[ccp4bb] how to overlap DNA

[Junfeng Liu]

 Dear All,
  Does anybody has the experience to overlap DNA in the  protein
complex? I have tried the LSQ in Coot and it works ok but  not
perfectly. Could you please tell me a better way to do that?Or can
Coot be used to overlap  DNA/RNA on their  back bone  by LSQ or SSM ?
At   the same time, are there some software or servers can be used to
 search the "homology DNA " in the database like the Dali on
protein?
  Thanks in advance!
  Best wishes
  leo

[ccp4bb] Workshop on Advanced Topics in EM Structure Determination

[Clint Potter]

The National Resource for Automated Molecular Microscopy

Announces

A Workshop on Advanced Topics in EM Structure Determination
 
November 11-16, 2012
 
National Resource for Automated Molecular Microscopy
The Scripps Research Institute (TSRI), La Jolla, California.

We invite applications to participate in a Workshop on EM Structure 
Determination of Challenging Macromolecules.  The workshop is aimed at 
students, postdocs and faculty that already have some experience practicing 
cryoEM.  We can accommodate a total of 100 participants.
 
A major goal of the workshop will be to discuss some of the challenges that we 
face in using cryoEM to solve the structure of macromolecules.  Topics to be 
discussed will include improvements in specimen preparation, imaging, 
processing and reconstruction, and methods for validation. The basic format of 
the course will be theoretical lectures in the mornings followed by practical 
demonstrations and panel discussions in the afternoon. Evenings will be 
reserved for poster presentations by participants and research talks by 
instructors.

The instructors for the course will include: Yifan Cheng (UCSF), Wah Chiu 
(Baylor), David DeRosier (Brandeis), Joachim Frank (Columbia), Bob Glaeser 
(LBL), Niko Grigorieff (Brandeis), Richard Henderson (MRC), Tilak Jain (TSRI), 
Gabe Lander (Berkeley), Steve Ludtke (Baylor), Pawel Penczek (U. Texas- 
Houston), John Rubinstein (Hospital for Sick Children, Toronto), Sjors Scheres 
(MRC), Holger Stark (Max Planck- Göttingen), Elizabeth Villa (MPI), and Tom 
Walz (Harvard).

Application forms may be found online at the workshop web page:
http://nramm.scripps.edu/?page_id=2424

A registration fee of $750 will be charged to participants from non-profit 
institutions. Some partial scholarship support may be available depending on 
the success of efforts to raise support. All meals will be provided as part of 
the workshop registration fee but participants will be expected to cover their 
own travel and lodging expenses. Cost of housing is estimated to be under 
$100/night for a shared room and transportation will be provided between the 
hotel and the workshop venue.  Further details on these and other matters will 
be provided once the registration process begins.

The application deadline is 1 July and a final selection of participants will 
be made by 15 August.

Please see all other information pertaining to the course at the web site:
http://nramm.scripps.edu/?page_id=2424
 

For other inquiries send email to:  nr...@scripps.edu

Organizers
Bridget Carragher, Clinton S. Potter and Ronald A. Milligan
National Resource for Automated Molecular Microscopy,
The Scripps Research Institute
 
The National Resource for Automated Molecular Microscopy is supported by grants 
from the National Institute of General Medical Sciences (GM103310).

-- 
Clint Potter, Professor,  Automated Molecular Imaging Group, Dept. of Cell 
Biology, Mailing Address:  The Scripps Research Institute,  MC CB129,  La 
Jolla, CA  92037
Ph: (858) 784-9050, Fax: (858) 784-9090, e-mail: cpot...@scripps.edu, URL 
http://ami.scripps.edu
Office Location: Room 118,  Carr-B Building,  3215 Merryfield Row, San Diego, 
CA 92121. Map and Directions: http://cimbio.scripps.edu/misc/building/
NRAMM: National Resource for Automated Molecular Microscopy 
http://nramm.scripps.edu

[ccp4bb] Workshop on image processing of electron crystallography data: Aug. 19-25, 2012

[Henning Stahlberg]

Workshop on Image Processing with 2dx

August 19-25, 2012, in Basel, Switzerland.

We invite for applications to participate in the fourth international workshop 
on electron crystallography of membrane proteins. This workshop will focus on 
data processing, with emphasis on 3D reconstructions from images of tilted 2D 
crystals. 

The hand-on workshop on the processing of images from cryo-electron microscopy 
of 2D crystals of membrane proteins (electron crystallography) will provide the 
theoretical background and practical applications in advanced image processing 
algorithms. The workshop will use the 2dx software system,  which is based on 
the MRC programs.  Theoretical morning lectures will be followed by practical 
exercises in the afternoon. Although we will provide iMacs for every 
participant, you are encouraged to bring your own laptop (Linux or OSX), or at 
least a portable hard-drive (USB2.0), onto which we will install the relevant 
software systems and test data during the workshop.  You are also welcome to 
bring your own dataset. 

Speakers and instructors include:
Marcel Arheit, C-CINA, Biozentrum, University of Basel, Switzerland.
Daniel Castano-Diez, C-CINA, Biozentrum, University of Basel, Switzerland
Anchi Cheng, Scripps, CA, USA.
Hans Hebert, Karolinska, Stockholm, Sweden.
Cristina Paulino, MPI for Biophysics, Frankfurt, Germany.
Sebastian Scherer, C-CINA, Biozentrum, University of Basel, Switzerland
Henning Stahlberg, C-CINA, Biozentrum, University of Basel, Switzerland.
Xiangyan Zeng, FVSU, GA, USA

The detailed program is available here:
http://www.2dx.unibas.ch/workshop/2012

A registration fee of 300 CHF (approx. $340) for participants from non-profit 
organizations includes lunch and snacks. Registration is open here: 
http://www.2dx.unibas.ch/workshop/2012/registration-for-the-workshop

Oganizers:
Marcel Arheit, Karen Bergmann, and Henning Stahlberg. 

All the best,

Henning Stahlberg.
Prof. for Structural Biology, C-CINA, Biozentrum, University Basel
Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland
http://c-cina.org | Tel. +41-61-387 32 62

[ccp4bb] Crystallographer - Principal Beamline Scientist (I04-1) position available at DIAMOND

[Martin Walsh]

Dear all,
We are in the process of recruiting a Senior Scientist at Diamond with 
responsibility for the MX beamline I04-1 which forms part of the MX village 
suite.
This provides an exciting opportunity to lead the operation and development of 
I04-1 through the direct management of a small team of scientists and 
interactions with the other four currently operational beamlines within the MX 
village at Diamond (http://www.diamond.ac.uk/Home/Beamlines/MX.html).

The Principal Beamline Scientist is expected to establish an internationally 
competitive research programme that complements the activities of the MX 
village (Structural biology, Crystallographic methods development and/or 
Instrumentation). To this end Diamond provides state of the art facilities for 
all aspects of structural biology and will fund a full time post-doctoral 
research associate, as well as supporting graduate students through sponsorship 
with academic institutions via the Diamond PhD studentship programme.

Full details of the post and how to apply can be found here:
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0732_TH.html

Informal inquires about the post can be directed directly to Martin Walsh 
either by telephone (+44 (0) 1235 778518) or via email: 
martin.wa...@diamond.ac.uk

The closing date is set at 2/6/2012
Martin

Re: [ccp4bb] ctruncate and anistropy correction

[Charles Ballard]

Hi Frank

this means that the anisotropy corrected data is used to calculate the twinning 
statistics, moments etc.  The corrected data is not used in the truncate 
procedure.

Charles

On 1 May 2012, at 19:28, Frank von Delft wrote:

> Hello, a colleague just pointed me to an innocuous sentence in the ctruncate:
> 
>"CTRUNCATE looks for anisotropy in the data and performs anisotropy 
> correction."
> 
> What exactly does that involve...?
> 
> phx.