Re: [ccp4bb] Create Links in PDB

[Paul Emsley]

On 04/04/14 20:45, Remie Fawaz-Touma wrote:

Hi all,

I need help creating links between units of sugar (ligands) in the PDB file 
before refining so that CCP4 recognizes the sugars are attached.

I tried the one suggestion I got before Extension > Make a Link,  but I get 
discontinued bonds instead of full bonds.



A dotted line is how Coot represents a LINK.  It will not use solid 
lines for LINKs. You don't need a solid line for Coot and Refmac to 
consider the residues as bonded.


If you examine the output PDB file, you will see a LINK record.

Paul.

[ccp4bb] EPSRC Centre for Doctoral Training in Cross-disciplinary Approaches to Non-Equilibrium Systems

[Lorenz, Chris]

EPSRC Centre for Doctoral Training in
Cross-Disciplinary Approaches to Non-Equilibrium Systems (CANES)

10 fully-funded 4-year PhD studentships at King's College London
Apply by 28 April 2014 for Sept 2014 entry (late consideration possible)

Non-equilibrium processes underpin many challenging problems across the natural 
sciences. The mission of CANES is to train a new generation of researchers in 
cross-disciplinary approaches to non-equilibrium systems, focussing on the 
three key strands of theoretical modelling, simulation and data-driven analysis 
(see ow.ly/vqCPG). It draws on a broad range of supervisor 
expertise in Mathematics, Physics, Chemistry, Informatics, Computational and 
Systems Biomedicine, Earth and Environmental Sciences, including partners at 
Imperial College London, University College London and Queen Mary London.

The training programme consists of a first year combining taught courses and 
research projects, leading to the award of an MSc. In years two to four, the 
programme will include open question sandpits, master classes, journal clubs 
and an annual retreat. Students will also be able to undertake internships at a 
broad range of industrial and international academic partners.

Funding for CANES students covers course fees, a stipend for living expenses 
(?15,863 per year), and conference travel and internship funds. The programme 
can support UK applicants as well as a limited number of students from the EU 
and overseas.

Applications are now invited from candidates with excellent undergraduate or 
equivalent qualifications in any relevant discipline including mathematics, 
physics, chemistry, engineering, materials science, biophysics, geophysical 
sciences and computer science. A strong background in quantitative science will 
be essential for students to take full advantage of the CANES training 
programme.

Please see http://www.kcl.ac.uk/canes/ for further details of how to apply.

Interested candidates should apply by 28 April 2014. Applications received 
after this date will be considered as long as places remain. Informal enquiries 
can be addressed to the CANES Director, Prof. Peter Sollich 
(peter.soll...@kcl.ac.uk).




Dr. Chris Lorenz
Senior Lecturer --- Senior Tutor
Theory & Simulation of Condensed Matter Group
Department of Physics
King's College London
Strand, London, WC2R 2LS
United Kingdom
020 7848 2639 (phone)

[ccp4bb] broken loggraph on 64 bit redhat: new style refmac graph popup after refmac from inside coot?

[hari jayaram]

Hi all,
I like running my refmac from inside coot and having the loggraph blt
graphs popup on completion.
loggraph graph pop ups seem broken on 64 bit redhat enterprise running ccp4
6.3 and ccp4 6.4 , both 64 bit versions. The window for the graph pops up
and then crashes with an error complaining of the loggraph.tcl script( see
below).

This script nor associated scripts have not changed in ccp4 for a while,
and everything works on 64 bit Ubuntu, so I am scared the error may like
with some redhat component.

I tried to compile a "native" blt instead of using the ccp4 supplied one to
see if that fixed things. Digging through the blt forums etc it seems that
many are abandoning blt to something like a replacement called wize. Also
judging from the forums several things in the blt 2.4 and older seem
to have issues with newer  tk flavors  like 8.5.

Regardless , given all this , are there any ways to auto popup the new
style qt based graphs when running refmac from within coot upon completion.


Sorry I am cross posting to coot, ccp4bb.

thanks for your help in advance.
hari

the error I see in refmac : view log graphs OR in coot on refmac completion
says:

"Error in startup script: syntax error in expression "10 11 12 + 12": extra
tokens at end of expression
while executing
"expr [string trim $ele] + $data(NCOLUMNS) "
(procedure "extract_tables_from_GRAPH" line 44)
invoked from within
"extract_tables_from_$filetype $input $arrayname"
(procedure "extract_tables_from_file" line 31)
invoked from within
"extract_tables_from_file $system(SCRIPT) $system(FORMAT) data"
invoked from within
"if { $system(SCRIPT) != "" } {
  if { ![ElementExists system FORMAT] || $system(FORMAT) == "" } {
 set system(FORMAT) [GetFileFormat $system(SCRI..."
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl"
line 2324)
invoked from within
"source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]"
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl" line 83)
"

[ccp4bb] IUCr Diffraction Data Deposition Working Group

[Jrh Gmail]

Dear Colleagues,
We wish to let you know that the Triennial report for 2011 to 2014 on 
diffraction data deposition matters, prepared by the IUCr Diffraction Data 
Deposition Working Group (DDD WG) is now available at:-
http://forums.iucr.org/viewtopic.php?f=21&t=343
Best wishes,

John, Brian and Tom 

John Helliwell Chair of the WG;
Brian McMahon Co-Chair of the WG;
Tom Terwilliger Member representing the IUCr Commission on Biological 
Macromolecules

[ccp4bb] [ccp4] Research Technician Position at EMBL Grenoble

[Marco Marcia]

Dear all
a Research Technician position is available in the group that I will 
establish at EMBL Grenoble, France.

All details and instructions for submitting applications can be found at:

www.embl.de/aboutus/jobs/searchjobs/index.php?newlang=1&ref=GR_00061

Application deadline is May 11th.
Please, forward this link to anyone you think may be interested.
Thank you.
Marco

--


_

Dr. Marco MARCIA
Yale University, KBT 834
266, Whitney Avenue
New Haven, CT - 06511
USA

phone (lab): +1-203-432-6370
phone (office): +1-203-432-5546
fax: +1-203-432-5316
email: marco.mar...@yale.edu
web: http://www.pylelab.org