We are offering RapiData 2012, the fourteenth offering of our popular course:

      Rapid Data Collection and Structure Solving at the NSLS: A Practical
             Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/.
Students could be at any level from advanced undergraduate to full professor.
The course should accommodate 48 students total.  We encourage all students to
bring their own specimens for data collection, and to bring old data for the
data-reduction and structure-solving tutorials.

Please read the Course Announcement at http://www.bnl.gov/RapiData/.
You'll see that many experts in the field will be available for lectures
and tutorials. You'll find the application materials on the Course
Application tab at this site.

For the tenth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 22 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography.  For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty (under 40
yrs).  Please apply for the course, and then contact R. Sweet
(sweet@...) if you are interested in applying for a scholarship.

In accordance with the standards of the International Union of
Crystallography, we observe the basic policy of non-discrimination,
affirming the right and freedom of scientists to associate in
international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race,
colour, language, age, or gender, in accordance with the Statutes of the
International Council for Science.  At this course no barriers will exist
beyond the application procedure that would prevent the participation of
bona fide scientists.

Please apply or send your students to our course,

Bob Sweet, Sonya Kiss, and Alex Soares

Course Announcement at http://www.bnl.gov/RapiData/

=========================================================================
           Robert M. Sweet                 E-Dress: sweet@...
           Group Leader, PXRR: Macromolecular               ^ (that's L
             Crystallography Research Resource at NSLS            not 1)
             http://px.nsls.bnl.gov/
           Biology Dept
           Brookhaven Nat'l Lab.           Phones:
           Upton, NY  11973                631 344 3401  (Office)
           U.S.A.                          631 344 2741  (Facsimile)
=========================================================================

SHIFTX2 (Protein chemical shift prediction program) version 1.07 is released at
Jan 04, 2012. It is updated its prediction models for the backbone and some side
chain Atoms and the performance of SHIFTX2 has been increased.

Website and Download: http://www.shiftx2.ca

Many seats are still available for RapiData 2012, the fourteenth offering
of our popular course:

      Rapid Data Collection and Structure Solving at the NSLS: A Practical
             Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/.
Students could be at any level from advanced undergraduate to full professor.
The course should accommodate 48 students total.  We encourage all students to
bring their own specimens for data collection, and to bring old data for the
data-reduction and structure-solving tutorials.

Please read the Course Announcement at http://www.bnl.gov/RapiData/.
You'll see that many experts in the field will be available for lectures
and tutorials. You'll find the application materials on the Course
Application tab at this site.

For the tenth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 22 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography.  For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty (under 40
yrs).  Please apply for the course, and then contact R. Sweet
(sweet@...) if you are interested in applying for a scholarship.

In accordance with the standards of the International Union of
Crystallography, we observe the basic policy of non-discrimination,
affirming the right and freedom of scientists to associate in
international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race,
colour, language, age, or gender, in accordance with the Statutes of the
International Council for Science.  At this course no barriers will exist
beyond the application procedure that would prevent the participation of
bona fide scientists.

Please apply or send your students to our course,

Bob Sweet, Sonya Kiss, and Alex Soares

Course Announcement at http://www.bnl.gov/RapiData/

=========================================================================
           Robert M. Sweet                 E-Dress: sweet@...
           Group Leader, PXRR: Macromolecular               ^ (that's L
             Crystallography Research Resource at NSLS            not 1)
             http://px.nsls.bnl.gov/
           Biology Dept
           Brookhaven Nat'l Lab.           Phones:
           Upton, NY  11973                631 344 3401  (Office)
           U.S.A.                          631 344 2741  (Facsimile)
=========================================================================

Structural Bioinformatics Lab, Department of Biotechnology & Bioinformatics, Korea University, Seoul Korea

Brainpool Research Associate – Full time, fixed term appointment for up to two years

 

The Structural Bioinformatics Lab is seeking a Brainpool Research Associate to carry out structural analysis (x-ray crystallography) and biophysical studies of complexes related to virus-host interaction. The group is led by Professor Kyung Hyun Kim and has over the years produced good results (PNAS, NAR, JGV). The research programme is funded by a grant from the Korean Federation of Science and technology Societies (www.brainpool.or.kr) to which both the applicant and our team apply together. Further details on the research group can be found at http://sbl.korea.ac.kr/.

 

Applicants should have a PhD in Structural Biology, Biophysics or a related area, with at least 5 years of research experience after Ph.D., or high profile publications in the highest impact journals.

 

Salary range will be from $45,000-$55,000 per annum plus plane ticket, moving expense and medical insurance. Initial salary for possibly the two months will be dependent on the skills and experience of the successful applicant.

 

Closing date for completed applications: 5 February 2012. To apply for this position please send emails to khkim@... with your resume.

 

Korea U is an equal opportunities employer and encourages applications from all candidates irrespective of gender, race, disability, sexual orientation, age, religion and belief or another protected characteristic.

 

Half of the seats are still available for RapiData 2012, the fourteenth
offering of our popular course:

      Rapid Data Collection and Structure Solving at the NSLS: A Practical
             Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/.
Students could be at any level from advanced undergraduate to full professor.
The course should accommodate 48 students total.  We encourage all students to
bring their own specimens for data collection, and to bring old data for the
data-reduction and structure-solving tutorials.

Please read the Course Announcement at http://www.bnl.gov/RapiData/.
You'll see that many experts in the field will be available for lectures
and tutorials. You'll find the application materials on the Course
Application tab at this site.

For the tenth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 22 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography.  For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty (under 40
yrs).  Please apply for the course, and then contact R. Sweet
(sweet@...) if you are interested in applying for a scholarship.

In accordance with the standards of the International Union of
Crystallography, we observe the basic policy of non-discrimination,
affirming the right and freedom of scientists to associate in
international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race,
colour, language, age, or gender, in accordance with the Statutes of the
International Council for Science.  At this course no barriers will exist
beyond the application procedure that would prevent the participation of
bona fide scientists.

Please apply or send your students to our course,

Bob Sweet, Sonya Kiss, and Alex Soares

Course Announcement at http://www.bnl.gov/RapiData/

=========================================================================
           Robert M. Sweet                 E-Dress: sweet@...
           Group Leader, PXRR: Macromolecular               ^ (that's L
             Crystallography Research Resource at NSLS            not 1)
             http://px.nsls.bnl.gov/
           Biology Dept
           Brookhaven Nat'l Lab.           Phones:
           Upton, NY  11973                631 344 3401  (Office)
           U.S.A.                          631 344 2741  (Facsimile)
=========================================================================

We are extending the deadline because seats are still available for
RapiData 2012, the fourteenth offering of our popular course:

      Rapid Data Collection and Structure Solving at the NSLS: A Practical
             Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/.
Students could be at any level from advanced undergraduate to full professor.
The course should accommodate 48 students total.  We encourage all students to
bring their own specimens for data collection, and to bring old data for the
data-reduction and structure-solving tutorials.

Please read the Course Announcement at http://www.bnl.gov/RapiData/.
You'll see that many experts in the field will be available for lectures
and tutorials. You'll find the application materials on the Course
Application tab at this site.

For the tenth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 22 April. The body of the
RapiData course really requires that students have a healthy knowledge of
crystallography.  For potential students who have some experience but are shaky
about fundamentals, this course will help. There will be a small additional fee
for the fundamentals course, to pay for Saturday night accomodations and food
on Sunday morning and noon.

Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty (under 40
yrs).  Please apply for the course, and then contact R. Sweet
(sweet@...) if you are interested in applying for a scholarship.

In accordance with the standards of the International Union of
Crystallography, we observe the basic policy of non-discrimination,
affirming the right and freedom of scientists to associate in
international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race,
colour, language, age, or gender, in accordance with the Statutes of the
International Council for Science.  At this course no barriers will exist
beyond the application procedure that would prevent the participation of
bona fide scientists.

Please apply or send your students to our course,

Bob Sweet, Sonya Kiss, and Alex Soares

Course Announcement at http://www.bnl.gov/RapiData/

=========================================================================
           Robert M. Sweet                 E-Dress: sweet@...
           Group Leader, PXRR: Macromolecular               ^ (that's L
             Crystallography Research Resource at NSLS            not 1)
             http://px.nsls.bnl.gov/
           Biology Dept
           Brookhaven Nat'l Lab.           Phones:
           Upton, NY  11973                631 344 3401  (Office)
           U.S.A.                          631 344 2741  (Facsimile)
=========================================================================

Hi All,
  I am facing the  same problem reported by Rob in 2002.
Is there any solution for this.
Many thanks.
Regards,
-Kiran

--- In cnsbb@yahoogroups.com, "rreutzel2002" <rreutzel@...> wrote:
>
> Hi,
> This is my first time posting so thanks in advance for any help.
> First a little background...I have been able to derivatize my crystal
> with K2PtI6 and was able to find one huge peak in P21212 with cns,
> fft(patterson) and shelxs so I am pretty sure the peak is there.  The
> problem is that when I try and compute SIR phases in cns I get a big
> problem saying the reflections selected is zero.  here's the error
> message:
> TAB isomorphous diff. for derivative 1:  of refl. selected for scal.
> and ref. target: 5815
>  Program version= 1.1 File version= 1.1
>  Minimum of      7366 elements =                 3.3000
>  Maximum of      7366 elements =                19.9278
>  ANOMalous=FALSe {OFF}
>  Sum of      7412 elements =              5815.0000
>  Program version= 1.1 File version= 1.1
> GETLOCANDPROB: "Fiso calculation"
>  Program version= 1.1 File version= 1.1
>  Sum of         0 elements =                 0.0000
>  %XPRED-ERR: zero atoms selected.
>  %XPRED error encountered: zero atoms selectected.
>    (CNS is in mode: SET ABORT=NORMal END)
> I just want to phase and it's giving me a lot of problems I have
> tinkered with most parameters and I was wondering if anyone has any
> ideas.
>
> thanks
> Rob
>

Hi all,

The Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new, improved
and updated versions of its tools and resources twice a year. Now it's time
for the winter update. Below is a brief description of new features and
services. As always, the URL http://pdbe.org will take you to the PDBe
website. Many of the features can be accessed through the "PDBe Tools" menu on
the left side of the front page, or you can use the shortcut URLs mentioned
below.

                    ------------------

The executive summary for the busy PI:

#1 - A browser of the PDB archive based on GO, the Gene Ontology
(http://pdbe.org/go)

#2 - A service to investigate the status of any PDB entry code ever released
(http://pdbe.org/status)

#3 - New and improved modules to carry out advanced analyses of the PDB
archive with a very simple interface (http://pdbe.org/express)

#4 - A new advanced search tool for EMDB (http://pdbe.org/emsearch)

#5 - New visual analysis pages and volume/model viewers for EMDB entries
(http://pdbe.org/emdb)

#6 - Improved atlas pages for PDB entries

#7 - BioBar made compatible with the latest version of Firefox
(http://pdbe.org/biobar)

#8 - Many other smaller (or "under-the-hood") improvements

                    ------------------

The nitty-gritty details for the eager structure user:

#1 - A new PDB archive browser has been added (see http://pdbe.org/browse for
an overview of all available browser modules). The new module allows analysis
of the archive by the GO terms (http://geneontology.org/) assigned to the
protein(s) in each entry. GO, or Gene Ontology, terms are assigned to UniProt
(http://uniprot.org/) entries and this annotation is mapped onto relevant
proteins or protein fragments in PDB entries as part of the SIFTS project
(http://pdbe.org/sifts). This means that for almost every protein in the PDB,
there is annotation about its molecular function, cellular component and
biological process. For example, if you want to find out what structures are
in the PDB related to programmed cell death, from which species, representing
which protein families, etc., the GO browser will give you the answer in
seconds. You can also traverse the GO "graph" interactively and select terms
above or below "programmed cell death", e.g. "autophagic cell death". You can
access the new PDB browser module at http://pdbe.org/go

#2 - PDBe have developed a new service to provide information about the status
of any or all entries (PDB codes) that are, have been, or will be part of the
archive. You can search in various ways, e.g. by PDB code (if you want to know
the status of an entry you deposited), by author or keyword (to find out what
the competition is doing), by method, by period and by status. So, if you want
to find out how many NMR entries were made obsolete in 2011, or how many
ribosome structures are on hold until publication, this is the tool for you.
Try it out at http://pdbe.org/status

#3 - PDBeMotif (http://pdbe.org/motif) is a very powerful tool for analysing
PDB entries in terms of structure, sequence and chemistry. However, it is also
quite complex to use. For this reason, we are developing small modules of
PDBeMotif (and other) functionality that are presented in such a way that they
are very easy to use by non-experts and provide answers to common but complex
questions. We have developed a new module to answer the question "Which
enzymes interact with this ligand?", and we have improved one of the earlier
modules. Try it out at http://pdbe.org/express

#4 - PDBe have developed a new and flexible search service for the EMDB
archive. Give it a go at http://pdbe.org/emsearch

#5 - EMDataBank serves summary pages about EMDB entries from RCSB and PDBe.
Both sites now serve pages with an OpenAstexViewer-based volume and model
viewer - for example:
http://www.ebi.ac.uk/emdb-srv/atlas/5119_openastexviewer.html - so you can
easily see how the fitted model from the PDB fits inside the volume from EMDB.
PDBe also serves visual map analysis pages - e.g.
http://www.ebi.ac.uk/emdb-srv/atlas/1564_mapoverview.html - with graphs and
static images that enable you to assess if the density was masked, if the
contour level is appropriate, how each of the PDB models fits inside the
density, etc.

#6 - The atlas pages for many PDB entries have been improved:
    * for entries with ligands for which there is bioactivity data available in
ChEMBL (https://www.ebi.ac.uk/chembl/), we include a widget on the ligand page
- try http://pdbe.org/1cbs/ligands - you can click on the graphs and further
explore the available data in ChEMBL
    * annotation (e.g., InterPro and GO classifications) for chimeric proteins
has been properly separated for the constituent proteins, e.g. for
http://pdbe.org/3rze
    * for entries containing fragments of proteins, the GO and other annotations
now pertain only to the fragment that was included in the sample, not the
entire UniProt sequence
    * if an entry has been released, but the experimental data is still on hold,
this is shown on the summary page, e.g. for http://pdbe.org/3tuw
    * if the experimental data for an entry has been used by a different set of
authors to re-refine the structure, a comment and a link is placed on the
summary page of both entries, e.g. http://pdbe.org/2gwx and
http://pdbe.org/2baw

#7 - Biobar is a bioinformatics-oriented browsing toolbar for Firefox that
provides access to major biological data resources directly from your browser.
BioBar has now been made compatible with the latest version of Firefox and a
couple of bugs have been fixed. For more information and installation of the
plug-in, surf to http://pdbe.org/biobar

PDBe maintains a list of publications (co-)authored by PDBe staff (at
http://pdbe.org/publications). If you would like to read more about PDBe
services, our paper in the 2012 Databases issue of NAR (Nucleic Acids
Research) is warmly recommended - open access is provided here:
http://nar.oxfordjournals.org/content/40/D1/D445

As always, we welcome constructive criticism, comments, suggestions, bug
reports, etc. through the feedback button at the top of any PDBe web page.

--Gerard

P.S.: In case you had forgotten, last year we released new features such as
Quips (http://pdbe.org/quips), a "slideshow widget" called PDBportfolio
(http://pdbe.org/portfolio), a compound-based and a taxonomy-based PDB browser
(http://pdbe.org/compounds and http://pdbe.org/taxonomy), PDB highlights
(http://pdbe.org/highlights), a user-friendly overview of every weekly release
(http://pdbe.org/latest) of both PDB (in terms of both entries and chemical
compounds) and EMDB (maps and headers), a widget to display coverage of a
UniProt entry in the PDB (http://pdbe.org/unipdb), easy-to-use analyses of the
PDB (http://pdbe.org/express), a tool for validation and analysis of NMR
models in the PDB (http:/pdbe.org/vivaldi), a data-mining tool for EMDB
(http://pdbe.org/emstats), and revamped NMR (http://pdbe.org/nmr) and
EM-related pages (http://pdbe.org/emdb).

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard@... ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin@...

Hi all,

As many of you know by now, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) regularly produces Quips, short interactive stories about
QUite Interesting Pdb Structures (http://pdbe.org/quips). Quips articles
address biologically interesting aspects of one or more PDB entries from a
structural perspective, using animated and interactive graphics views and
usually a mini-tutorial or suggestions for further exploration using PDBe
tools, services and resources.

Today a new interactive Quips story was released, exploring the structure of
bacterial polymerase III and in particular the beta-clamp and its interaction
with DNA. The accompanying mini-tutorial shows how you can explore a structure
further and produce your own customised views using the OpenAstexViewer (which
is used in Quips for 3D animations and graphics).

To access this Quips episode, point your browser at:
http://pdbe.org/quips?story=BetaClamp

To go straight to the OpenAstexViewer tutorial, surf to:
http://pdbe.org/quips?story=BetaClamp&auxpage=AVtut

There is also an RSS feed that informs you whenever there is a new Quips
article available. For links to this and several other feeds, see
http://pdbe.org/rss

If you have an interesting structure whose story you would like to tell (with
our help) in the form of a Quips article, please contact us at pdbe@...

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard@... ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin@...

Hi all,

In April we will once again organise the EMBO practical course on
"Computational structural biology - from data to structure to function". The
application deadline is only a week away - 24 February.

For more information about the course and how to apply, surf to:

          http://www.ebi.ac.uk/training/onsite/120416_structures.html

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard@... ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin@...

Hi

Please tell me how to install CNS 1.3 on ubuntu on i686 architecture.

Is binary installation (cns_solve_1.3_all_intel-mac_linux.tar.gz) possible on
i686 or source installer file of CNS 1.3 (cns_solve_1.3_all.tar.gz) should be
used and compiled.

Thanks
Kumud Agarwal
Post-Graduate Student in Bioinformatics
IIT Bombay
India

Take a look at this thread

http://tech.groups.yahoo.com/group/cnsbb/message/2124

Once again, I don't really know what the problem is since I can neither
reproduce it nor get others who have this problem to thoroughly
troubleshoot.

On Wed, 2012-02-22 at 22:36 +0800, kumud agarwal wrote:
>
> Hi
>
>
>
> I have been trying to install CNS 1.3 (using source installer -
> cns_solve_1.3_all.tar.gz) on ubuntu on i686 architecture.
>
>
> After giving make install command using gfortran as compiler I got
> following error :
>
>
> gcc -o to_cns -O to_cns.c -lm
> to_cns.c: In function ‘get_hkl_refs’:
> to_cns.c:431:8: warning: ignoring return value of ‘fgets’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c: In function ‘read_reflections’:
> to_cns.c:282:15: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:335:15: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c: In function ‘read_header’:
> to_cns.c:231:11: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:232:11: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:233:10: warning: ignoring return value of ‘fgets’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:234:10: warning: ignoring return value of ‘fgets’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:242:11: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:249:12: warning: ignoring return value of ‘fgets’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:252:13: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:256:13: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> to_cns.c:265:13: warning: ignoring return value of ‘fscanf’, declared
> with attribute warn_unused_result [-Wunused-result]
> g++ -o cluster_struc -O cluster_struc.cpp -lm
> cluster_struc.cpp: In function ‘int main(int, char**)’:
> cluster_struc.cpp:122:24: warning: ignoring return value of ‘char*
> fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
> [-Wunused-result]
> lex refloat.l
> make[4]: lex: Command not found
> make[4]: *** [refloat] Error 127
> make[3]: *** [utils] Error 2
> make[2]: *** [compile-utils] Error 2
> make[1]: *** [utils] Error 2
>
> flags:
>  fortran -> [gfortran] -w -O3  -funroll-loops -ffast-math
>        c -> [gcc] -O -DCNS_ARCH_TYPE_LINUX
>     link -> [gfortran] -w
>
> compiling: angledb.f
> compiling: aria.f
> compiling: ariass.f
> compiling: arical.f
> .....
>
>
> in the end it showed
>
>
>
> compiling: machine_c.c
>
> linking: cns_solve
>
> created executable file cns_solve-1202221517.exe
>
>
> but when I gave cns_solve command I got below message :
>
>
> prof-OptiPlex-390:~/cns_solve_1.3> source cns_solve_env
>
> prof-OptiPlex-390:~/cns_solve_1.3> cns_solve
>  %SETFPEPS increase value of MXFPEPS2 and recompile
>  %SETFPEPS error encountered: Could not determine machine epsilon
>    (CNS is in mode: SET ABORT=NORMal END)
>  WARNING: program encountered a fatal error.
>     However, in interactive mode, program execution
>     will continue.  Proceed at your own risk.
>  Program will stop immediately.
>           ============================================================
>            Maximum dynamic memory allocation:           0 bytes
>            Maximum dynamic memory overhead:             0 bytes
>            Program started at:  on
>            Program stopped at: 15:19:11 on 22-Feb-2012
>            CPU time used:       0.0000 seconds
>           ============================================================
> prof-OptiPlex-390:~/cns_solve_1.3>
>
> Please tell me what is the problem here?
> How can I solve this error?
>
> Thanks
> Kumud Agarwal
> Postgraduate Student in Bioinformatics
> IIT Bombay
> India
>
>
>
>
>
>
>
>
>
>
>
>
>

--
After much deep and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
                                     Julian, King of Lemurs

Hi all,

As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) has
launched a number of PDB archive browsers in the past two years. These allow
users to explore and analyse what is in the PDB based on concepts and
classifications they are familiar with, such as the EC system, chemical
compounds, taxonomy or amino-acid sequences (see http://pdbe.org/browse for
more information).

The most recent addition is a browser that is based on the GO system
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The SIFTS project (http://pdbe.org/sifts) maps GO annotations from UniProt to
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* molecular function, the elemental activities of a gene product at the
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To start exploring, surf to http://pdbe.org/go

In the left panel you can either:

- click on one of the three examples and then hit the Submit button

- start exploring the GO classification by expanding the molecular_function,
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- start typing a term in the input box (above the Submit button). Once you
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Once you have selected a GO term that is of interest to you, the browser will
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click on the image to get a bigger version.) In the central panel, the "PDB
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- which ligands are found in these entries?

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- from which taxa have structures been determined?

- who has determined these structures?

For instance, if your are interested in "purine nucleotide biosynthetic
process", you may find that:

- there are 310 relevant structures in the PDB

- the most common ligands are Mg, SO4, PO4, GDP, K, CL, AMP and ADP

- the structures are mostly of the alpha/beta type (82%), with 45% of all
domains adopting a 3-layer ABA sandwich fold

- 70% of the entries contain homo-oligomeric structures (and 50% of those are
homodimers, but there are also 5 homohexameric structures)

- the set of entries covers 43 different Pfam families

- there are 11 proteins in 5 distinct entries from Yersinia pestis

- R.B. Honzatko is the most prolific depositor of PDB entries in this category
(useful to know if you are looking for collaborators or referees)

As you can see, the GO browser can be used to explore many aspects of what is
known in terms of 3D structures for proteins with a given function, role or
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If you have any questions, comments or suggestions, please use the button
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---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard@... ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin@...

Dear All,

I was generated topologies/parameters for a new residue in a peptide. The
generate.inp created a correct peptide bond from the new residue to the next
residue in the generated .pdb file and produced an .mtf file, which I used as an
input for the anneal.inp. During the annealing the peptide bond was not hold in
place anymore and the peptide was severed into two pieces. Anyone has any idea
where the problem could be?

Thanks a lot for any help,
Krisztina

Most likely, there is some error in topology.  Please post your
topology/parameter/link files for the unconventional residue.

On Sun, 2012-03-04 at 20:18 +0000, feher_krisztina wrote:
>
> Dear All,
>
> I was generated topologies/parameters for a new residue in a peptide.
> The generate.inp created a correct peptide bond from the new residue
> to the next residue in the generated .pdb file and produced an .mtf
> file, which I used as an input for the anneal.inp. During the
> annealing the peptide bond was not hold in place anymore and the
> peptide was severed into two pieces. Anyone has any idea where the
> problem could be?
>
> Thanks a lot for any help,
> Krisztina
>
>
>
>
>

Yes.  I have had this happen when I had to create a novel amino acid
(oxidized cysteine) and didn't set it up to 'link' with the normal amino
acids.

On 3/4/2012 8:15 PM, Ed Pozharski wrote:
> Most likely, there is some error in topology.  Please post your
> topology/parameter/link files for the unconventional residue.
>
> On Sun, 2012-03-04 at 20:18 +0000, feher_krisztina wrote:
>>
>> Dear All,
>>
>> I was generated topologies/parameters for a new residue in a peptide.
>> The generate.inp created a correct peptide bond from the new residue
>> to the next residue in the generated .pdb file and produced an .mtf
>> file, which I used as an input for the anneal.inp. During the
>> annealing the peptide bond was not hold in place anymore and the
>> peptide was severed into two pieces. Anyone has any idea where the
>> problem could be?
>>
>> Thanks a lot for any help,
>> Krisztina
>>
>>
>>
>>
>>
>
>
>
> ------------------------------------
>
> --------------------------------------------------------
> List information at http://groups.yahoo.com/group/cnsbb.
> Posting is only allowed for members of this list.
>
> Yahoo! Groups Links
>
>
>

I am running CNS 1.2 calculations of NMR structure of symmetric DNA
duplex (like (CGAAATTTCG)2 ) and would like to use NCS restraints
included in the "anneal.inp" file. There are written:

{======================== other restraint data ========================}
...............................
{* NCS-restraints file *}
{* example is in inputs/xtal_data/eg1_ncs_restrain.dat *}
{===>} nmr.ncs.file="";

  Unfortunately I cannot find the example of "eg1_ncs_restrain.dat" file in
both CNS 1.2 or 1.3 versions (and the "ncs.def" file does not look
working for this case).
  Could anybody send me an example for "ncs_restrain.dat" file which I could
use for my symmetric dimer calculations? Or may some other ideas how to
place symmetry restraints for NMR structure calculations.

I solved this puzzle with help of the XPLOR manual. The absent NCS file
"ncs_restrain.dat" for symmetry in NMR structure calculations should be
like:

flags
include ncs
end

ncs restraints

  group
  equi (segid A and resid 1:10 and not hydrogen)
  equi (segid B and resid 1:10 and not hydrogen)
  weight-ncs=300
  sigb=1.0
  end

// etc.
  end

  Segid for symmetric parts should be different (A and B), just one segid A
(see below) is not working:

  equi (segid A and resid 1:10 and not hydrogen)
  equi (segid A and resid 21:30 and not hydrogen)

  Alexey


-----------------------------------------------------

>  I am running CNS 1.2 calculations of NMR structure of symmetric DNA
> duplex (like (CGAAATTTCG)2 ) and would like to use NCS restraints
> included in the "anneal.inp" file. There are written:
>
> {======================== other restraint data ========================}
> ...............................
> {* NCS-restraints file *}
> {* example is in inputs/xtal_data/eg1_ncs_restrain.dat *}
> {===>} nmr.ncs.file="";
>
>  Unfortunately I cannot find the example of "eg1_ncs_restrain.dat" file in
> both CNS 1.2 or 1.3 versions (and the "ncs.def" file does not look
> working for this case).
>  Could anybody send me an example for "ncs_restrain.dat" file which I
> could
> use for my symmetric dimer calculations? Or may some other ideas how to
> place symmetry restraints for NMR structure calculations.
>
>

Hi Everyone,

I was wondering if the cns libraries have definitions for 2-mercaptoethanol and
2-hydroxyethyl disulfide. If not, how can I generate those definitions?

Thanks,
Matt @ CSU

Use Hic-Up database, e.g

http://xray.bmc.uu.se/hicup/BME/index.html

Otherwise, xplo2d is a standalone program (part of USF) and prodrg is a
server you can use.

On Mon, 2012-03-26 at 17:26 +0000, mscsu wrote:
>
> Hi Everyone,
>
> I was wondering if the cns libraries have definitions for
> 2-mercaptoethanol and 2-hydroxyethyl disulfide. If not, how can I
> generate those definitions?
>
> Thanks,
> Matt @ CSU
>
>
>
>
>

--
I don't know why the sacrifice thing didn't work.
Science behind it seemed so solid.
                                     Julian, King of Lemurs

Hi Everyone
I was wondering if anyone has a working topology and param file (CNS) for one of
the following ligands with protons to allow me to do a structure calculation
with NMR restraints.
M7GDP (pdb identifer M7G)  7-methyguanosine 5' diphosphate
or M7GTP (identifer MGT) (7-methyguanosine 5' triphosphate)

I have tried using hiccup, but I cannot get the H's attached or read into CNS. I
have aslo used the PRODRG siter to do this, but I am getting some weird
geometries from my calculations!! I'm not sure if his is due to bad noe
restraints or a poor top/par file.
Thanks in advance.
Mike

Dear Colleagues,

   on behalf of the selection committee I'd like to draw your attention to the
the Trueblood award:

	 http://www.amercrystalassn.org/content/pages/main-award-descriptions

   This will next be awarded in 2013, however nominations are sought now so that
the winner can be announcement this Summer. The award will be presented at the
2013 ACA meeting. Please follow this link to obtain the nomination form:

	 http://www.amercrystalassn.org/documents/ACAnomNEW.pdf

   Note that the deadline for nominations is May 1st, which should be sent to
marcia@.... Here is a summary of the award:

Kenneth N. Trueblood Award To recognize exceptional achievement in computational
or chemical crystallography. The award is established in memory of Professor
Kenneth N. Trueblood, UCLA 1949-1998, who was a major force in the early use of
computers and the development of crystallographic computer programs. He applied
these programs to the examination of chemical and molecular details of many
structures at the frontiers of research. His contribution to the famous work on
vitamin B12 is one example. Professor Trueblood was a leader in the development
of techniques for analysis of anisotropic motion and was also a superb teacher
and a lucid author. Established in 2001, the award will be given every three
years and consist of an honorarium of $1,500 and up to $1,500 in travel expenses
to accept the award.

--
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

Building 64, Room 248
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ LBenvenue@... ][ 1-510-495-2506 ]
--

Dear All,
  I installed cns-solve.1.21 coupled with Aria2. When I tried to run aria2 I got
the error message as:
   EntityValueError: USER ERROR <aria.cns.CNSSettings> File
"/Users/fengh/Aria23/src/py/aria/cns.py", line 2855 in load_from_element
CNSSettings: Value "" for entity "local_executable" (Path) is invalid.
Path "" does not exist.
  Can you figure out where is the problem.

Thank you,

Han

Since the error is raised by Aria23/src/py/aria/cns.py, this is not a
CNS-question.  Try asking your question in Aria discussion board.

On Wed, 2012-04-04 at 16:16 +0000, f570518 wrote:
>
> Dear All,
> I installed cns-solve.1.21 coupled with Aria2. When I tried to run
> aria2 I got the error message as:
> EntityValueError: USER ERROR <aria.cns.CNSSettings> File
> "/Users/fengh/Aria23/src/py/aria/cns.py", line 2855 in
> load_from_element
> CNSSettings: Value "" for entity "local_executable" (Path) is invalid.
> Path "" does not exist.
> Can you figure out where is the problem.
>
> Thank you,
>
> Han
>
>
>
>
>

--
After much deep and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
                                     Julian, King of Lemurs

Hi,

I have a situation in which I would like to have different scale factors for NOE
and hydrogen bond restraints using annealing. I looked on the "input files" tab
on http://cns-online.org/v1.3/ and selected anneal.inp under the NMR section. I
see that this template allows for several NOE restraint files and a hydrogen
bond restraint file. Currently I have one of each. I would like, while doing my
annealing starting from a model (of a transmembrane alpha helical structure) to
maintain secondary structure while allowing the helices to move. I have hydrogen
bond restraints for the intra-helical hydrogen bonds that should maintain the
secondary structure. For the NOE restraints file (currently I have only one but
would like to include multiple ones later) I have distances between C_alpha's. I
would like to make the Hydrogen bonds strong and the NOE's weak, but it seems
that they are both linked to the "NOE scale factor" field in the template. If I
make the scale factor large (say 75) I get no movement of any residue. If I make
it week (say 0.1) I get spaghetti. I ran a test in which I entered only the
hydrogen bond restraints and no NOEs at a scale of 75 and got helices strewn
about. That tells me that the hydrogen bond restraints work to hold the
secondary structure and that it was not (just) the NOE restraints.
The lines in the restraint files take the form
assign ( resid # and name A) (resid # and name B) d dm dp
The energy for the biharmonic restraints is
min(ceil, S Kb T/ 2 c^2 * (R - d)^2)
I think S is the NOE scale factor. ceil is 30 by default and I don't see that as
changed in anneal.inp c = dm if R < d and dp if R > d.
Given all of that, I thought that if I lowered S so that the helices could move
but pumped up (1/c^2) for only the hydrogen bond restraints to compensate (that
is, lower dm and dp by 1/Sqrt(factor)), I could keep the helical shape while
allowing the helices to move while remaining weakly tethered together. I had
scale = 0.1 and factor set to 1000 and it didn't work. Recall that originally
scale = 75 did work to maintain secondary structure. 75/0.1 only equals 750, so
a factor of 1000 should have been sufficient. I tried a factor of 10,000 and
still no luck.

Is there a way to set different scale factors for restraints from different
restraint files, be it among the NOE restraint files or between the NOE and
hydrogen bond restraint files using anneal.inp?