Hi all,

Someone pointed me to this:
http://cdn3.spiegel.de/images/image-287176-galleryV9-qokb.jpg

Apparently, it is a page from this book:
http://www.amazon.co.uk/Science-Ink-Tattoos-Obsessed/dp/1402783604

Personally, if I had to get a tramp stamp, it would obviously be of 1cbs
(http://pdbe.org/1cbs)

--Gerard

******************************************************************
                             Gerard J. Kleywegt

        http://xray.bmc.uu.se/gerard   mailto:gerard@...
******************************************************************
     The opinions in this message are fictional.  Any similarity
     to actual opinions, living or dead, is purely coincidental.
******************************************************************
     Little known gastromathematical curiosity: let "z" be the
     radius and "a" the thickness of a pizza. Then the volume
              of that pizza is equal to pi*z*z*a !
******************************************************************

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)
=========================================================================

Hi all,

I am running OSX Lion server (10.7.2) on a Mac Pro desktop (8 cores) and have installed CNS version 1.21 but I can not get CNS to run using cns_solve etc. I also tried CNS 1.3 and had the same problem, but I installed cns1.2 last week on one of our mac minis OS X 10.6 without a problem. I am using the tcsh shell (but the bash shell with the cns_solve_env_sh file gives the same error).

After sourcing the cns_solve_env:

% cns_solve

cns_solve: Command not found

After trying to alias cns_solve in the csh.cshrc file:

% cns_solve 

/usr/local/cns_solve_1.21/cns_solve_env: Permission denied

% echo $CNS_SOLVE

/usr/local/cns_solve_1.21

I left the machine arch as unknown in the cns_solve_env and I tried setting CNS_ARCH to mac-intel-darwin and each time I get the same response

% echo $CNS_ARCH

unknown-x86_64-Darwin

% uname -a

Darwin server.urmc.private 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug  9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64

% env | grep -i cns

CNS_SOLVE=/usr/local/cns_solve_1.21

CNS_ARCH=unknown-x86_64-Darwin

CNS_LIB=/usr/local/cns_solve_1.21/libraries

CNS_MODULE=/usr/local/cns_solve_1.21/modules

CNS_TOPPAR=/usr/local/cns_solve_1.21/libraries/toppar

CNS_CONFDB=/usr/local/cns_solve_1.21/libraries/confdb

CNS_XTALLIB=/usr/local/cns_solve_1.21/libraries/xtal

CNS_NMRLIB=/usr/local/cns_solve_1.21/libraries/nmr

CNS_XRAYLIB=/usr/local/cns_solve_1.21/libraries/xray

CNS_XTALMODULE=/usr/local/cns_solve_1.21/modules/xtal

CNS_NMRMODULE=/usr/local/cns_solve_1.21/modules/nmr

CNS_HELPLIB=/usr/local/cns_solve_1.21/helplib

Any ideas on how to fix this? 

Jermaine Jenkins (JJ)

URMC Rochester NY

Hello Jermaine,

> I am running OSX Lion server (10.7.2) on a Mac Pro desktop (8 cores) and
> have installed CNS version 1.21 but I can not get CNS to run using
> cns_solve etc.

The $CNS_SOLVE/bin/getarch script in 1.21 doesn't understand the 64-bit
kernel in OS X 10.7. Download the latest CNS 1.3 release and copy the
'getarch' script into the 1.21 installation, and that part will be fixed.

I just tested our 1.21 installation on 10.7, and it works fine after making
that change.

-ben

--
| Ben Eisenbraun
| SBGrid Consortium                          | http://sbgrid.org       |
| Harvard Medical School                     | http://hms.harvard.edu  |

Dear all

I am trying to install cns1.3 on an ubuntu linux system. I downloaded:

http://cns-online.org/download/v1.3/cns_solve_1.3_all.tar.gz
and then after gunzip and tar, I compiled using:

make install compiler=gfortran

as the other two compilers:pgf95 and ifort both gave error messages.

It looked OK at that point but when I tried running the distributed test process
by doing:

----------------
cd $CNS_INST
check if a directory called "test" exists. If not, create one by "mkdir test"
cd test
run_tests -link
run_tests *.inp
run_diffs *.inp
-------------

I see that all the *.out files in test contain:

%SETFPEPS increase value of MXFPEPS2 and recompile
%SETFPEPS error encountered: Could not determine machine epsilon

Previously in this form someone (Ed) suggested increasing the value of MXFPEPS2
from 1024. I tried 2048, 4096 and 8192 but then got different error messages in
*.out files:

SETFPEPS Machine epsilon determined to be  0.494-323
  %SETFPEPS error encountered: Machine epsilon value is too small


I would be very grateful if anyone has the solution for what I need to do.

Thanks very much,

Michelle

On Thu, 2011-12-15 at 21:16 +0000, michelle_honiton wrote:
> Previously in this form someone (Ed) suggested increasing the value of
> MXFPEPS2 from 1024. I tried 2048, 4096 and 8192 but then got different
> error messages in *.out files:
>

This is the third time this came up, so there must be some similarity in
the setups.

What happened with the original post was that we started troubleshooting
and then once we put the write statements to see what is going on it
compiled without a problem.  So unfortunately I do not really know what
the problem is, but if you want to try the same troubleshooting we can
do that.

To start, post the 'uname -a' and 'cat /etc/lsb-release' output.  This
might be some 32/64-bit issue.

Also, do the pre-compiled binaries work for you?

Cheers,

Ed.

--
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,

If you should suffer from Christmas Disease, and you were to cut yourself
while carving the turkey, you could be in trouble! Find out why in the last
episode for 2011 of Quips, PDBe's collection of interactive stories about
QUite Interesting Pdb Structures.

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

The accompanying mini-tutorial shows you how to carry out a fragment search
with PDBeChem so as to identify all small molecules in the PDB archive that
contain a benzothiophene moiety.

---

On behalf of all PDBe staff: best wishes for the coming holiday season and a
well-structured 2012! (Unless you're working on natively unfolded proteins, in
which case we wish you an unstructured or partially structured 2012, of
course.)

--Gerard

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

On Sun, 2011-12-25 at 23:58 +0530, sunil tewary wrote:
> Please help if anybody knows how to break it.

Most likely your CNS_SOLVE environmental variable is not set properly.
Check your cns_solve_env.  To verify, you can also go back to the
command line and execute "echo $CNS_TOPPAR", it should return the folder
that contains the topology files.  If it exists, check if it has
protein.top in it, its absence is why you run fails.

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
(http://pdbe.org/go). GO stands for Gene Ontology, a major bioinformatics
initiative with the aim of standardizing the representation of gene and gene
product attributes across species and databases (http://geneontology.org/).
The SIFTS project (http://pdbe.org/sifts) maps GO annotations from UniProt to
all proteins and protein fragments that occur in the PDB. These GO terms
describe:

* molecular function, the elemental activities of a gene product at the
molecular level (e.g., catalysis of free radical formation)

* cellular component, the localisation of a gene product in a cell or its
extracellular environment (e.g., outer membrane-bounded periplasmic space)

* biological process, operations or sets of molecular events with a defined
beginning and end, pertinent to the functioning of integrated living units:
cells, tissues, organs, and organisms (e.g., neuron apoptosis)

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,
cellular_component or biological_process term. Clicking on any of these will
expand the classification to show the underlying terms, and these can be
clicked on for further drilling. If a term is shown on a grey background, it
means that there are no proteins in the PDB that have been annotated with that
term.

- start typing a term in the input box (above the Submit button). Once you
have typed a few characters, an auto-complete function will show you a list of
all the matching GO terms. Select any one of these and hit the Submit button.

Once you have selected a GO term that is of interest to you, the browser will
load all PDB entries that contain a protein (fragment) that has been annotated
with that term in the central panel of the browser. (The right panel contains
more information about the GO term and how it fits in the GO classification -
click on the image to get a bigger version.) In the central panel, the "PDB
entries" tab shows a simple list of the PDB entries. However, there are other
tabs that provide different views on this set of entries, such as:

- which ligands are found in these entries?

- what folds are represented (CATH)?

- what quaternary structures occur (PISA)?

- what sequence families are present (Pfam)?

- 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
localisation.

If you have any questions, comments or suggestions, please use the button
marked "FEEDBACK" in the top right corner of any PDBe webpage.

---
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
>>
>>
>>
>>
>>
>
>
>
> ------------------------------------
>
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>
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>
>
>