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
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
To
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
ter
ear 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 <mailto:vic...@embl-hamburg.de>>
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
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 start
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
tlab.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@JISCMA
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.
Vi
=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
.
For details see:
http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=53392&aid=15470
Please apply online through www.embl.org/jobs
With best regards,
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_
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
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
Dear Karthikeyan,
It may indeed be too long length of your PATH variable.
Can you also type
echo $PATH | wc -c
and see what the output is? On my Mac it is 641.
With best regards,
Victor
On 07/03/2013 14:38, S. Karthikeyan wrote:
Dear CCP4BB members,
I am trying to run arp_warp classic (7.3
Just a few additional ideas on the significance of the presented values
of the correlation coefficient.
For samples of size N from a bivariate normal with correlation r, its
standard deviation is approximately
StDev(R) = (1 - R^2)/sqrt(N – 1) - note that it depends on the number of
points used
e/training/events/2012/ESMAX-12/index.html
The deadline for applications is October 1st, 2012.
The organising committee - Michele Cianci, Johanna Kallio, Ronan Keegan,
Eugene Krissinel, Victor Lamzin, Andrey Lebedev, Thomas Schneider
I can only confirm what Alex said. And the structure was neither a
globin or zyme or psin!
Victor
Quoting aaleshin :
I and Victor Lamzin solved our first protein structure (3A
resolution) in 80-s using pure MIR and a home made (Russian)
diffractometer...
Alex
On Jun 6, 2012, at 1:42
Dear Tony, Tongqing, Tim,
Adding some alanine spacer is good for a simple reason - during
sequence docking ARP/wARP checks the distance between the ends of the
fragments.
Imagine you have two chains, 10 residues each. If you concatenate them
together, terminal residues belonging to differ
Dear Bernard,
arp_waters is a very old code and it gets even older as we speak.
Try to use ARP/wARP version 7.2, where you can run the same task:
from the command line ($warpbin/auto_solvent.sh)
from the CCP4i GUI (ARP/wARP Solvent)
from ArpNavigator (Model Solvent)
There should be both 32 and
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 buildi
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 fr
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
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 Navigat
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 i
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
b
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
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
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
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
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 o
Dear Jian,
This bug (ARP/wARP not being able on some computer platforms to
recognise version number if it starts from zero) was fixed about half a
year ago. Please go to www.arp-warp.org and download the 7.1.1 patch.
After installing the patch the problem should go.
With best regards,
Victor
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
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
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
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
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
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 mo
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/w
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
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 wrote:
Dear Madravi,
Probably the buffer was not flashed out to the log file.
Does the error stay if
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
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
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 ele
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.
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 th
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
sour
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
(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
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
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
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,
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
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.
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
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 deprecat
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
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 th
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 com
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 brok
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.
--
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.
--
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 Septemb
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)
nce 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
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
We are happy to announce the release of ARP/wARP 7.0.1. To download
please visit as usual http://www.arp-warp.org
As the version number implies this release contains bug fixes and only
minor enhancement of the functionality. Most noteworthy:
* Installation problems (mostly related to the use
ion 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
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,
P
This is just a gentle reminder - the deadline for the applications to
the M2M course is in 1 week.
=
We would like to announce the Practical Course on Training in methods
for Macromolecular Crystallography M2M-7: From Measurement to M
James Holton wrote:
Perhaps the best way to settle this is to put it out to a challenge:
does anybody have a map calculated with an average
FOM(fromsomeprogram) < 0.5 that they were able to trace?
I saw ARP/wARP iteratively tracing such densities if the resolution was
1.5 A or higher - a b
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
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.
•
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, 20
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