Dear All,
I am attempting to refine a structure with BeF3- as a ligand.
Initially I received the error message;

%XRASSOC-ERR: missing SCATter definition for (each of the atoms)

I redefined scatter.lib, and was able to proceed with minimize.inp,
bgroup.inp, and bindividual.inp without error. However, when I
attempted to add water using water_pick.inp, I again encountered the
above error message.

Has anyone encountered this problem before? Any suggestions?
Thanks!
Mike
UCHSC

We are offering RapiData 2009, the eleventh 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 19-24 April 2009.  Students could be at any level from
advanced undergraduate to full professor.  48 students will be accepted; 24
will bring their own specimens for data collection.  Please read the course
description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many
experts in the field will be available for lectures and tutorials, and you'll
find the application materials at this site.

For the seventh time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 19 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.  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,

Alex Soares, Sal Sclafani, and Bob Sweet

=========================================================================
          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 using CNS 1.2. can you please let me know what should be the
input in get_ncs_matrices.inp

i do not get what i need to fill in place of:

segid AAAA and name CA

thanks in advance
jasmita

Hi Jasmita,

have a look at http://cns-online.org/v1.21/ -> Tutorial -> Selecting
Atoms.

Best regards, Daniel

--
Daniel Schlieper                     email: daniel.schlieper@...
Biochemie der Pflanzen               phone: +49 211 8115232
Heinrich-Heine-Universitaet          fax  : +49 211 8113569
40225 Duesseldorf, Germany           http://www.biologie.uni-duesseldorf.de

On Wed, 7 Jan 2009, mita_jhj wrote:

> hi all,
>
> i am using CNS 1.2. can you please let me know what should be the
> input in get_ncs_matrices.inp
>
> i do not get what i need to fill in place of:
>
> segid AAAA and name CA
>
> thanks in advance
> jasmita
>
>

Hi

I am trying determine the phase of a structure by Single Isomorphous
Replacement Anomalous Scattering (SIRAS).
When I use the input file "ir_phase.inp", the following error occurs. What
are the problems?  Could you give me suggestions?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Program version= 1.2 File version= 1.2
  Minimum of     32138 elements =                 2.7500
  Maximum of     32138 elements =                29.7337
  ANOMalous=TRUE {ON}
  Sum of     83129 elements =             25912.0000
  Sum of     83129 elements =                 0.0000
  ERROR: Anomalous form factors (f'') are zero for all
atoms
  associated with LOC f_peak.

      -> Check atom selection for LOC f_peak
      -> Check form factor library.
      -> Are you using an anomalous form factor library?
  %  error encountered: ABORT statement specified.
    (CNS is in mode: SET ABORT=NORMal END)
  *****************************************************
  ABORT mode will terminate program execution.
  *****************************************************
  Program will stop immediately.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Best regards.


-------------------------------------
Masaki Unno, PhD.

Inst. of Multidisciplinary Research for Advanced Materials,
Tohoku University

2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan
Tel: +22-217-5117
Fax: +22-217-5118

Candidates should have a Ph.D. in structural biology or related fields (Chemistry, Physics, Biochemistry, Biophysics, Molecular Biology); experience in biological NMR or macromolecular crystal structure determination, including protein crystallization, data collection/processing, structure determination and model refinement a plus. Please send your CV and the names and contact information for three references to Ms. Janet Zambotti (NMR) or Dr. Laurie Betts (X-ray crystallography) to the following e-mail address:

Hi citizens:

I haven't calculated SIR or MIR phases in CNS since upgrading from 1.1 to 1.2. 
Today I
tried calculating SIRAS phases for a demonstration RNA phasing tutorial I use
for my
research group.

Using CNS 1.1 and one Br RNA derivative, I could calculate beautiful, nearly
perfect 3Å
maps like this:

http://www.chemistry.ucsc.edu/%7Ewgscott/courses/chem200a/xtal_tutorial/map.jpg

Using CNS 1.2 (and then 1.21) the maps are completely uninterpretable.  The
Pattersons
look fine and the Br site is found readily.  But phasing somehow now goes
terribly wrong.

If I instead phase in CCP4's mlphare, and then solvent-flatten in CNS, the maps
look
decent (though not quite as good -- I used to use this to demonstrate solving
with 1
derivative in CNS worked better than with 2 derivatives in mlphare).

Was there a significant change in how (SIRAS or other) phases are calculated
between 1.1
and 1.2.x?  I'm using the new input file but am trying to keep everything else
constant. (I
also used the old one as a control -- same result).

I've been using cns on OS X intel, ppc, and linux, fwiw.

Thanks for any insight or suggestions.

Bill Scott

The other parameter you may consider is treatment of missing
reflections.  AFAIK, ccp4 maps substitute Fc for missing data.  True,
these days most people just load the mtz file in coot, but this follows
the same rule since it uses the FWT etc. columns, which are complete.
This may sound like a bad idea (BIAS!), but in fact it's better than
excluding those reflections (what are you doing by this is setting them
to zero - obviously wrong).

Fortunately, CNS has the fill_in parameter, although its default value
is false.  Consider setting it to true (I had one case when it was
absolutely necessary because of ice rings and severe map distortion due
to missing resolution shell).

On Thu, 2009-01-22 at 23:28 -0800, Xie Jiabao wrote:
> Dear all,
>
> Are test reflections omitted while calculating electron density maps
> in cns?
>
> Best regards,
>
> Xie
>
>
>
>
>
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

The application deadline is 8AM EST Monday 9 February for RapiData 2009,
the eleventh 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 19-24 April 2009. Students could be at any level from
advanced undergraduate to full professor. 48 students will be accepted; 24
will bring their own specimens for data collection. Please read the course
description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many
experts in the field will be available for lectures and tutorials, and you'll
find the application materials at this site.

For the seventh time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 19 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. 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,

Alex Soares, Sal Sclafani, and Bob Sweet

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

I'm trying to install CNS on a Dell 2.8GHz Pentium 4 HT Poweredge SC420
2 GB Unbuntu 8.10 Intrepid ibex.  I downloaded cns_solve_1.21 and moveed
it to my /usr/local/xtal/ directory.  I changed CNS_SOLVE to
'usr/local/xtal/cns_solve_env.' Then I typed 'make install' and get the
following error:

craig-desktop:/usr/local/xtal/cns_solve_1.21> make install
Installation directory: /usr/local/xtal/cns_solve_1.21/intel-i686-linux
copying files in instlib directory linux to intel-i686-linux
0read.me
arch_env
machine_c.c
machine_f.f
Makefile.header.1.ifort
Makefile.header.2.gfortran
Makefile.header.3.pgf95
Makefile.header.4.ifort_mp
Using Makefile template for compiler: gfortran
removing old source files
linking source files to intel-i686-linux/source
linking machine_f.f to source directory
linking machine_c.c to source directory
linking generic fft file to source directory
making Makefile in source directory
testing Fortran and C compilers
compiling: gcc -O -DCNS_ARCH_TYPE_LINUX
C compiler passes test
compiling: gfortran -w -O3 -malign-double -funroll-loops -ffast-math
linking: gfortran -w
Segmentation fault
***** ERROR: problem with Fortran compiler *****
make[3]: *** [fortran-test] Error 2
make[2]: *** [compiler-test] Error 2
make[1]: *** [compiler-test] Error 2
compiler problems - stopping installation
please check compilers before retrying installation
make: *** [install] Error 1

So it looks like I have a problem with my gfortran compiler but I don't
know how to proceed

I am trying to install cns version 1.1 (don't ask) on a 64-bit Linux
(AMD) machine running CENTOS.  When I downloaded
the general tar file and then tried to run make install (after source
the cns_solve_env) got the following

sed: -e expression #1, char 11: Invalid range end
the architecture of the machine is unknown - CNS_ARCH=unknown-x86_64-
Linux

What else do I need to do?

THanks


Laurie Betts
University of Pittsburgh
X-ray Crystallography Facility Manager
Department of Structural Biology
3501 Fifth Avenue,
Pittsburgh, PA 15260
412-383-5839
lab117@...

The application deadline is 8AM EST Monday 9 February for RapiData 2009,
the eleventh 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 19-24 April 2009. Students could be at any level
from advanced undergraduate to full professor. 48 students will be
accepted; 24 will bring their own specimens for data collection. Please
read the course description at http://www.px.nsls.bnl.gov/RapiData2009/.
You'll see that many experts in the field will be available for lectures
and tutorials, and you'll find the application materials at this site.

For the seventh time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 19 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. 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,

Alex Soares, Sal Sclafani, and Bob Sweet

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

Dear cnsbb,

I am trying to energy minimize a structure to which I have manually
added a Mg2+ ion (I have ensured that the Mg has a 2+ charge). I have
successfully run generate.inp and minimize.inp (with wa=0), but most
of the resultant distances between the Mg2+ and it's neighbours (3
Asps and 3 waters) are too long (2.4 - 2.9 Ang). I was wondering if I
could specifically restrain these distances, but I am struggling to
find an example of how to do it.

Any help much appreciated.

Dave Lawson

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

Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.lawson@...
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm

Dear cnsbb,

I am trying to energy minimize a structure to which I have manually
added a Mg2+ ion (I have ensured that the Mg has a 2+ charge). I have
successfully run generate.inp and minimize.inp (with wa=0), but most
of the resultant distances between the Mg2+ and it's neighbours (3
Asps and 3 waters) are too long (2.4 - 2.9 Ang). I was wondering if I
could specifically restrain these distances, but I am struggling to
find an example of how to do it.

Any help much appreciated.

Dave Lawson

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

Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.lawson@bbsrc.ac.uk
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm

Hi all,
I am new to this group, so sorry if I am repeating somethings. I
cannot figure out how to name glutamine He21 and He22 (IUPAC) so CNS
will recognize the atom. Same problem with arginine Hh11/12/21/22. I
have tried # and * and get nowhere.
I would appreciate any help.
Thanks,
Vicki

Hi all,
I am new to this group, so sorry if I am repeating somethings. I
cannot figure out how to name glutamine He21 and He22 (IUPAC) so CNS
will recognize the atom. Same problem with arginine Hh11/12/21/22. I
have tried # and * and get nowhere.
I would appreciate any help.
Thanks,
Vicki

Dear all,

Could someone advise me how to install CNS1.1 on Mac (intel) OS X
10.5.6? I searched the CNSBB archive and downloaded a version from
Logan Donaldson, but the binary could not work.

I wanted to install CNS1.1 because COOT can convert the two
coefficient files generated by model_map.inp into MTZ file. But these
two files are not produced by CNS1.2. Is there any way to fulfill the
same function using CNS1.2?

Thanks in advance!

Tiancen
Shanghai Institute of Materia Medica
Chinese Academy of Sciences

Hi everyone, this is my first post on the CNS bulletin board.  Thanks in advance
for any help!

I am currently having a problem with composite omit maps in cns version 1.2.  I
have
previously used these with much success on different structures.  My current
structure is in
spacegroup P1.  The maps that CNS gives me contain "normal" looking regions as
well as
regions of dramatically reduced and spotty density.  The problem areas have
density similar
to the solvent regions.  These regions appear to be separated by straight lines
that look
something like unit cell edges/angles.  I have edited the cns .inp file to make
the map over
my pdb as well as over my asymmetric unit and the same thing happens in either
case.  I also
converted the map coefficients into a format readable by coot using sftools and
the same
thing happened.  This leads me to believe that the error is not in how the map
is
drawn/calculated but is something more fundamental.  I have checked and
rechecked my .inp
files and downloaded and edited new .inp files from the cns website, but the
same thing
happens every time.  Any ideas?

Thanks!

Nathan Thomsen
Graduate Student
UC Berkeley

Except that ifort costs $900 (academic price is $360, and academic use
does *not* qualify for non-commercial software development).  You can
get around it once by using an evaluation copy, but it only works for 30
days, so one will be out of luck when the next version of CNS is
released.

It would be nice if Intel would give ifort away for free (after all,
they are not a software company and how much is fortran used these days
anyway), but they don't.  By the way, does gfortran compilation work on
amd machines?  I guess amd binaries will then run on intel processors,
but will be similarly slower compared to ifort version.

On Thu, 2009-03-05 at 13:39 +0000, Boaz Shaanan wrote:
> Hi,
>
> The best solution (it's Axel's advice) is to use the intel compiler.
> It worked like a charm for me.
>             Boaz
> ----- Original Message -----
> From: jbauer6@...
> Date: Thursday, March 5, 2009 9:46
> Subject: [cnsbb] issues with compiling cns 1.21 using gfortran 4.3
> To: cnsbb@yahoogroups.com
>
> > For those who are having difficulty compiling cns v. 1.21 under
> > Linux using gfortran 4.3 (fortran compiler fails test):
> >
> > The problem seems to be the -malign-double switch. The
> > documentation for gcc says that binary files compiled with this
> > switch may not be compatible with those compiled without it (and
> > probably won't link). Mine wasn't and it's quite possible that
> > others also were not. Here are three possible solutions:
> >
> > 1. Use the binary if you can (probably the best solution)
> > 2. Drop the -malign-double switch. You can do this by editing
> >
> > $CNS_SOLVE/instlib/machine/supported/linux/arch_env
> >
> > and commenting out lines 27-30:
> >
> > #
> > # set -malign-double flag on intel-based machines
> > #
> > #setenv CNS_MALIGN_I86 ""
> > #if ( $CNS_ARCH =~ *-i[3456789]86-* ) then
> > #  setenv CNS_MALIGN_I86 "-malign-double"
> > #endif
> > #
> >
> > Then run make install and things should work, hopefully. This
> > will solve the compiler test problem on i686 processors, but not
> > x64 ones.
> >
> > 3. Or you could re-compile the gfortran libraries using the -
> > malign-double switch. I haven't bothered to do this, so I don't
> > know how well it would work out.
> >
> > -malign-double is supposed to give a small performance boost on
> > Pentium processors at the expense of using more memory. Removing
> > it may make CNS run more slowly, but probably won't affect
> > anything else. After dropping this switch, CNS successfully
> > compiled and linked. My installation passed all of the tests,
> > but did run more slowly (on an older and slower computer with a
> > rather small amount of memory) than Dr. Brunger's.
> >
> > Hope this helps,
> >
> > Jacob Bauer
> >
> >
> >
> >
> >
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220 ; Fax: 646-1710
> Skype: boaz.shaanan
>
> ‎
>
>
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

Hi everyone,
I tried to use alpha and beta carbon shifts for structure calculation with cns
1.1, but it seems the syntax of my file is incorrect. I already looked it up in
the syntax manual on the cns homepage but it still doesn't work. Maybe someone
can give me an example how the syntax should look like?
Thanks a lot!
Simone

Has anyone looked at the possibility of paralleling CNS for a GPU (NVIDIA CUDA
specifically)?