Is there a good reason to have this CD/CD1 conversion when reading a PDB
file?  All it takes, in my understanding, to avoid this is to modify the
protein.top and protein_rep.param to reflect the new atom name.  In a
similar fashion, * versus ' in nucleic acids can be easily fixed so that
there is no need to convert pdb files when going to Coot and back.  Am I
missing some potential problem?

--
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 /

dear friends,
     Is there a good reason to have this CD/CD1 conversion when reading a PDB
file? All it takes, in my understanding, to avoid this is to modify the
protein.top and protein_rep.param to reflect the new atom name. In a
similar fashion, * versus ' in nucleic acids can be easily fixed so that
there is no need to convert pdb files when going to Coot and back. Am I
missing some potential problem?

http\\rangefindecamera.50webs.com

in the tutorial, the section "enantiomorph ambiguity" groups the 22
enantiomorphic space groups into 11 pairs, each pair related by a center of
inversion.

in particular, "P 61 2 2" is related to "P 63 2 2" -- my understanding was that
"P 61 2 2" is related to "P 65 2 2" by inversion (and indistiguishable by
systematic absences), while "P 63 2 2" is not chiral.  "P 65 2 2" is not found
on this list.

i suspect i am ignorant or missing some key points - any help appreciated.

-bryan (have to use "salmonrushdee" temporarily)

Dear cnsbb,

How to use pre-compiled linux(32-bit; with bash shell) binaries to get the
compilers to work in CNS ver 1.21.

Please see below the complete process done and suggest.

# cd cns
# ls
cns_solve_1.21  cns_solve_1.21_all-mp.tar
# cd cns_solve_1.21
# ls

bin            cns_solve_original  inputs     License   Readme  utils
Changes        doc                 instlib    Makefile  source
cns_solve_env  helplib             libraries  modules   test

# nedit cns_solve_env
# make install

Installation directory: cns_solve_1.21/intel-i686-linux
copying files in instlib directory linux to intel-i686-linux
0read.me
Makefile.header.1.ifort
Makefile.header.2.gfortran
Makefile.header.3.pgf95
Makefile.header.4.ifort_mp
arch_env
machine_c.c
machine_f.f
Using Makefile template for compiler: gfortran
making source directory in intel-i686-linux
making bin directory in intel-i686-linux
making utils directory in intel-i686-linux
making test directory in intel-i686-linux
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
making compiler-test directory in intel-i686-linux
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

# cd intel-i686-linux
# ls

0read.me       machine_c.c              Makefile.header.2.gfortran  test
arch_env       machine_f.f              Makefile.header.3.pgf95     utils
bin            Makefile.header          Makefile.header.4.ifort_mp
compiler-test  Makefile.header.1.ifort  source

# nedit 0read.me

# make install compiler=gfortran

Installation directory: cns_solve_1.21/intel-i686-linux
copying files in instlib directory linux to intel-i686-linux
0read.me
Makefile.header.1.ifort
Makefile.header.2.gfortran
Makefile.header.3.pgf95
Makefile.header.4.ifort_mp
arch_env
machine_c.c
machine_f.f
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
------------------------------------------------------
Can anyone Now tell me How to proceed. Thanks in advance.
Regards,
stella joe

Stella Joe schrieb:
>
>
>
> Dear cnsbb,
>
> after editing the cns_solve_env file as follows:
>
> setenv CNS_SOLVE '/softwares/cns/cns_solve_1.21'
> setenv CNS_SOLVE $CNS_SOLVE
>
> didnot run the install script.
>
> i tried to source the file.
> but i get the following message:
>
> # source cns_solve_env
> bash: setenv: command not found
> bash: setenv: command not found
> bash: setenv: command not found
> bash: cns_solve_env: line 39: syntax error near unexpected token `setenv'
> bash: cns_solve_env: line 39: `  if ( ! $?CNS_ARCH ) setenv CNS_ARCH
> `$CNS_SOLVE/bin/getarch`'
>

setenv is specific for csh or tcsh. You have to use export at bash:

export CNS_SOLVE='/softwares/cns/cns_solve_1.21'

justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

Stella,

Under the bash shell you use 'export' and not 'setenv' (C shell command)
to set environmental variables:

export=CNS_SOLVE '/softwares/cns/cns_solve_1.21'

HTH,
Iain

Stella Joe wrote:
>
>
> Dear cnsbb,
>
> after editing the cns_solve_env file as follows:
>
> setenv CNS_SOLVE '/softwares/cns/cns_solve_1.21'
> setenv CNS_SOLVE $CNS_SOLVE
>
> didnot run the install script.
>
> i tried to source the file.
> but i get the following message:
>
> # source cns_solve_env
> bash: setenv: command not found
> bash: setenv: command not found
> bash: setenv: command not found
> bash: cns_solve_env: line 39: syntax error near unexpected token `setenv'
> bash: cns_solve_env: line 39: `  if ( ! $?CNS_ARCH ) setenv CNS_ARCH
> `$CNS_SOLVE/bin/getarch`'
>
> how to go about now. my system is bin/bash with 32-bit linux
>
> thanks and regards,
> stella joe
>
>
>
>
>
> ------------------------------------------------------------------------
>
>
> No virus found in this incoming message.
> Checked by AVG - www.avg.com
> Version: 8.5.339 / Virus Database: 270.12.49/2149 - Release Date: 06/01/09
17:55:00
>
>

Yeah, misplaced '='...

Clearly wasn't awake enough then as you'd already replied anyway !

Justin wrote:
> Iain Kerr schrieb:
>
>>
>> Stella,
>>
>> Under the bash shell you use 'export' and not 'setenv' (C shell command)
>> to set environmental variables:
>>
>> export=CNS_SOLVE '/softwares/cns/cns_solve_1.21'
>>
>>
>
> That won't work either:
>
>
> export CNS_SOLVE='/softwares/cns/cns_solve_1.21'
>
>

Dear All,

I have been doing calculations with Haddock that uses CNS. But I get
the series of error messages below when the program reads
generate.inp. The names I am using in my structure files are not very
large, and the same protocol runs well in another computer.
Does anyone already saw problems like this?

Thanks,

Roberto

  %DEFMACSET-ERR: parameter too long:

this message was repeated several times untill:


  %NEXTF-ERR: EOF or ERROR encountered on input:

several times and finally:
  %PARSER error encountered: Encountered too many parsing errors.
    (CNS is in mode: SET ABORT=NORMal END)
  *****************************************************
  ABORT mode will terminate program execution.

Hi Roberto,
Check if you forgot a " in your input file.

Cheers,
christian


Roberto Kopke Salinas wrote:
>
>
>
> Dear All,
>
> I have been doing calculations with Haddock that uses CNS. But I get
> the series of error messages below when the program reads
> generate.inp. The names I am using in my structure files are not very
> large, and the same protocol runs well in another computer.
> Does anyone already saw problems like this?
>
> Thanks,
>
> Roberto
>
> %DEFMACSET-ERR: parameter too long:
>
> this message was repeated several times untill:
>
> %NEXTF-ERR: EOF or ERROR encountered on input:
>
> several times and finally:
> %PARSER error encountered: Encountered too many parsing errors.
> (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
>
>
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_______________________________________________________________________

Dr. Christian Biert�mpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health              phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03          fax:   +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________

Hello,

I am trying to install some CNS Solve 1.2 for a fellow researcher and have run
into a compile problem.

`uname -a` is: Linux uridine 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005
x86_64 x86_64 x86_64 GNU/Linux

`g77 -v` gives:
Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.3/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--disable-checking --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-languages=c,c++,objc,java,f77
--enable-java-awt=gtk --host=x86_64-redhat-linux
Thread model: posix
gcc version 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)

I pasted the output of the failed `make g77install` command here:
http://pastebin.com/m298ebd9d

In short, it seems to compile everything correctly except for xscale.f.

I am competent at sysadmining and C, bash, etc, but I don't know any Fortran at
all, or what the error means. The error it gives is several variations of the
following:
xscale.f: In subroutine `xsclsq2':
xscale.f:850:
         &                   MAXSET,TGSET,HPSFSET,TYPESF,ERROR,
                             1
xscale.f:868: (continued):
          DOUBLE COMPLEX ARG(maxset)
                             2
Invalid declaration of or reference to symbol `maxset' at (2) [initially seen at
  (1)]

Has anyone else seen anything like this? How can I correct the error and install
CNS?

Thanks for you helps,
~jws

Hi-

I have a bromine in my ligand, and it always refines with a much higher b-factor
than the rest of the ligand, and correspondingly, a bunch of negative density
and distorted b-factors for the adjacent atoms.

I am wondering if the non-bonded term in my parameter file is way off.  I am
using xplo2d to generate my top/par files.  The nonbonded term is:

NONBonded BR  0.3200   3.884   0.3200 3.884

Thanks -

Christine

>This message is intended for the use of the named recipient(s) only and may
contain confidential and/or proprietary information. If you are not the intended
recipient, please contact the sender and delete this message. Any unauthorized
use of the information contained in this message is prohibited.

Hi All,

I am trying to install CNS_solve_1.2 on my suse11.1 linux
I have configure CNS
But when i type the command of : make install
i m not able to install
I get the following reply

bash: setenv: command not found
bash: setenv: command not found
bash: setenv: command not found
bash: cns_solve_env: line 39: syntax error unexpected token `setenv'
bash: cns_solve_env: line 39: `if (!$?CNS_ARCH) setenv CNS_ARCH
`CNS_SOLVE/bin/getarch

If someone can help me out, I would be happy

Thanking you

Ramasree.D

Since our recent upgrade of the lustre filesystem on our cluster to version 1.8,
we have been having issues with cns. Specifically the command 'set
display=&coordinate_outfile end' fails.

  CNSsolve> set display=&coordinate_outfile end
  %ASSFIL-ERR: error opening file b_test.pdb
  %ASSFIL error encountered: Error accessing file
    (CNS is in mode: SET ABORT=NORMal END)
  *****************************************************
  ABORT mode will terminate program execution.
  *****************************************************
  Program will stop immediately.

It's impossible to say what exactly went wrong - please post the
define() part of your density_modify.inp - apparently one or more
selections are malformed.

On Thu, 2009-07-23 at 03:47 +0800, JingHua LU wrote:
>
> Dear ALL:
>
>      I got a problem to run density modification in CNS.
>
>       Would you give me some troubleshooting?
>
>        The following is what I did:
> 1) I calculated the phase using model_phase.inp after annealing
> refinement,
>
> 2) edit the density_modify.inp and input two reflection data,
> original .cv and model_phase.hkl from model_phase.inp.
>
> When I run density_modify.inp, there came an error messenge:
>
> data type mismatch, selection must be a logical expression.
>
>     Thanks a lot,
>
> Jinghua
>
>
>
>
>
> ______________________________________________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！
>
>
>
--
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 /

Is it stuck or it just quits (try "ps -Af | grep cns_solve" to see if
cns_solve is still running).  If it quits, it may be related to the
stacksize limitation, remove it this way:

ulimit -s unlimited

prior to running cns_solve (this is for bash, it is "limit stacksize
unliited" for tcsh, as far as I remember).

On Sun, 2009-08-02 at 14:43 -0700, Xie Jiabao wrote:
>
> Dear all,
>
> I am trying to carry out simulated annealing, energy minimization and
> Bfactor refinement of my model using refine.inp in cns1.21. The
> protein model has 2 protein chains (145 residues each) in the
> asymmetric unit with 142 water molecules. I tried to run the script
> with auto setting of torsion_maxlength, torsion_maxtree and
> torsion_maxchain and with water molecules fixed. However, the run was
> aborted with the message that there were too many trees, and the
> parameter torsion_maxtree should be increased. I next increased the
> parameter torsion_maxtree to 145 and reran the program. In this
> instance the process is running but execution seems stuck at the
> following step (I am reproducing the last few lines of the log file).
>  Torsion Topology>         fix group ( &atom_rigid )
>  SELRPN:      0 atoms have been selected out of   2416
>  Torsion Topology>
>  Torsion Topology>       end
>  Torsion Dynamics>       nstep=0
>  Torsion Dynamics>       cmremove=true
>  Torsion Dynamics>     end
>  DTOREST2: number of groups       1207
>  DTOREST2: number of joints       1205
>  DTOREST2: total number of closed loops          0
>  DTOREST2: number of trees          2
>  DTOREST2: total number of chains        486
>  DTOREST2: maximum number of chains in any tree        243
>  DTOREST2: overall maximum chain length          8
>
>
> I have tried removing water molecules from the model and rerunning the
> script with auto selection of torsion_maxlength, torsion_maxtree and
> torsion_maxchain. Program execution again seems stuck at the same
> step.
>
> Can someone please explain to me what is going on and how do I solve
> this program?
>
> Thanks in advance,
>
> Xie
>
>
>
>
>
>
>
>
--

I wanted to let everyone know that there appears to be a typo in
difference_distance.inp for v1.1 and v1.2.

The following lines

      evaluate ($dist1=sqrt(($xm2-$xm1)^2+($ym2-$ym1)^2+($ym2-$ym1)^2))

      evaluate ($dist2=sqrt(($xc2-$xc1)^2+($yc2-$yc1)^2+($yc2-$yc1)^2))


should be changed to

      evaluate ($dist1=sqrt(($xm2-$xm1)^2+($ym2-$ym1)^2+($zm2-$zm1)^2))

      evaluate ($dist2=sqrt(($xc2-$xc1)^2+($yc2-$yc1)^2+($zc2-$zc1)^2))


Jack


--
John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tannerjj@...
http://www.chem.missouri.edu/TannerGroup/tanner.html