows
  or suspects that the local geometry is different, before
  deciding to abandon NCS restraints. This was certainly
  true in the bad old days when “loose” (as opposed to
  strict) NCS restraints were used and “bound” each chain
  more-or-less to a single chain’s geometry, even though one
  was refining all extant chains. Using so-called “loose”
  NCS restraints, I once had a loop pulled out of electron
  density during refinement and the tip moved ~6 Å!
   
  However, for the last 5 years or so,
  BUSTER, which I use, and REFMAC (and presumably PHENIX)
  have used LSSR (local secondary structure restraints)
  where the maximum “pull” to uniformity tops out at a
  certain value. I have not rigorously followed my own
  advice above to run parallel refinements, but I have yet
  to find a case where LSSR-type NCS restraints have “hurt”
  the refinement down to at least ~1.5 Å resolution.

   
  To give credit where it is due, Oliver
  Smart, who implemented LSSR in BUSTER, attributed the
  concept to George Sheldrick.
   
  Steven
   
  --
  Date:    Mon, 20 Apr 2015 10:38:27
+
  From:    Reza Khayat rkha...@ccny.cuny.edu
  Subject: Re: [ccp4bb] on NCS restraint
   
  Hi,
   
  The purpose of NCS is to reduce the
degrees of freedom in order to avoid over refinement -not
only to expedite refinement. Strict or restrained NCS should
be applied at lower resolutions (2.7Å) or data
completeness. Forgo NCS If you have a complete and better
than 2.5Å dataset. Also, you can define the regions where
NCS is applied and thus avoid loops/regions where the NCS is
violated.
   
  Best wishes,
  Reza

[ccp4bb] postdoctoral position in methods development for biological structure determination

[Victor Lamzin]

Dear Colleagues,

I would like to draw your attention to the following job vacancy at the 
EMBL in Hamburg:


Postdoctoral position in the area of Research and Scientific Software 
Development for Biological Structure Determination


http://www.embl-hamburg.de/jobs/searchjobs/index.php?ref=HH_00080

If you are interested in this position, please apply online through 
www.embl.org/jobs


The deadline for applications is 24th May 2015.

With best regards,
Victor Lamzin

[ccp4bb] Research software developer at EMBL Hamburg

[Victor Lamzin]

Dear Colleagues,

There is a staff member vacancy for a Research Software Developer at the 
EMBL Unit in Hamburg, Germany. The post holder will have a leading role 
in technical implementation and scientific development of the ARP/wARP 
software (www.arp-warp.org) for crystallographic structure determination 
and the building of macromolecular models in 3D electron density maps 
generated from X-ray diffraction data. Important tasks will include 
compilation, packaging and benchmarking of the software, as well as 
support for end-users.


The deadline for applications is 8th March 2015.

For details see:
http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=53392aid=15470

Please apply online through www.embl.org/jobs

With best regards,
Victor Lamzin

Re: [ccp4bb] R free flag missing after ARP/wARP?

[Victor Lamzin]

  
  

  Dear Lu,
  
  The MTZ file produced at the end of the ARP/wARP protein model
  building is created by Refmac and contains the following:
  
  1. New columns created for the built model: (FC, PHIC, FC_ALL,
  PHIC_ALL, FWT, PHWT, DELFWT, PHDELWT, FOM, FC_ALL_LS, PHIC_ALL_LS)
  
  2. Columns from the input data file that were used for the
  refinement - structure factor amplitudes and their estimated
  standard deviations scaled to those calculated from the model. If
  Rfree flag was used, the FREE column is also copied to the output
  MTZ file.
  
  Since you chose not to use Rfree for model building, the Rfree
  flag was not copied to the output.
  
  Historically, the default for ARP/wARP protein model building is
  not to use Rfree. Some years ago we did observe a number of cases
  where setting a part of the data aside for cross-validation
  resulted in lower observation-to-parameter ratio and poorer model
  building. We also thought that the auto-traced model (if built)
  could itself serve as a validation criterion. In contrast, for
  ARP/wARP building the solvent structure only, the use of Rfree is
  a default.
  
  Over the recent years much has improved, notably Refmac's
  likelihood targets. I am sure that in many cases the use of Rfree
  could now be advantageous for protein model building. We will try
  to repeat extensive benchmarking with different ARP/wARP
  protocols, so that many default parameters could be improved.
  
  With best regards,
  Victor
  
  
  
  
  On 20/10/2014 04:41, luzuok wrote:


  
Dear all,
    I was using ARP/wARP in ccp4i, the input mtz file
  certainly has free R flag, but the output mzt file doesn't
  have the free R flag label? 
I chose " do not use the Free R flag" in the ARP/wARP GUI.
  Can anyone tell me what's wrong with this? 

best reagrds!
Lu Zuokun


--
  卢作焜
  南开大学新生物站A202

  
  
  
  


  

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] Postdoctoral opportunity at the EMBL Hamburg

[Victor Lamzin]

Dear All,

We are seeking a highly motivated researcher, preferably a fresh PhD 
graduate, for a postdoctoral position in the area of in silico 
ligand-based drug design 
(http://www.embl-hamburg.de/training/postdocs/08-eipod/application/04_2013_project_ideas/lamzin.pdf). 



The position is within the EMBL Interdisciplinary Postdoctoral Programme 
(EIPOD, http://www.embl-hamburg.de/training/postdocs/08-eipod/index.html).


The postholder will be primarily working on computational modelling of 
small molecule shapes and protein-ligand interactions. The project may 
also require to perform biochemical or biophysical assays.


If you are interested in applying for the position, please send your CV 
to me at vic...@embl-hamburg.de


The deadline for the applications is September 10.

With best regards,
Victor Lamzin

European Molecular Biology Laboratory, Hamburg Unit
Deputy Head and Group Leader
c/o DESY Notkestrasse 85
22603 Hamburg, Germany

Re: [ccp4bb] Problem in running ARP_WARP in CCP4i

[Victor Lamzin]

Dear Karthikeyan,

It may indeed be too long length of your PATH variable.

Can you also type
echo $PATH | wc -c
and see what the output is? On my Mac it is 641.

With best regards,
Victor



On 07/03/2013 14:38, S. Karthikeyan wrote:

Dear CCP4BB members,

I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in
CentOS system. However, it gives the following error even for the example files
provided with Arp/Warp. Any suggestions are welcome.


---
BFONT COLOR=#FF!--SUMMARY_BEGIN--
QUITTING ... ARP/wARP module stopped with an error message:
/home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh

!--SUMMARY_END--/FONT/B


If I try to run through command line it gives the following error:


auto_tracing.sh datafile ../psp.mtz

Thu Mar  7 19:09:18 IST 2013


Word too long.

QUITTING ... ARP/wARP module stopped with an error message:
/home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh

---
Thanking you

With regards
S. Karthikeyan





__
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Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202

Re: [ccp4bb] PNAS on fraud

[Victor Lamzin]

Just a few additional ideas on the significance of the presented values 
of the correlation coefficient.


For samples of size N from a bivariate normal with correlation r, its 
standard deviation is approximately
StDev(R) = (1 - R^2)/sqrt(N – 1) - note that it depends on the number of 
points used to calculate CC. One good reference is Hotelling, H. (1953). 
New light on the correlation coefficient and its transforms. Journal of 
the Royal Statistical Society, Series B, 15(2), 193-232. For the three 
cases mentioned in Figure 3, fraud, error and duplicates the correlation 
coefficients and their standard deviationa are respectively:


0.294 0.031 (almost 10 times above its standard deviation)
0.338 0.042 (also well above standard deviation)
0.119 0.045 (2.5 times above standard deviation, what the authors call 
'slight' correlation)



A distribution of CC is not Gaussian, which is often inconvenient. One 
can do a Fischer's z-transformation to obtain z-statistics

z = (1/2)ln((1+R)/(1-R))
which is approximately normally distributed with standard deviation 
1/sqrt(N-3) and then do z-score tests on it. For the same three cases 
the values of normally distributed z and their standard deviation are 
very similar to the values obtained from the approximation above.


0.303 0.034
0.352 0.048
0.120 0.045

With best regards,
Victor






On 18/10/2012 19:52, DUMAS Philippe (UDS) wrote:
  
Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit:


I had a look to this PNAS paper by Fang et al.
I am a bit surprised by their interpretation of their Fig. 3: they claim that 
here exists a highly signficant correlation between Impact factor and number of 
retractations. Personnaly,  I would have concluded to a complete lack of 
correlation...
Should I retract this judgment?
Philippe Dumas
  

Dear CCP4 followers,

Maybe you are already aware of this interesting study in PNAS regarding the
prevalence of fraud vs. 'real' error in paper retractions:

Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the
majority of retracted scientific publications. Proc Natl Acad Sci U S A
109(42): 17028-33.

http://www.pnas.org/content/109/42/17028.abstract

There were also a few comments on related stuff such as fake peer review in
the Chronicle of Higher Education. As not all may
have access to that journal, I have put the 3 relevant pdf links on my web

http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf
http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf
http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf


Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
  
  
  
  

[ccp4bb] joint EMBL-CCP4 training course in macromolecular crystallography

[Victor Lamzin]

We would like to announce a joint EMBL-CCP4 training course European 
School for Macromolecular Crystallography (ESMAX), which will build 
upon the traditions of the forefront of training in structural biology – 
the M2M workshops and the CCP4 crystallography schools. The first 
ESMAX-2012 course will take place at the EMBL Hamburg Outstation, the 
DESY synchrotron site during the period:


Monday November 19th to Monday November 26th, 2012.

The ESMAX-2012 course will include a range of activities addressing 
essential steps in determining biomolecular structures. In particular, 
the courses will have practicals on the use of synchrotron radiation and 
beamline equipment, sample handling and carrying out an experiment, 
followed by an intense course on data processing, structure solution, 
model building and validation using top-ranked software packages.


Speakers and tutors include G. Bourenkov (Hamburg), C. Carolan 
(Hamburg), M. Cianci (Hamburg), Z. Dauter (Argonne), K. Diederichs 
(Konstanz), W. Kabsch (Heidelberg), J. Kallio (Hamburg), R. Keegan 
(Didcot), E. Krissinel (Didcot), V. Lamzin (Hamburg), A. Lebedev 
(Didcot), B. Lohkamp (Stockholm), W. Minor (Charlottesville), G. 
Murshudov (Cambridge), S. Panjikar (Melbourne), N. Pannu (Leiden), H. 
Powell (Cambridge), T. Schneider (Hamburg), T. Schwede (Basel), T. 
Wiegels (Hamburg).


The number of places is restricted to 20. Applications can be made 
electronically via the link 
http://www.embl-hamburg.de/training/events/2012/ESMAX-12/index.html


The deadline for applications is October 1st, 2012.

The organising committee - Michele Cianci, Johanna Kallio, Ronan Keegan, 
Eugene Krissinel, Victor Lamzin, Andrey Lebedev, Thomas Schneider

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

[Victor Lamzin]

I can only confirm what Alex said. And the structure was neither a  
globin or zyme or psin!


Victor


Quoting aaleshin aales...@burnham.org:

I and Victor Lamzin solved our first protein structure (3A  
resolution) in 80-s using pure MIR and a home made (Russian)  
diffractometer...


Alex

On Jun 6, 2012, at 1:42 PM, Boaz Shaanan wrote:

So if get the gist of the thread right, am I correct in assuming  
that the last protein structures to be solved strictly by MIR  are  
haemoglobin/myoglobin, lysozyme and chymotrypsin and perhaps one or  
two more in the late sixties? In which case the answer  to the  
original question about MIR being obsolete, is yes it is since a  
long time?


 Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil  
Evans [p...@mrc-lmb.cam.ac.uk]

Sent: Wednesday, June 06, 2012 6:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous  
replacement an obsolete technique?


No they were not useless! I used them

(probably better now with cryo data though)

Phil

On 6 Jun 2012, at 16:02, Dyda wrote:

I suspect that pure MIR (without anomalous) was always a fiction.  
I doubt that anyone has ever used it. Heavy atoms always give

an anomalous signal



Phil


I suspect that there was a time when the anomalous signal in data  
sets was fictional.
Before the invent of flash freezing, systematic errors due to  
decay and the need
of scaling together many derivative data sets collected on  
multiple crystals could render
weak anomalous signal useless. Therefore MIR was needed. Also,  
current hardware/software

produces much better reduced data, so weak signals can become useful.

Fred

?[32m***
Fred Dyda, Ph.D.   Phone:301-402-4496
Laboratory of Molecular BiologyFax: 301-496-0201
DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov
Bldg. 5. Room 303
Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
Google maps coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***?[m

Re: [ccp4bb] arp_waters still available?

[Victor Lamzin]

Dear Bernard,

arp_waters is a very old code and it gets even older as we speak.

Try to use ARP/wARP version 7.2, where you can run the same task:
from the command line ($warpbin/auto_solvent.sh)
from the CCP4i GUI (ARP/wARP Solvent)
from ArpNavigator (Model Solvent)

There should be both 32 and 64-bit versions.

Best regards,
Victor


On 05/04/2012 05:23, Bernhard Rupp (Hofkristallrat a.D.) wrote:

Dear Developers,

in some older scripts I still call the ccp4 version of arp_waters, which
worked well for dummy atom picking.
It does not seem to be included in recent 64 bit CCP4 packages. Does anyone
perhaps have
a precompiled 64 bit version of arp_waters that might run on RHEL62?

Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-

No animals were hurt or killed during the
production of this email.
-

[ccp4bb] research software developer vacancy at EMBL Hamburg

[Victor Lamzin]

Dear all,

There is a staff member vacancy for a Research Software Developer at the 
EMBL Unit in Hamburg, Germany. The post holder will have a leading role 
in technical implementation and scientific development of the ARP/wARP 
software for crystallographic structure determination and the building 
of macromolecular models in 3D electron density maps generated from 
X-ray diffraction and, potentially, from electron microscopy and 
free-electron laser based data.


Application deadline is 22nd April, 2012.

For details see:

http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=48242aid=15470

With best regards,
Victor

[ccp4bb] Biology infrastructure at the XFEL

[Victor Lamzin]

The European Molecular Biology Laboratory (EMBL) and the European  
X-ray Free Electron Laser (XFEL) at DESY, Hamburg, Germany, have a  
keen interest in the development of FEL-based applications in  
structural biology. Within this framework the EMBL, together with  
international collaborators from Russia, Sweden and Germany, propose  
to construct a biology infrastructure at the XFEL facility (expected  
completion in 2016) to enable biological experiments using the high  
brilliance, ultrashort pulse duration and high repetition rate  
coherent X-ray radiation.


The proposed biological sample infrastructure facility will provide:
- support to the international life-science community in generation  
and handling of challenging samples in immediate proximity to XFEL  
instruments.
- appropriate selection, quality control and evaluation of samples,  
including correlative imaging, immediately prior to XFEL experiments.
- standardized technology for data interpretation, including  
computation and validation of structural models.


In order to ensure efficient operation of the facility and provide  
optimal services for the international biological community we seek  
your input to identify the requirements necessary to support these  
novel biological imaging experiments. We would appreciate your input  
in the web-based questionnaire available at  
http://www.embl-hamburg.de/xfel_cgi-bin/questionnaire


The results of this survey will be used to identify the most pressing  
needs that should be taken into account during planning and  
construction of the infrastructure.


We thank you in advance for your cooperation.

Re: [ccp4bb] loop building with ARP/wARP

[Victor Lamzin]

Dear Greg,

Try ARP/wARP 7.2, released a few days ago, which is better, more  
stable and should have improved flash of error messages to the log  
files.


ARP/wARP Loopy will not build a 33-residue loop at once, but Classic  
model building may get the gap shortened.


Go to www.arp-warp.org for download. In parallel, from the same page  
you can submit Classic protein model building for remote execution in  
Hamburg, which also has ARP/wARP 7.2 installed.


Please get back if problems remain.

With best regards,
Victor


Quoting Gregory Bowman gdbow...@jhu.edu:


Hi all,

I have a large disordered loop (33aa) for a 2.0 Å dataset for which  
the rest of the structure is well-defined, and phases are decent  
(Rwork=19.6, Rfree=24.6). I can see some broken up density at one  
end, but have been unable to convincingly build into into this  
region manually. I would like to try arp/warp to improve density or  
possibly extend the loop termini but have been thwarted by some  
technical problems and would appreciate any advice. I've installed  
ccp4 6.2.0 on Mac OS X (10.6.8) with fink, both as 32-bit and 64-bit  
to allow me to run ARP/wARP (version 7.1) from the ccp4i GUI. I've  
been unable to get loopy to work, and also the standard ARP/wARP  
classic.


When I run ARP/wARP Loops  (a.k.a. loopy), I get the message in  
the log file:  Couldn't find any loop to build, loopy will simple  
copy the pdb file. The program is able to read the sequence .pir  
file and match it to the structure, and seems from the sequence  
alignment to identify the regions of the sequence for which there is  
no structure. I'm guessing that I'm not putting some obvious  
parameter into the GUI/starting script, but I don't know what that  
might be. The script generated from the GUI (21_loopy.def) is pasted  
below.


When I try to run ARP/wARP classic for loop building, I get the  
following message in the logfile:


QUITTING ... ARP/wARP module stopped with an error message:
REFMAC
*** Look for error message in the file:
/Users/gbowman/Greg/20_warpNtrace_refine.last.log

At the end of the warpNtrace_refine.last.log file, the program  
reports what seem to be close contacts. Since I don't see this in  
the structure, and don't have any problems or errors like this when  
I refine the structure with REMAC, is this from rebuilding, and is  
this the problem that halts REFMAC?


Thanks!
Greg

= = = = = =
20_warpNtrace_refine.last.log
= = = = = =
snip
 Input file :restraints.pdb
  NUMBER OF MONOMERS IN THE LIBRARY  : 11465
with complete description: 11465
  NUMBER OF MODIFICATIONS:53
  NUMBER OF LINKS:66
  I am reading libraries. Please wait.
  - energy parameters
  - monomers description (links  mod )
BFONT COLOR=#FF!--SUMMARY_BEGIN--
!--SUMMARY_END--/FONT/B
  Number of atoms:2463
  Number of residues : 859
  Number of chains   :   3
  I am reading library. Please wait.
mon_lib.cif
  INFO: link is found (not be used) dist=   1.907 ideal_dist=   1.432
ch:AA   res:   8  GLY  at:CA  .-ch:AA   res:  50   
TYR  at:OH  .

  INFO: link is found (not be used) dist=   2.126 ideal_dist=   1.645
ch:AA   res:  13  ARG  at:NH1 .-ch:AA   res:  54   
MET  at:SD  .

  INFO: link is found (not be used) dist=   1.820 ideal_dist=   1.462
ch:AA   res:  13  ARG  at:NH1 .-ch:AA   res:  54   
MET  at:CE  .

  INFO: link is found (not be used) dist=   1.757 ideal_dist=   1.395
ch:AA   res:  13  ARG  at:NE  .-ch:AA   res: 119   
PHE  at:CD1 .

  INFO: link is found (not be used) dist=   1.572 ideal_dist=   1.462
ch:AA   res:  13  ARG  at:NH2 .-ch:AA   res: 125   
LEU  at:CD2 .

  INFO: link is found (not be used) dist=   1.751 ideal_dist=   1.513
ch:AA   res:  33  ILE  at:CG2 .-ch:AA   res:  39   
PRO  at:CG  .

  INFO: link is found (not be used) dist=   1.451 ideal_dist=   1.513
ch:AA   res:  33  ILE  at:CG2 .-ch:AA   res:  39   
PRO  at:CD  .

  INFO: link is found (not be used) dist=   1.759 ideal_dist=   1.524
ch:AA   res:  58  LYS  at:CD  .-ch:AA   res: 130   
LEU  at:CB  .

  INFO: link is found (not be used) dist=   1.725 ideal_dist=   1.513
ch:AA   res:  58  LYS  at:CD  .-ch:AA   res: 130   
LEU  at:CD1 .

  INFO: link is found (not be used) dist=   1.578 ideal_dist=   1.524
ch:AA   res:  83  ARG  at:CD  .-ch:AA   res: 101   
PRO  at:CG  .

  INFO: link is found (not be used) dist=   1.843 ideal_dist=   1.457
ch:AA   res:  83  ARG  at:NE  .-ch:AA   res: 101   
PRO  at:CB  .

  INFO: link is found (not be used) dist=   0.666 ideal_dist=   1.457
ch:AA   

[ccp4bb] Software release ARP/wARP version 7.2

[Victor Lamzin]

Dear All,

We are happy to announce the release of ARP/wARP version 7.2. Please
visit http://www.arp-warp.org for details, software download or remote
submission of protein model building.

The major implementations and improvements are:

 * The functionality of the graphics front-end, Arp Navigator, has been
   considerably extended.
 * Auto-NCS detection coupled with enhanced protein chain tracing helps
   obtain more complete models, particularly at resolution lower than
   2.5 A.
 * Automated ligand building can screen a cocktail of candidates and
   has an option to model bound ligands that are partially ordered.
 * Supported computer platforms are Mac powerpc, Mac Intel and Linux
   (including 32 and 64-bit versions).
 * The ARP/wARP installer has been updated on all platforms so that its
   use should be simpler for the users. Users of Mac OSX Intel can also
   download and install a native application packaged in a DMG file.
 * There should be full compatibility of ARP/wARP 7.2 with with CCP4
   6.1.13 and Refmac 5.5.0109.

Victor and Tassos on behalf of the ARP/wARP developers.

Re: [ccp4bb] Arp/Wrap problem while model building

[Victor Lamzin]

Dear Rojan,

On 09/07/2011 09:56, Rojan Shrestha wrote:


Hello,

I am facing a problem in running “auto_tracing” in arp/wrap. At first 
I have tried using command line mode however I missed R-free value. I 
have added the “freelabin “ FREE=FREE ”” and have got an error


“Refmac_5.5.0102: Error in label assignments in LABIN”



If your free column in the MTZ file is called 'FREE', then on the 
command line simply use

freelabin FREE

In another way, I used ccp4i, here also the error was appeared as 
“Cannot extract ARP/wARP asymmetric unit limit.”




Most likely ARP/wARP is not sourced. Type 'echo $warpbin' and see 
whether the outcome is something like:

/arp_warp/arp_warp_7.1/bin/bin-i386-Darwin

Please get back if there are problems.

With best regards,
Victor

[ccp4bb] research software developer vacancy at EMBL Hamburg

[Victor Lamzin]

Dear all,

There is a staff member vacancy for a Research Software Developer at  
the EMBL Unit in Hamburg, Germany. The post holder will have a leading  
role in technical implementation and scientific development of the  
ARP/wARP software for crystallographic structure determination and the  
building of macromolecular models in 3D electron density maps  
generated from X-ray diffraction and, potentially, from electron  
microscopy and free-electron laser based data.


Application deadline is 13th March, 2011.

For details see:

http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=41327aid=15470

With best regards,
Victor

[ccp4bb] Synchrotron Beamline Facilities 2011 at EMBL Hamburg

[Victor Lamzin]

Call for access to Synchrotron Beamline Facilities 2011

EMBL Hamburg, Germany

We announce a call for synchrotron beam time applications in biological
small-angle scattering (SAXS) and X-ray crystallography (PX).
Up to 32 weeks of beam time will be available at the DORIS storage ring
at the synchrotron DESY from March 2011 to February 2012.

On the DORIS storage ring, EMBL Hamburg will operate the beamlines
in SAXS (responsible scientist Dmitri Svergun) and PX (responsible
scientist Victor Lamzin).

Electronic beam proposal forms and a detailed description of the DORIS
beamlines are available at www.embl-hamburg.de (click on 'Access to
Infrastructures'). The deadline for submission of proposals is
January, 31st, 2011. An external Priorities Committee will assess the
proposals.

EMBL is constructing three new beamlines for applications in PX and
SAXS at the Petra-III synchrotron storage ring, which are expected
to become available in 2011-2012 (responsible scientist Thomas Schneider).

For further information and for potential participation in the
commissioning as test users see www.embl-hamburg.de/services/petra

A high-throughput crystallisation facility at the EMBL-Hamburg
(responsible scientist Jochen Mueller-Dieckmann) is available to 
external users,

see www.embl-hamburg.de/facilities/access_infrastructures/htpx).

For further information
tel. 40-89902-110,
s...@embl-hamburg.de (SAXS)
b...@embl-hamburg.de (PX)

Access to the EMBL Hamburg facilities will in part be supported by the
European Commission, Research Infrastructure Action under the FP7
projects ELISA and PCUBE.

[ccp4bb] synchrotron beam time at EMBL Hamburg 2011

[Victor Lamzin]

 Call for access to Synchrotron Beamline Facilities 2011

  EMBL Hamburg, Germany

We announce a call for synchrotron beam time applications in biological
small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32
weeks of beam time will be available at the DORIS storage ring at the
synchrotron DESY from March 2011 to February 2012.

On the DORIS storage ring, EMBL Hamburg will operate the beamlines in
SAXS (responsible scientist Dmitri Svergun) and PX (responsible
scientist Victor Lamzin).

Electronic beam proposal forms and a detailed description of the DORIS
beamlines will be available from January, 15th, 2011 at www.embl-hamburg.de
(click on 'Access to Infrastructures'). The deadline for submission of
proposals is January, 31st, 2011. An external Priorities Committee will
assess the proposals.

EMBL is constructing three new beamlines for applications in PX and SAXS
at the Petra-III synchrotron storage ring, which are expected to become
available in 2011-2012 (responsible scientist Thomas Schneider). For
further information and for potential participation in the commissioning
as test users see www.embl-hamburg.de/services/petra

A high-throughput crystallisation facility at the EMBL-Hamburg
(responsible scientist Jochen Mueller-Dieckmann) is available to external
users, see www.embl-hamburg.de/facilities/access_infrastructures/htpx).

For further information
tel. 40-89902-110,
s...@embl-hamburg.de (SAXS)
b...@embl-hamburg.de (PX)

Access to the EMBL Hamburg facilities will in part be supported by the
European Commission, Research Infrastructure Action under the FP7
projects ELISA and PCUBE.

[ccp4bb] Citations in supplementary material

[Victor Lamzin]

Dear All,

I would like to bring to your attention the recent Editorial in Acta 
Cryst D (http://journals.iucr.org/d/issues/2010/12/00/issconts.html), 
which highlights the long-standing issue of under-citation of papers 
published in the IUCr journals. The Editorial, having looked at the 
papers published in 2009 in Nature, Science, Cell and PNAS, concluded:


'almost half of all references to publications in IUCr journals end up 
being published in the supplementary material only... Not only does this 
mean that the impact factor of IUCr journals should be higher, but also 
that the real overall numbers of citations of methods papers are much 
higher than what is reported, for instance, by the Web of Science'


Although this topic may seem to concern mostly methods developers, I 
think the whole research community will only benefit from more fair 
credit that we all give to our colleagues via referencing their 
publications. What do you think?


Victor

Re: [ccp4bb] Fill map/mask with dummy atoms?

[Victor Lamzin]

Dear Dirk,

For filling an input map you can try ARP/wARP in an 'old-fashion' way. 
The script below should place DUM atoms (1.1 times the requested number) 
into the highest density. Prepare your map in the CCP4 format, for 
example in P1, extended to cover the asymmetric unit in full (0 1 0 1 0 1).


Please let me know if you need info on additional keywords to have 
further controls, e.g. inter-dummy-atom distances or density thresholds.


With best regards,
Victor

#!/bin/csh -f
#
set sym = 'space group number, presumably 1'
set cell= 'cell parameters'
set resol   = 'rmin rmax'
set number_of_atoms = 'number of atoms to fill'
#
set mapin   = 'input map file name'
set xyzout1 = 'output PDB file name'
#
$warpbin/arp_warp EOF
MODE MIRBUILD
FILES CCP4 MAPFIND $mapin XYZOUT1 $xyzout1
SYMM ${sym}
CELL ${cell}
RESOLUTION ${resol}
MIRBUILD ATOMS $number_of_atoms MODELS 1 RESN DUM
END



On 13/10/2010 13:00, Dirk Kostrewa wrote:

 Dear CCP4ers,

is there a program around that allows to fill an input map or mask 
with dummy atoms?


Best regards,

Dirk.

[ccp4bb] EMBL Interdisciplinary Postdocs

[Victor Lamzin]

Dear All,

We have an opening for a postdoctoral position within the EMBL 
interdisciplinary postdocs initiative (EIPOD). The project on 'Combined 
computational methods for macromolecules' aims at interpretation of 
macromolecular crystallography data at a resolution from 4 to 10 A, 
making use of crystallographic and electron microscopy image analysis 
methods. At the same time the project aims at an enhanced interpretation 
of electron microscopy data by making use of advanced crystallographic 
modelling tools.


The deadline for applications is August 31, and for further details 
please refer to

http://www.embl-hamburg.de/training/postdocs/eipod/index.html
and
http://www.embl-hamburg.de/training/postdocs/eipod/app2010/lamzin.pdf

Best regards,
Victor

[ccp4bb] staff scientist position at the EMBL in Hamburg, Germany

[Victor Lamzin]

STAFF SCIENTIST IN BIOLOGICAL X-RAY CRYSTALLOGRAPHY WITH SYNCHROTRON 
RADIATION


European Molecular Biology Laboratory, Hamburg, Germany

A position is available at the Structural Biology Unit of the EMBL in 
Hamburg. The Unit utilises synchrotron radiation at the German 
Synchrotron Research Centre (DESY) for research in structural biology. 
EMBL operates synchrotron beamlines at the DORIS-III storage ring (until 
the end of 2012), which are used by hundreds of external visitors per 
year as well as local research groups. EMBL is also building an 
integrated facility for structural biology at the new PETRA III storage 
ring at DESY, Hamburg, which will include the operation of world-class 
synchrotron radiation beamlines, providing an ideal research environment 
for future challenges in structural biology. We are seeking a scientist 
who will be involved in support of our crystallographic synchrotron 
beamline facilities initially at DORIS and subsequently at PETRA III.


The post holder will be affiliated to the group of Victor Lamzin 
(http://www.embl-hamburg.de/research/unit/lamzin/index.html) and will be 
expected to carry out research projects in, e.g.:

• Research and technology development for X-ray crystallography
• Automation and integration of user-friendly synchrotron radiation data 
acquisition facilities
• Research in structural biology on, e.g. projects of medical relevance, 
teaming up with ongoing research projects at the EMBL
• Collaborations with external research groups on challenging structural 
biology and technology development projects


Applicants should have a PhD in a relevant field, postdoctoral training, 
significant research accomplishments and expertise in macromolecular 
crystallography. Excellent communication and social skills and a good 
command of English are required. An initial contract of 3 years will be 
offered to the successful candidate. This can be renewed, depending on 
circumstances at the time of the review.


Closing date for applications is 13 June 2010

For further information please look at 
http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_039/index.html


To apply, please email a cover letter, CV (in English) and contact 
information of three professional references quoting ref. no. W/10/039 
in the subject line, to applicat...@embl.de

General enquiries may be sent to j...@embl.de

[ccp4bb] beamline technician position at the EMBL in Hamburg, Germany

[Victor Lamzin]

BEAMLINE TECHNICIAN

European Molecular Biology Laboratory, Hamburg, Germany

A position is available at the Structural Biology Unit of the EMBL in 
Hamburg. The Unit utilises synchrotron radiation at the German 
Synchrotron Research Centre (DESY) for research in structural biology. 
EMBL operates synchrotron beamlines, which are used by hundreds of 
external visitors per year as well as local research groups. EMBL is 
also building an integrated facility for structural biology at the new 
PETRA III storage ring at DESY, Hamburg, which will include the 
operation from 2011 of world-class synchrotron radiation beamlines in 
biological macromolecular crystallography and small angle X-ray 
scattering, providing an ideal research environment for future 
challenges in structural biology.


The Beamline Technician will be involved in the support of the external 
visitors at our beamlines in macromolecular crystallography at DORIS and 
beamlines at PETRA. This includes maintenance and servicing of beamline 
end-station infrastructure, log-book keeping and direct responsibility 
for beamline cryogenic equipment. (S)he is expected to actively interact 
with a broad variety of international visitors and improve the 
efficiency of the experimental support. The post holder will be expected 
to take responsibility for the administration of (pre-frozen) crystals 
shipped to EMBL Hamburg for data collection.


The ideal candidate should have a technician or engineering degree in 
electronics or electro-mechanics, physics technical assistant or a 
related discipline. Experience in cryogenics, vacuum technology and 
control electronics is desirable. Skills in Macintosh/PC desktop 
software are essential; familiarity with control software like LabVIEW, 
TwinCAD or SPS programming would be an advantage. Knowledge about 
macromolecular crystallography is a plus. Excellent communication and 
social skills and a good command of English are required. An initial 
contract of 3 years will be offered to the successful candidate. This 
can be renewed, depending on circumstances at the time of the review.


Closing date for applications is 13 June 2010

For further information please look at 
http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_038/index.html


To apply, please email a cover letter, CV (in English) and contact 
information of three professional references quoting ref. no. W/10/038 
in the subject line, to applicat...@embl.de

General enquiries may be sent to j...@embl.de

Re: [ccp4bb] YATQ (yet another twinning question) - may involve pirates

[Victor Lamzin]

Hi,

ARP/wARP as of version 7.1 generates instructions for Refmac to carry 
out twin refinement during protein model building. Refmac version 5.5.16 
or higher is required.


ARP/wARP is not yet making active use of NCS for tracing protein chains. 
This development is almost accomplished and will be out in the next release.


Best regards,
Victor



Garib Murshudov wrote:
I hope Kevin will respond soon. I think he has done (or is planning to 
do) to twinning and ncs in his pipeline of model building.
I think something like that may already be in new ARP/wARP (Victor and 
Tasos will correct me if I am wrong)


regards
Garib

[ccp4bb] staff scientist position at the EMBL in Hamburg, Germany

[Victor Lamzin]

STAFF SCIENTIST IN BIOLOGICAL X-RAY CRYSTALLOGRAPHY WITH SYNCHROTRON 
RADIATION


European Molecular Biology Laboratory, Hamburg, Germany

A position is available at the Structural Biology Unit of the EMBL in 
Hamburg. The Unit utilises synchrotron radiation at the German 
Synchrotron Research Centre (DESY) for research in structural biology. 
EMBL operates synchrotron beamlines at the DORIS-III storage ring (until 
the end of 2012), which are used by hundreds of external visitors per 
year as well as local research groups. EMBL is also building an 
integrated facility for structural biology at the new PETRA III storage 
ring at DESY, Hamburg, which will include the operation of world-class 
synchrotron radiation beamlines, providing an ideal research environment 
for future challenges in structural biology. We are seeking a scientist 
who will be involved in support of our crystallographic synchrotron 
beamline facilities initially at DORIS and subsequently at PETRA III.


The post holder will be affiliated to the group of Victor Lamzin 
(http://www.embl-hamburg.de/research/unit/lamzin/index.html) and will be 
expected to carry out research projects in, e.g.:

• Research and technology development for X-ray crystallography
• Automation and integration of user-friendly synchrotron radiation data 
acquisition facilities
• Research in structural biology on, e.g. projects of medical relevance, 
teaming up with ongoing research projects at the EMBL
• Collaborations with external research groups on challenging structural 
biology and technology development projects


Applicants should have a PhD in a relevant field, postdoctoral training, 
significant research accomplishments and expertise in macromolecular 
crystallography. Excellent communication and social skills and a good 
command of English are required. An initial contract of 3 years will be 
offered to the successful candidate. This can be renewed, depending on 
circumstances at the time of the review.


Closing date for applications is 13 June 2010

For further information please look at 
http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_039/index.html


To apply, please email a cover letter, CV (in English) and contact 
information of three professional references quoting ref. no. W/10/039 
in the subject line, to applicat...@embl.de

General enquiries may be sent to j...@embl.de

[ccp4bb] beamline technician position at the EMBL in Hamburg, Germany

[Victor Lamzin]

BEAMLINE TECHNICIAN

European Molecular Biology Laboratory, Hamburg, Germany

A position is available at the Structural Biology Unit of the EMBL in 
Hamburg. The Unit utilises synchrotron radiation at the German 
Synchrotron Research Centre (DESY) for research in structural biology. 
EMBL operates synchrotron beamlines, which are used by hundreds of 
external visitors per year as well as local research groups. EMBL is 
also building an integrated facility for structural biology at the new 
PETRA III storage ring at DESY, Hamburg, which will include the 
operation from 2011 of world-class synchrotron radiation beamlines in 
biological macromolecular crystallography and small angle X-ray 
scattering, providing an ideal research environment for future 
challenges in structural biology.


The Beamline Technician will be involved in the support of the external 
visitors at our beamlines in macromolecular crystallography at DORIS and 
beamlines at PETRA. This includes maintenance and servicing of beamline 
end-station infrastructure, log-book keeping and direct responsibility 
for beamline cryogenic equipment. (S)he is expected to actively interact 
with a broad variety of international visitors and improve the 
efficiency of the experimental support. The post holder will be expected 
to take responsibility for the administration of (pre-frozen) crystals 
shipped to EMBL Hamburg for data collection.


The ideal candidate should have a technician or engineering degree in 
electronics or electro-mechanics, physics technical assistant or a 
related discipline. Experience in cryogenics, vacuum technology and 
control electronics is desirable. Skills in Macintosh/PC desktop 
software are essential; familiarity with control software like LabVIEW, 
TwinCAD or SPS programming would be an advantage. Knowledge about 
macromolecular crystallography is a plus. Excellent communication and 
social skills and a good command of English are required. An initial 
contract of 3 years will be offered to the successful candidate. This 
can be renewed, depending on circumstances at the time of the review.


Closing date for applications is 13 June 2010

For further information please look at 
http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_038/index.html


To apply, please email a cover letter, CV (in English) and contact 
information of three professional references quoting ref. no. W/10/038 
in the subject line, to applicat...@embl.de

General enquiries may be sent to j...@embl.de

Re: [ccp4bb] arp/warp

[Victor Lamzin]

Dear Rafael,

We have seen this already twice, it is a bug, sorry. The fix is being 
made and, when ready within a day or two, we will announce it.


With best regards,
Victor



Rafael Counago wrote:

Dear all,

I am getting an error message when I run arp/warp using CCP4i.

*/QUITTING ... ARP/wARP module stopped with an error message:
RESTRAINTS

*** Look for error message in the file:
/home/rafael/MAD/CCP4/2_warpNtrace_build.last.log

[1] 11549/*


The only error message I can find on the above file is:

/*:1: parser error : Document is empty
XMLOutputFilename = 'snow_log.xml'
^
Parameter Stream does NOT contain XML, this is the reason for the 
previous message (parser error).
Will try to parse it as a variable file (each line being a 
'variableName=value' pair).*/


Any ideas?

Cheers,

Rafael.

[ccp4bb] patch to ARP_wARP 7.1

[Victor Lamzin]

Dear All,

Following very useful feedback, we have made a patch #1 to ARP/wARP 
version 7.1, which addresses the following issues:


CCP4i GUI and command line module 'ARP/wARP solvent':
1. Assignment of Rfree
2. Reference to the log file containing the error message

CCP4i GUI and command line module 'ARP/wARP protein building Classic':
1. Occasional stops of the RESTRAINTS program

To download the patch, please visit www.arp-warp.org and further link to 
Frequently Asked Questions.


Best regards,
Victor (and the ARP/wARP team)

Re: [ccp4bb] arp_warp 7.1 and CCP4 6.1.3

[Victor Lamzin]

Dear Pedro,

This was fixed in ARP/wARP version 7.1 in January this year. We informed 
all who downloaded the software before the fix, but perhaps missed you.


Just go now to www.arp-warp.org, download the package and install - 
everything should be fine.


Best regards,
Victor


Pedro M. Matias wrote:

Hi.

I don't know whether other people had this problem, but I've tried to 
install arp_warp 7.1 with CCP4 6.1.3 and the installation failed 
because the refmac version is 5.5.0109. There's a conditional branch 
in the installation script that extracts the 0109 from this and does 
not like the leading zero.


Solution (to be tried): re-compile refmac5 changing the version number 
to 5.5.109


Pedro Matias

Re: [ccp4bb] problem with ARP/wARP module in CCP4

[Victor Lamzin]

Dear Vimal, Jayashankar, Madravi,

Thanks for your Emails. I don't really know what the problem might be;  
perhaps some of you could send me the data and the input parameters so  
that I can reproduce the error locally. ARP/wARP is definitely not  
resolution-limited (well, within limits of its applicability).


Regarding the practicality, one thing I would suggest you to try with  
CCP4i ARP/wARP GUI is to turn Rfree off and let me know if this helps.  
Otherwise you should always be able to build the solvent structure  
with two alternative ARP/wARP possibilities, which run the same  
sequence of the programs anyway:

1. command line script: $warpbin/warp_solvent.sh
2. graphics front end: $warpbin/arpnavigator

I look forward to hearing from you.

With best regards,
Victor


Quoting vimal parkash vimal.park...@helsinki.fi:


Hi,
   I faced the same problem with my 2.8Å structure. But it was  
alright with high resolution structure - so I thought the program is  
resolution limited.


Regards,
Vimal

Quoting Jayashankar s.jayashan...@gmail.com:


Dear Victor,

I faced the same problem and  got the same error for arpwarp solvent module,
and I have even communicated you through my system admin for arp warp
classic module
giving some trouble.

sincerely

S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.


On Fri, Mar 5, 2010 at 7:40 PM, Victor Lamzin vic...@embl-hamburg.dewrote:


Dear Madravi,

Probably the buffer was not flashed out to the log file.

Does the error stay if you run it from the command line,
$warpbin/auto_solvent.sh ?

Best regards,
Victor



Nalam, Madhavi wrote:


Hello:
I am using CCP4i version 6.1.2

I am trying to run the job ARP/wARP solvent building within CCP4. I used
the default values for running the job. The log file after the  
run is pasted

below.

I looked in the file (sm14b_unique1_warp_solvent_last.log) for an error
message but the file is empty. Can anyone suggest what/where I should be
looking into?
Thanks,
Madhavi

5 ARP refinement cycles will be run in total
Atoms will be removed if below 1.0 sigmas in 2mFoDFc map
Atoms will be added if above 3.4 sigmas in mFoDFc map

Refmac Refinement Parameters:
  1 REFMAC cycle(s) in each ARP cycle
  Weight for restraints is set to AUTO
  Scaling protocol  SIMPLE LSSC ANIS
  FreeR will be used for monitoring and sigmaa calculations


QUITTING ... ARP/wARP module stopped with an error message:
REFMAC5

*** Look for error message in the file:
sm14b_unique1_warp_solvent_last.log

[1] 6836

#CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 05 Mar 2010  11:00:42
#CCP4I TERMINATION OUTPUT_FILES
/home/nalamm/angie/struc_soln/6_arp_warp_solvent.par angie
#CCP4I MESSAGE Task completed successfully

Re: [ccp4bb] problem with ARP/wARP module in CCP4

[Victor Lamzin]

Dear Madravi,

Probably the buffer was not flashed out to the log file.

Does the error stay if you run it from the command line, 
$warpbin/auto_solvent.sh ?


Best regards,
Victor


Nalam, Madhavi wrote:

Hello:
I am using CCP4i version 6.1.2

I am trying to run the job ARP/wARP solvent building within CCP4. I used the 
default values for running the job. The log file after the run is pasted below.

I looked in the file (sm14b_unique1_warp_solvent_last.log) for an error message 
but the file is empty. Can anyone suggest what/where I should be looking into?
Thanks,
Madhavi

  5 ARP refinement cycles will be run in total
  Atoms will be removed if below 1.0 sigmas in 2mFoDFc map
  Atoms will be added if above 3.4 sigmas in mFoDFc map

  Refmac Refinement Parameters:
1 REFMAC cycle(s) in each ARP cycle
Weight for restraints is set to AUTO
Scaling protocol  SIMPLE LSSC ANIS
FreeR will be used for monitoring and sigmaa calculations


QUITTING ... ARP/wARP module stopped with an error message:
REFMAC5

*** Look for error message in the file: 
sm14b_unique1_warp_solvent_last.log


[1] 6836

#CCP4I TERMINATION STATUS 1 
#CCP4I TERMINATION TIME 05 Mar 2010  11:00:42

#CCP4I TERMINATION OUTPUT_FILES  
/home/nalamm/angie/struc_soln/6_arp_warp_solvent.par angie
#CCP4I MESSAGE Task completed successfully

  

[ccp4bb] Synchrotron beam time 2010 at EMBL Hamburg

[Victor Lamzin]

This is just a gentle reminder that the deadline for beam time 2010 at  
EMBL Hamburg is today, January 13.


With best regards,
Victor



 Call for access to Synchrotron Beamline Facilities 2010

  EMBL Hamburg, Germany

We announce a call for synchrotron beam time applications in biological
small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32
weeks of beam time will be available at the DORIS storage ring (DESY)
from March 2010 to February 2011.

EMBL Hamburg will operate the following beamlines:

Beamline  New featuresScientist responsible

X33SAXS   Automated and remote operation  Dmitri Svergun
X11PX MAR555 Flat Panel detector  Santosh Panjikar
X12PX MAD, S-SAD, fluorescence analysis   Andrea Schmidt
X13PX Microspec, expert data collection   Matthew Groves

The deadline for submission of proposals is January 13, 2010.
An external Priorities Committee will assess the proposals.

Electronic beam proposal forms and a detailed description of the
beamline facilities are available at www.embl-hamburg.de
(click on 'Access to Infrastructures').

Additional EMBL services can be found at www.embl-hamburg.de/facilities

EMBL is constructing three new beamlines for applications in biological
X-ray crystallography (PX) and small-angle scattering (SAXS) at the Petra-III
synchrotron storage ring, which are scheduled to be available from 2011.
See www.embl-hamburg.de/services/petra for further information.

For further information
tel. +49-40-89902-110,
s...@embl-hamburg.de (SAXS)
b...@embl-hamburg.de (PX).

Access to the EMBL Hamburg facilities will be supported by the European
Commission, Research Infrastructure Action under the FP7 ELISA (European
Light Sources Activities).

[ccp4bb] ARP_wARP 7.1 release

[Victor Lamzin]

Dear All,

We are happy to announce the release of ARP/wARP version 7.1.

Please visit http://www.arp-warp.org for details and software download.

The major implementations and improvements are:

• A prototype of the molecular graphics ARP/wARP front-end, allowing the 
display of molecules and electron densities.
• A prototype version of the new module for building poly-nucleotides 
(DNA or RNA).
• Improved and faster protein chain tracing with higher performance at 
lower resolution.
• The loop building as well as helix/strand building are now also 
inherent parts of protein model building, resulting in enhanced model 
completeness.
• Refinement procedures during automated model building have been 
enhanced in the new versions of our preferred refinement engine, REFMAC, 
notably including the implementation of 'conditional restraints'.
• Direct use of experimental single-wavelength anomalous diffraction 
data (SAD) during model building is now also possible.

• Improved performance of automated ligand building.
• Supported computer platforms are Mac powerpc, Mac Intel and Linux 
(including 32 and 64-bit versions and itanium).


Merry Xmas and Happy New Year!

Victor and Tassos on behalf of the ARP/wARP developers' team.

[ccp4bb] Call for Beamline 2010 at EMBL Hamburg

[Victor Lamzin]

Call for access to Synchrotron Beamline Facilities 2010

 EMBL Hamburg, Germany

We announce a call for synchrotron beam time applications in biological
small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32
weeks of beam time will be available at the DORIS storage ring (DESY)
from March 2010 to February 2011.

EMBL Hamburg will operate the following beamlines:

Beamline  New featuresScientist responsible

X33SAXS   Automated and remote operation  Dmitri Svergun
X11PX MAR555 Flat Panel detector  Santosh Panjikar
X12PX MAD, S-SAD, fluorescence analysis   Andrea Schmidt
X13PX Microspec, expert data collection   Matthew Groves

The deadline for submission of proposals is January 13, 2010.
An external Priorities Committee will assess the proposals.

Electronic beam proposal forms and a detailed description of the
beamline facilities are available at www.embl-hamburg.de
(click on 'Access to Infrastructures').

Additional EMBL services can be found at www.embl-hamburg.de/facilities

EMBL is constructing three new beamlines for applications in biological
X-ray crystallography (PX) and small-angle scattering (SAXS) at the 
Petra-III

synchrotron storage ring, which are scheduled to be available from 2011.
See www.embl-hamburg.de/services/petra for further information.

For further information
tel. +49-40-89902-110,
s...@embl-hamburg.de (SAXS)
b...@embl-hamburg.de (PX).

Access to the EMBL Hamburg facilities will be supported by the European
Commission, Research Infrastructure Action under the FP7 ELISA (European
Light Sources Activities).

Re: [ccp4bb] AU limts not read - arp/warp ccp4i interface

[Victor Lamzin]

Dear Narayanan,

If you set the space group to P2221 (#17), ARP/wARP 7.0 will accept it. 
If you would like to stay with the space group P2212 (#2017), please 
wait for the coming ARP/wARP 7.1 version.


Best regards,
Victor


Narayanan Ramasubbu wrote:

Hi:
I tried to run arp/warp using the gui. My original mtz file  (space 
group p222) is read correctly and I see the AU limits in the Crystal 
parameters.
I then tried to change the space group using CAD/SORTMTZ export to 
.sca and manually change the space group to P2212 and  then used 
scalepack2mtz to generate an mtz file.
The space group is correctly converetd and the SYMM is fine. But 
arp/warp comes up with AU limits error.

Please help.
Subbu

Re: [ccp4bb] Arp/Warp in Ubuntu

[Victor Lamzin]

Dear Yuan,

Most likely your ARP/wARP settings are not sourced.

1. Quit CCP4i
2. Modify your ./cshrc (or .bashrc) so that it sources CCP4 first and 
ARP/wARP then. Below is one example of .cshrc:


#
# Setup CCP4
source /Users/victor/xtal/ccp4/ccp4-6.0.2/include/ccp4.setup
#
# Setup ARP/wARP
source /Users/victor/xtal/arp_warp/arp_warp_7.0.1/arpwarp_setup.csh
#

3. Open a new terminal window and start CCP4i.

With best regards,
Victor

SHANG Yuan wrote:

Hi,
  Does anyone know how to Plugging ARP/wARP GUI into CCP4i interface? I
followed http://www.embl-hamburg.de/arp-cgi-bin/FAQ7.0_1.pl, but always
get a warning Can not get environment variable for wardoc with a
subsequent Application Error Error:bad window path name \.warning...
  Under Ubuntu, I can find the place for me to input the administrator's
code..
  Thanks in advance.

Yuan SHANG

  

[ccp4bb] Practical Course for Macromolecular Crystallography M2M-2009

[Victor Lamzin]

1 week is left to the deadline for applications to

the Practical Course on Training in methods for Macromolecular 
Crystallography M2M-2009: From Measurement to Model.


The course will take place at the EMBL Hamburg Outstation, the DESY 
synchrotron site during the period:

Wednesday October 21st - Wednesday October 28th, 2009.

The M2M course series was established in 1993 and has been at the 
forefront of training in structural biology, covering the essential 
steps in determining biomolecular structures.


The M2M-2009 course will include practicals at synchrotron beamlines for 
macromolecular crystallography, computational tutorials and lectures on 
the use of synchrotron radiation and beamline equipment, sample handling 
and carrying out an experiment. Topics will also include data 
processing, structure solution, model building and validation.


Invited speakers include K. Bartels (Norderstedt), T. Beck (Goettingen), 
A. Brunger (Stanford), Z. Dauter (Argonne), W. Kabsch (Heidelberg), W. 
Minor (Charlottesville), G. Murshudov (York), A. Perrakis (Amsterdam), 
H. Powell (Cambridge), T. Terwilliger (Los Alamos) and A. Vagin (York). 
Internal speakers from the EMBL are G. Bourenkov, M. Cianchi, S. 
Fiedler, M. Groves, V. Lamzin, G. Langer, S. Panjikar, U. Ristau, A. 
Schmidt, T. Schneider, P. Tucker, D. Watts and M. Weiss.


The course is primarily supported by the European Macromolecular 
Crystallography Infrastructure network (MAXINF2), EC Contract No 505977.


The number of places is restricted to 20. Applications can be made 
electronically via the link 
http://www.embl-hamburg.de/workshops/2009/m2m9/index.html


The deadline for applications is September 10th, 2009.

The organising committee - Victor Lamzin, Santosh Panjikar, Thomas 
Schneider, Paul Tucker, Manfred Weiss

[ccp4bb] Practical Course for Macromolecular Crystallography M2M-2009

[Victor Lamzin]

This is a gentle reminder that 30 days is left until the deadline for 
applications to the Practical Course on Training in methods for 
Macromolecular Crystallography M2M-2009: From Measurement to Model. The 
course will take place at the EMBL Hamburg Outstation, the DESY 
synchrotron site during the period:


Wednesday October 21st - Wednesday October 28th, 2009.

The M2M course series was established in 1993 and has been at the 
forefront of training in structural biology, covering the essential 
steps in determining biomolecular structures.


The M2M-2009 course will include practicals at synchrotron beamlines for 
macromolecular crystallography, computational tutorials and lectures on 
the use of synchrotron radiation and beamline equipment, sample handling 
and carrying out an experiment. Topics will also include data 
processing, structure solution, model building and validation.


Invited speakers include K. Bartels (Norderstedt), T. Beck (Goettingen), 
A. Brunger (Stanford), Z. Dauter (Argonne), W. Kabsch (Heidelberg), W. 
Minor (Charlottesville), G. Murshudov (York), A. Perrakis (Amsterdam), 
H. Powell (Cambridge), T. Terwilliger (Los Alamos) and A. Vagin (York). 
Internal speakers from the EMBL are G. Bourenkov, M. Cianchi, S. 
Fiedler, M. Groves, V. Lamzin, G. Langer, S. Panjikar, U. Ristau, A. 
Schmidt, T. Schneider, P. Tucker, D. Watts and M. Weiss.


The course is primarily supported by the European Macromolecular 
Crystallography Infrastructure network (MAXINF2), EC Contract No 505977.


The number of places is restricted to 20. Applications can be made 
electronically via the link 
http://www.embl-hamburg.de/workshops/2009/m2m9/index.html


The deadline for applications is September 10th, 2009.

The organising committee - Victor Lamzin, Santosh Panjikar, Thomas 
Schneider, Paul Tucker, Manfred Weiss

[ccp4bb] Practical Course for Macromolecular Crystallography M2M-2009

[Victor Lamzin]

This is the second announcement of the Practical Course on Training in 
methods for Macromolecular Crystallography M2M-2009: From Measurement to 
Model. The course will take place at the EMBL Hamburg Outstation, the 
DESY synchrotron site during the period:


Wednesday October 21st - Wednesday October 28th, 2009.

The M2M course series was established in 1993 and has been at the 
forefront of training in structural biology, covering the essential 
steps in determining biomolecular structures.


The M2M-2009 course will include practicals at synchrotron beamlines for 
macromolecular crystallography, computational tutorials and lectures on 
the use of synchrotron radiation and beamline equipment, sample handling 
and carrying out an experiment. Topics will also include data 
processing, structure solution, model building and validation.


Invited speakers include K. Bartels (Norderstedt), T. Beck (Goettingen), 
A. Brunger (Stanford), Z. Dauter (Argonne), W. Kabsch (Heidelberg), W. 
Minor (Charlottesville), G. Murshudov (York), A. Perrakis (Amsterdam), 
H. Powell (Cambridge), T. Terwilliger (Los Alamos) and A. Vagin (York). 
Internal speakers from the EMBL are G. Bourenkov, M. Cianchi, S. 
Fiedler, M. Groves, V. Lamzin, G. Langer, S. Panjikar, U. Ristau, A. 
Schmidt, T. Schneider, P. Tucker, D. Watts and M. Weiss.


The course is primarily supported by the European Macromolecular 
Crystallography Infrastructure network (MAXINF2), EC Contract No 505977.


The number of places is restricted to 20. Applications can be made 
electronically via the link 
http://www.embl-hamburg.de/workshops/2009/m2m9/index.html


The deadline for applications is September 10th, 2009.

The organising committee - Victor Lamzin, Santosh Panjikar, Thomas 
Schneider, Paul Tucker, Manfred Weiss

[ccp4bb] Practical Course for Macromolecular Crystallography M2M-2009

[Victor Lamzin]

We would like to announce the Practical Course on Training in methods 
for Macromolecular Crystallography M2M-2009: From Measurement to Model. 
The course will take place at the EMBL Hamburg Outstation, the DESY 
synchrotron site during the period:


Wednesday October 21st - Wednesday October 28th, 2009.

The M2M course series was established in 1993 and has been at the 
forefront of training in structural biology, covering the essential 
steps in determining biomolecular structures.


The M2M-2009 course will include practicals at synchrotron beamlines for 
macromolecular crystallography, computational tutorials and lectures on 
the use of synchrotron radiation and beamline equipment, sample handling 
and carrying out an experiment. Topics will also include data 
processing, structure solution, model building and validation.


Invited speakers include K. Bartels (Norderstedt), T. Beck (Goettingen), 
A. Brunger (Stanford), Z. Dauter (Argonne), W. Kabsch (Heidelberg), W. 
Minor (Charlottesville), G. Murshudov (York), A. Perrakis (Amsterdam), 
H. Powell (Cambridge), T. Terwilliger (Los Alamos) and A. Vagin (York). 
Internal speakers from the EMBL are G. Bourenkov, M. Cianchi, S. 
Fiedler, M. Groves, V. Lamzin, G. Langer, S. Panjikar, U. Ristau, A. 
Schmidt, T. Schneider, P. Tucker, D. Watts and M. Weiss.


The course is primarily supported by the European Macromolecular 
Crystallography Infrastructure network (MAXINF2), EC Contract No 505977.


The number of places is restricted to 20. Applications can be made 
electronically via the link 
http://www.embl-hamburg.de/workshops/2009/m2m9/index.html


The deadline for applications is September 10th, 2009.

The organising committee - Victor Lamzin, Santosh Panjikar, Thomas 
Schneider, Paul Tucker, Manfred Weiss

Re: [ccp4bb] Error ARP/wARP MODE_WILSON

[Victor Lamzin]

Dear Kristof,

This is a bug we are aware of. It will go as of the next release but for 
the moment the easiest is if we send you a fixed executable. What is 
your computer platform (please type 'uname' and let me know the output) ?


With best regards,
Victor

Kristof Van Hecke wrote:

Dear all,

When refining a DNA-structure (poor data, resolution 2.5) and using 
ARP/wARP Solvent 7.0.1. for water divining with CCP4 6.1.1 and GUI 
2.0.4, I get the following error:


QUITTING ... ARP/wARP module stopped with an error message:
ARP_WARP_MODE_WILSON


When checking the warp_wilson_log file, I get:


Comments:  Overall fit of the data to the Wilson curve:

Comments:  Problems   Resolution range   5.15  to   4.89
Comments:  Problems   Resolution range   4.89  to   4.67
Comments:  Problems   Resolution range   2.89  to   2.84
Comments:  Possible reasons - missing overloads

Solvent content1.00


Computed solvent content is too high - check your input

* ERROR *

I was kind of surprised, because with the same data! and an older 
version of ARP/wARP, which was integrated in the Refmac5 program, I did 
not get any errors of this kind..!?


Is there a way to circumvent this please..?


Many thanks

Kristof Van Hecke




Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

  

Re: [ccp4bb] ARP/WARP - Can not get environment variable for warpdoc

[Victor Lamzin]

Please make sure you source arpwarp_setup.csh (or .bash) after you 
source CCP4, this should cure the problem. Instructions on how to source 
arpwarp_setup are printed when you install ARP/wARP with the install.sh 
script.


Best regards,
Victor


Sridhar Prasad wrote:

I installed CPP4 version 6.1.1 on a Linux laptop which is running ubuntu.

Following which I also installed ARP/WARP 7.0.1 version.However, when I attempt 
to launch ARP/WARP using the CCP4I GUI interface, I get the following message

Can not get environment variable for warpdoc.

Could someone please help me with fixing this problem.

Thanks
Sridhar

  

[ccp4bb] ARP/wARP and computer platforms

[Victor Lamzin]

We were collecting information on computer platforms that people would 
like ARP/wARP to run on.


126 people responded with 296 platform choices. The latter grouped as 
follows:


Linux i686   26%
Linux x86_64 24%
Linux ia644%
 total Linux54%

Mac powerpc   9%
Mac Intel 10.48%
Mac Intel 10.5   21%
 total Mac  38%

Windows   5%
IRIX64 mips   2%
Other platforms   1%

In addition, we asked about CCP4 version used:
CCP4 6.x only98%
CCP4 5.x only 2%
Both 5.x and 6.x  6%

Many thanks for participation in the questionnaire!

With best regards,
Victor

[ccp4bb] ARP/wARP and computer platforms

[Victor Lamzin]

We are collecting information on computer platforms that people would 
like ARP/wARP to run on. To access the questionnaire please go to 
http://www.embl-hamburg.de/ARP/platinf_new.shtml


Thank you for your cooperation.

With best regards,
Victor

Re: [ccp4bb] Replacement for arp_waters?

[Victor Lamzin]

Dear David,

You can use ARP/wARP 7.0.1 (www.arp-warp.org), which should be better 
than old arp_waters. Either the ARP/wARP GUI module 'ARP solvent' or a 
command line script auto_solvent.sh


Best regards,
Victor


David J. Schuller wrote:

I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a
program in the suite which fills the role formerly filled by arp_waters,
of automatically adding waters?

Cheers,
-  
===

You can't possibly be a scientist if you mind people
thinking that you're a fool. - Wonko the Sane
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

  

[ccp4bb] application for synchrotron beam time 2009 at EMBL Hamburg

[Victor Lamzin]

Dear Colleagues,

This is just a gentle reminder that the deadline for applications
for synchrotron beam time 2009 at the EMBL Hamburg is on January 13.

With best regards,
Victor Lamzin


Call for access to Synchrotron Beamline Facilities 2009 


 EMBL Hamburg, Germany

We announce a call for synchrotron beam time applications in biological 
small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32 
weeks of beam time will be available at the DORIS storage ring (DESY) 
from March 2009 to February 2010.


EMBL Hamburg will operate the following beamlines:

Beamline  New featuresScientist responsible

X33SAXS   Automated and remote operation  Dmitri Svergun
X11PX MAR555 Flat Panel detector  Paul Tucker
X12PX MAD, S-SAD, fluorescence analysis   Manfred Weiss
X13PX Microspec, expert data collection   Matthew Groves
BW7A*  PX High flux, multilayer opticsAndrea Schmidt
BW7B*  PX Automated sample changer MARVIN Santosh Panjikar

*These beamlines are used as Petra-III test facilities and therefore will 
be only temporarily available.


The deadline for submission of proposals is January 13, 2009.
An external Priorities Committee will assess the proposals.

Electronic beam proposal forms and a detailed description of the beamline 
facilities are available at www.embl-hamburg.de and 
www.embl-hamburg.de/facilities


Access to the EMBL Hamburg high-throughput crystallisation facility is 
available via www.embl-hamburg.de/services/crystallisation


EMBL is constructing three new beamlines for applications in biological 
X-ray crystallography (PX) and small-angle scattering (SAXS) at the Petra-III 
synchrotron storage ring, which are scheduled to be available from 2010/11. 
See www.embl-hamburg.de/services/petra for further information.


For further information 
tel. +49-40-89902-110, 
s...@embl-hamburg.de (SAXS)

b...@embl-hamburg.de (PX).

Access to the EMBL Hamburg facilities will be supported by the European 
Commission, Research Infrastructure Action under the FP7 ELISA (European 
Light Sources Activities).

[ccp4bb] Applications for synchrotron beam time 2009 at EMBL Hamburg

[Victor Lamzin]

Call for access to Synchrotron Beamline Facilities 2009

 EMBL Hamburg, Germany

We announce a call for synchrotron beam time applications in biological
small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32
weeks of beam time will be available at the DORIS storage ring (DESY)
from March 2009 to February 2010.

EMBL Hamburg will operate the following beamlines:

Beamline  New featuresScientist responsible

X33SAXS   Automated and remote operation  Dmitri Svergun
X11PX MAR555 Flat Panel detector  Paul Tucker
X12PX MAD, S-SAD, fluorescence analysis   Manfred Weiss
X13PX Microspec, expert data collection   Matthew Groves
BW7A*  PX High flux, multilayer opticsAndrea Schmidt
BW7B*  PX Automated sample changer MARVIN Santosh Panjikar

*These beamlines are used as Petra-III test facilities and therefore will
be only temporarily available.

The deadline for submission of proposals is January 13, 2009.
An external Priorities Committee will assess the proposals.

Electronic beam proposal forms and a detailed description of the beamline
facilities are available at www.embl-hamburg.de and
www.embl-hamburg.de/facilities

Access to the EMBL Hamburg high-throughput crystallisation facility is
available via www.embl-hamburg.de/services/crystallisation

EMBL is constructing three new beamlines for applications in biological
X-ray crystallography (PX) and small-angle scattering (SAXS) at the 
Petra-III

synchrotron storage ring, which are scheduled to be available from 2010/11.
See www.embl-hamburg.de/services/petra for further information.

For further information
tel. +49-40-89902-110,
s...@embl-hamburg.de (SAXS)
b...@embl-hamburg.de (PX).

Access to the EMBL Hamburg facilities will be supported by the European
Commission, Research Infrastructure Action under the FP7 ELISA (European
Light Sources Activities).

Re: [ccp4bb] refmac 5.5.0068 error

[Victor Lamzin]

Dear Michael,

ARP/wARP should recognise this refmac version with no problem. Before 
typing './install.sh' just do 'refmac5 -i' to check that refmac is 
executed fine and CCP4 environment is setup.


If the problem remains please get back to us with details on the 
ARP/wARP version number and computer operating system.


Best regards,
Victor


 Michael Jackson wrote:

 hello,
 Thank you for the reply about the refmac 5.5.0066 error. I downloaded 
refmac 5.5.0068 but there appears to be a problem for ARPwARP to 
recognise the version.  I reinstalled ARPwARP and the install shell 
script freezes when it looks for the refmac file.

Re: [ccp4bb] Arp/warp space group P 21 2 21

[Victor Lamzin]

Dear Phil,

One reason has been simplicity - many ARP/wARP modules operate with 
space group number only. For space group 18 this would mean P21212. 
Using space group name might be less robust - I remember some 
compatibility problems when CCP4 introduced spaces into space group 
names, this broke some of the parsers, including simple-minded ones from 
ARP/wARP.


If there is, however, a strong wish for ARP/wARP to support 
'unconventionally' indexed space groups - then we will certainly try to 
introduce it.


With best regards,
Victor



PhilEvans wrote:

Is there a reason why Arp/warp doesn't like space group P 21 2 21?

Phil

[ccp4bb] Call for synchrotron beam time at EMBL Hamburg

[Victor Lamzin]

Dear Colleague,

This is a gentle reminder of our call for beam time applications
at EMBL Hamburg that we circulated a few weeks ago.
We kindly ask you to complete your beam time proposal
by the deadline of ---  16 May 2008 

If you have already taken action, you can ignore this message.

---
EMBL HAMBURG UNIT

   Call for access to Synchrotron Beamline Facilities 2008

We announce a call for synchrotron beam time applications in biological
X-ray crystallography (PX) and small-angle scattering (SAXS).
Up to 12 weeks of beam time will be available at the DORIS storage ring
(DESY) during the period September 2008 until December 2008.
The EMBL Outstation will operate the following beamlines:

BeamlineTypeWavelength Scientist responsible
X11 PX  0.80 A Paul Tucker
X12 PX  tuneable   Manfred Weiss
X13 PX  0.80 A Matthew Groves
X33 SAXS1.5 A  Dmitri Svergun, Manfred Roessle

The deadline for submission of proposals is May 16th, 2008. An external
Priorities Committee will assess the proposals.

Electronic beam proposal forms and detailed description of the beamline
facilities are available via the web links
http://www.embl-hamburg.de and http://www.embl-hamburg.de/services

In parallel, EMBL-Hamburg is constructing three new beamlines for
applications in biological X-ray crystallography (PX) and small-angle
scattering (SAXS) at the Petra-III synchrotron storage ring, with an
expected opening in 2010/11. Further information can be obtained under
http://www.embl-hamburg.de/services/petra.

Two of the DORIS-III beamlines (BW7A, BW7B) will be used as test
beamlines for future Petra-III applications. Depending on circumstances,
they may become temporarily available to the external user community.

Applications to use the EMBL-Hamburg high-throughput crystallisation
facility can be made at any time at
http://www.embl-hamburg.de/services/crystallisation

Further information can be obtained by tel. +49-40-89902-110,
(fax +49-40-89902-149), Email [EMAIL PROTECTED] (PX),
[EMAIL PROTECTED] (SAXS).

Access to the EMBL Hamburg facilities is supported by the European
Commission, Research Infrastructure Action under the FP6 'Structuring the
European Research Area Specific Programme', Contract Number
RII3-CT-2004-506008.

---

[ccp4bb] Synchrotron beam time at EMBL Hamburg

[Victor Lamzin]

This is a gentle reminder of our call for beam time applications at EMBL Hamburg that 
we circulated a few weeks ago. We kindly ask you to complete your beam time proposal 
by the deadline of ---  16 May 2008 

If you have already taken action, please ignore this message.

---
 EMBL HAMBURG UNIT

Call for access to Synchrotron Beamline Facilities 2008

We announce a call for synchrotron beam time applications in biological
X-ray crystallography (PX) and small-angle scattering (SAXS).
Up to 12 weeks of beam time will be available at the DORIS storage ring
(DESY) during the period September 2008 until December 2008.
The EMBL Outstation will operate the following beamlines:

BeamlineTypeWavelength Scientist responsible 


X11 PX  0.80 A Paul Tucker
X12 PX  tuneable   Manfred Weiss
X13 PX  0.80 A Matthew Groves
X33 SAXS1.5 A  Dmitri Svergun, Manfred Roessle

The deadline for submission of proposals is May 16th, 2008. An external
Priorities Committee will assess the proposals.

Electronic beam proposal forms and detailed description of the beamline
facilities are available via the web links
http://www.embl-hamburg.de and http://www.embl-hamburg.de/services

In parallel, EMBL-Hamburg is constructing three new beamlines for
applications in biological X-ray crystallography (PX) and small-angle
scattering (SAXS) at the Petra-III synchrotron storage ring, with an
expected opening in 2010/11. Further information can be obtained under
http://www.embl-hamburg.de/services/petra.

Two of the DORIS-III beamlines (BW7A, BW7B) will be used as test
beamlines for future Petra-III applications. Depending on circumstances,
they may become temporarily available to the external user community.

Applications to use the EMBL-Hamburg high-throughput crystallisation
facility can be made at any time at
http://www.embl-hamburg.de/services/crystallisation

Further information can be obtained by tel. +49-40-89902-110,
(fax +49-40-89902-149), Email [EMAIL PROTECTED] (PX),
[EMAIL PROTECTED] (SAXS).

Access to the EMBL Hamburg facilities is supported by the European
Commission, Research Infrastructure Action under the FP6 'Structuring the
European Research Area Specific Programme', Contract Number
RII3-CT-2004-506008.

[ccp4bb] Synchrotron beam time 2008 at the EMBL Hamburg

[Victor Lamzin]

   Call for access to Synchrotron Beamline Facilities 2008

We announce a call for synchrotron beam time applications in biological
X-ray crystallography (PX) and small-angle scattering (SAXS).
Up to 12 weeks of beam time will be available at the DORIS storage ring
(DESY) during the period September 2008 until December 2008.
The EMBL Outstation will operate the following beamlines:

BeamlineTypeWavelength Scientist responsible

X11 PX  0.80 A Paul Tucker
X12 PX  tuneable   Manfred Weiss
X13 PX  0.80 A Matthew Groves
X33 SAXS1.5 A  Dmitri Svergun, Manfred Roessle

The deadline for submission of proposals is May 16th, 2008. An external
Priorities Committee will assess the proposals.

Electronic beam proposal forms and detailed description of the beamline
facilities are available via the web links
http://www.embl-hamburg.de and http://www.embl-hamburg.de/services

In parallel, EMBL-Hamburg is constructing three new beamlines for
applications in biological X-ray crystallography (PX) and small-angle
scattering (SAXS) at the Petra-III synchrotron storage ring, with an
expected opening in 2010/11. Further information can be obtained under
http://www.embl-hamburg.de/services/petra.

Two of the DORIS-III beamlines (BW7A, BW7B) will be used as test
beamlines for future Petra-III applications. Depending on circumstances,
they may become temporarily available to the external user community.

Applications to use the EMBL-Hamburg high-throughput crystallisation
facility can be made at any time at
http://www.embl-hamburg.de/services/crystallisation

Further information can be obtained by tel. +49-40-89902-110,
(fax +49-40-89902-149), Email [EMAIL PROTECTED] (PX),
[EMAIL PROTECTED] (SAXS).

Access to the EMBL Hamburg facilities is supported by the European
Commission, Research Infrastructure Action under the FP6 'Structuring the
European Research Area Specific Programme', Contract Number
RII3-CT-2004-506008.

[ccp4bb] Synchrotrons and Lasers for Structural Systems Biology

[Victor Lamzin]

This is just a gentle reminder than the deadline for the registration to 
attend the Symposium on Synchrotrons and Lasers for Structural Systems 
Biology is on April 5th, 2008.



We would like to announce the Symposium on Synchrotrons and Lasers for
Structural Systems Biology to be held on 16th April 2008 at the
premises of the EMBL/DESY in Hamburg, Germany. International experts in
the field of the use of synchrotron radiation in biological research
will present their point of view on how the new synchrotron light
sources including the X-ray free electron lasers under development will
shape biological structural research in the next decades to come.

The symposium will be followed by the 4th Annual Meeting of the
EC-funded BIOXHIT project, 17th - 18th April 2008. Project’s highlights
will be presented in the area of crystallisation technologies,
synchrotron beamlines, beamline endstations and data collection, data
processing and structure determination, databases and networking,
training, implementation and dissemination.

Attendance to the meetings is free of charge.

The registration deadline for the symposium and the BIOXHIT Meeting is
Saturday, 5th April 2008, http://www.structures-in-biology.org

Gerard Bricogne, Kim Henrick, Victor Lamzin, Sine Larsen, Sean
McSweeney, Colin Nave, Anastassis Perrakis, Manfred Weiss (the
organising committee)

[ccp4bb] Synchrotrons and Lasers for Structural Systems Biology

[Victor Lamzin]

We would like to announce the Symposium on Synchrotrons and Lasers for 
Structural Systems Biology to be held on 16th April 2008 at the 
premises of the EMBL/DESY in Hamburg, Germany. International experts in 
the field of the use of synchrotron radiation in biological research 
will present their point of view on how the new synchrotron light 
sources including the X-ray free electron lasers under development will 
shape biological structural research in the next decades to come.


The symposium will be followed by the 4th Annual Meeting of the 
EC-funded BIOXHIT project, 17th - 18th April 2008. Project’s highlights 
will be presented in the area of crystallisation technologies, 
synchrotron beamlines, beamline endstations and data collection, data 
processing and structure determination, databases and networking, 
training, implementation and dissemination.


Attendance to the meetings is free of charge.

The registration deadline for the symposium and the BIOXHIT Meeting is 
Saturday, 5th April 2008, http://www.structures-in-biology.org


Gerard Bricogne, Kim Henrick, Victor Lamzin, Sine Larsen, Sean 
McSweeney, Colin Nave, Anastassis Perrakis, Manfred Weiss (the 
organising committee)

[ccp4bb] Senior technical officer in MX at the EMBL in Hamburg

[Victor Lamzin]

SENIOR TECHNICAL OFFICER IN MACROMOLECULAR CRYSTALLOGRAPHY AT THE EMBL, 
HAMBURG


A position is available at the Structural Biology Unit of the EMBL in 
Hamburg. The task will be to provide technical coordination 
(programming, compilation, benchmarking and evaluation tests) as well as 
scientific assistance (development of algorithms and improved protocols 
for the end-users) to the on-going ARP/wARP activities at the EMBL. The 
successful candidate is also expected to be involved in enhancement of 
local crystallographic beamline-related software infrastructure, 
cooperate with related software development activities at the EMBL (e.g. 
BEST and AutoRickshaw) and participate in collaborative projects with 
the external users.


The ideal candidate should hold a PhD in a relevant field, sufficient 
research accomplishments and expertise in X-ray crystal structure 
termination techniques. Broad knowledge of statistics, pattern 
recognition techniques as well as extensive experience in scientific 
programming (FORTRAN, C or C++) are required. In addition, excellent 
communication and presentation skills as well as ability to work in 
international environment are essential. A contract of 3 years will be 
offered to the successful candidate.


Closing date for applications is 12 January 2008.

For further information please look at www.embl-hamburg.de and 
www.arp-warp.org or send me an Email at [EMAIL PROTECTED]


To apply please send a CV, including covering letter, a description of 
current and planned research activities, list of publications, and the 
names and addresses of three referees quoting ref. no. W/07/182 in the 
subject line to: [EMAIL PROTECTED]


Victor Lamzin

[ccp4bb] Postdoctoral position at EMBL in Hamburg

[Victor Lamzin]

POSTDOCTORAL POSITION AT THE EMBL, HAMBURG

Scientific Programming and Algorithm Developing in Macromolecular 
Crystallography


A postdoctoral position is available at the Structural Biology Unit of 
the EMBL in Hamburg. The postholder will work in a stimulating 
international environment on the ARP/wARP software project for 
macromolecular crystallography. The research will involve development 
and programming for modelling of bound ligands in protein-ligand complexes.


The ideal candidate should hold a PhD in a relevant field and have a 
sound scientific record. Familiarity with pattern recognition techniques 
and statistics, programming experience (FORTRAN, C or C++) as well as 
good communication, interpersonal and presentation skills are essential. 
Experience in X-ray crystallography will be considered as an advantage. 
A contract for up to 4 years will be offered to the successful candidate.


Closing date for applications is 12 January 2008.

For further information please look at www.embl-hamburg.de and 
www.arp-warp.org or send me an Email at [EMAIL PROTECTED] 
mailto:[EMAIL PROTECTED]


To apply please send a CV, including covering letter, a description of 
current and planned research activities, list of publications, and the 
names and addresses of three referees quoting ref. no. W/07/PD/20 in the 
subject line to: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]


Victor Lamzin

Re: [ccp4bb] arp/warp in p22121

[Victor Lamzin]

Dear Florian,

ARP/wARP supports 65 space groups where proteins crystallise and it 
indeed uses the Hermann-Mauguin convention as given in the International 
Tables. The space group P22121 (number 3018 in the CCP4 symop.lib) is 
not supported by ARP/wARP. The standard for it would be number 18, 
P21212. The easiest is to re-index your data.


The error message 'cannot extract asymmetric unit limits' should then 
also disappear.


Victor

PS. Actually, Tassos has already replied while I was typing this message.


Florian Schmitzberger wrote:

Dear All,

I am trying to build a molecular replacement model in arp/warp in space group P22121. 
Refmac alone seems to be fine with refining the model in P22121; but arp/warp fails, as far 
as I can see at the first Refmac refinement stage. In the log-file it says this space group is 
not supported.


I am wondering whether arp/warp needs the Hermann-Mauguin convention space group 
P21212.  I suppose I will need to reindex in P21212 in order to use arp/warp? (the diffraction 
data were indexed in XDS, scaled in SCALA, and then run through CAD to change the space 
group from P222 to P22121). I am using arp/warp via the ccp4i interface.


Also, arp/warp gives the following message when I load the mtz file cannot extract 
arp/warp asymmetric unit limits, the job will fail if run. (i did run arp/warp successfully with 
other mtz-files).


Thank you in advance for any comments!

Florian


  

[ccp4bb] Practical Course in Macromolecular Crystallography M2M-7

[Victor Lamzin]

This is just a gentle reminder - the deadline for the applications to 
the M2M course is in 1 month.


=

We would like to announce the Practical Course on Training in methods 
for Macromolecular Crystallography M2M-7: From Measurement to Model. The 
course will take place at the EMBL Hamburg Outstation on the DESY 
synchrotron site in Hamburg on:


Wednesday November 21st - Wednesday November 28th, 2007.

The course will include beamline practicals, computational tutorials 
and/or lectures on beamline hardware, crystal handling, carrying out a 
data collection experiment, data processing, model validation, phasing 
and phase improvement, model building and refinement. There will also be 
lectures on synchrotron radiation, detectors, data collection strategy, 
radiation damage, density modification, use of maximum likelihood and 
software for structure determination.


Invited speakers include K. Bartels (Norderstedt), Z. Dauter (APS), E. 
Garman (Oxford), W. Kabsch (Heidelberg), A. Leslie (LBM, Cambridge), W. 
Minor (Virginia), G. Murshudov (York), A. Perrakis (Amsterdam), J. 
Richardson (Duke) and T. Terwilliger (Los Alamos). Internal speakers 
from EMBL are G. Bourenkov, C. Hermes, V. Lamzin, S. Panjikar, A. 
Schmidt, T. Schneider, P. Tucker and M. Weiss.


The course is primarily supported by the European Macromolecular 
Crystallography Infrastructure network (MAXINF2), EC Contract No 505977.


The number of places is restricted to 20. Applications can be made 
electronically via the link 
http://www.embl-hamburg.de/workshops/2007/m2m7/. The deadline for 
applications is September 28th, 2007.


The organising committee - V. Lamzin, S. Panjikar, P. Tucker, M. Weiss

[ccp4bb] ARP_wARP 7.0 release

[Victor Lamzin]

Dear all,

We are happy to announce the release of ARP/wARP version 7.0

Please visit http://www.arp-warp.org for details and software download.

The major improvements are:

• A new module for ultra-fast low resolution tracing of helical and 
beta-stranded fragments at resolution down to 4.5 A.
• Improved and faster chain tracing, working at lower resolution than 
before, for both 'Classic' and 'flex-wARP' modules.
• Flex-wARP, a control system which automatically defines the sequence 
of the steps to be taken during iterative model building.
• Considerably advanced automated ligand building with ~80% success in 
site identification and ~70% in ligand constructions.
• An option for ‘cocktail screening’; the most likely ligand is 
identified and built from a list of potential compounds.
• Improved fragment sequence docking with empirical targets extracted 
from experimental datasets.
• A validation program ElAl (originated from G. Kleywegt) based on 
statistical density targets from the EDS implemented in flex-wARP.

• A standalone module for side chain building and refinement.
• A module for building loops between fragments implemented in flex-wARP 
and provided standalone.
• The solvent building module with incremental improvements as a 
dedicated module.
• Remote job submission at the EMBL Hamburg cluster directly from the 
web in addition to the CCP4i GUI.

• Command-line job submission for most ARP/wARP tasks.
• ARP/wARP is now running on Mac powerpc, Mac Intel, some flavours of 
Linuxes (i32 and 64-bit ) as well as alpha-Tru64 and mips-IRIX64.


Victor and Tassos on behalf of the ARP/wARP developers' team.