Hi everybody!
I'm new to both CNS and CHI. I downloaded and installed the binary for CNS 1.21
from the web and CHI1.1 from Paul on a machine running Fedora 8. I created the
chi_param file and I got the following problem while executing chi_create.


============================================================
            Running on machine: odisea (x86_64/Linux,64-bit)
                                with  2 threads
            Program started by: gus
            Program started at: 14:37:02 on 02-Dec-2009
============================================================

  FFT3C: Using FFTPACK4.1

  CNSsolve>{* To generate oligomer with sequence separated by a specified
  CNSsolve>   distance *}
  CNSsolve>
  CNSsolve>{* Cut down the output volume a bit *}
  CNSsolve>set message=off end
  CNSsolve>set echo=off end
  MISCOM: file exists
  %ASSFIL-ERR: error opening file results/create.out
  %ASSFIL error encountered: Error accessing file
    (CNS is in mode: SET ABORT=NORMal END)
  *****************************************************
  ABORT mode will terminate program execution.
  *****************************************************
  Program will stop immediately.

Any idea about how to solve it?
Many thanks,

Gustavo

What "doc file"?

On Thu, 2009-12-03 at 10:20 +0530, hussain hussain123 wrote:
>
> Dear all,
>
> I'm trying to fit the inhibitor in the electron density map using
> Hic-Up . but i'm facingproblem in converting the doc file to cns
> readable file(cns format) for further refinement.
>
>      so can any one help me  please...?
>
>
>
> Regards,
> Hussain,
>
>
>
>
>


--

Are you running CNS on windows?  Anyway, my question is what file
contains and why do you need to "convert" it?  All the input files for
CNS are in plain text.

On Fri, 2009-12-04 at 11:47 +0530, hussain hussain123 wrote:
> micro soft word file..2003 version


--

On Wed, Nov 04, 2009 at 02:53:48PM -0800, Axel Brunger wrote:
> It turns out that this is a "feature" of the latest ifort compiler.
> For some reason
> this compiler has problems with the variable names CLASSNAME and
> CLASSINDEX that
> are used in the source files angledb.f and rama.f.
>
> Attached are files that fix the problem.  Please try again.

I can confirm that the attached files are correcting the same issue on
our CentOS-5 x86_64 machines.

[tru@liberte cns_solve_1.21]$ ifort -V
Intel(R) Fortran Intel(R) 64 Compiler Professional for applications running on
Intel(R) 64, Version 11.1    Build 20090827 Package ID: l_cprof_p_11.1.056
Copyright (C) 1985-2009 Intel Corporation.  All rights reserved.

Thanks

Tru
PS: attached the patch file resulting from diff' ing Axel files
and the cns_solve_1.21/source/{angledb,rama}.f files
--
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru@... | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

We are offering RapiData 2010, the twelvth 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 11-16 April 2010.  Students could be at any level
from advanced undergraduate to full professor.  The course should
accommodate 48 students total. All students are encouraged 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 eighth time we will hold a short lecture course on the
fundamentals of crystallography for roughly five hours on Sunday 11 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,

Bob Sweet, Sal Sclafani, 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)
=========================================================================

Dear all,

we've been using the *allhdg topology and parameter files in the hope of
being able to minimize some models (without experimental data). However
we end up getting values of E(ELEC) of 0.0000 so somehow we're missing
the magic to make CNS actually calculate these values (and yes, the flag
for elec is on), or maybe some multiplicative constant is zero.

Can anybody help?

thanks,

Kay
--
Kay Diederichs                http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@...    Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
necessary capabilities, just ignore the attached signature "smime.p7s".

Kay,

are you using model_minimize.inp or something homemade?

Ed.

On Tue, 2009-12-15 at 17:05 +0100, Kay Diederichs wrote:
> Dear all,
>
> we've been using the *allhdg topology and parameter files in the hope of
> being able to minimize some models (without experimental data). However
> we end up getting values of E(ELEC) of 0.0000 so somehow we're missing
> the magic to make CNS actually calculate these values (and yes, the flag
> for elec is on), or maybe some multiplicative constant is zero.
>
> Can anybody help?
>
> thanks,
>
> Kay


--
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 /

Kay Diederichs schrieb:
> Dear all,
>
> we've been using the *allhdg topology and parameter files in the hope of
> being able to minimize some models (without experimental data). However
> we end up getting values of E(ELEC) of 0.0000 so somehow we're missing
> the magic to make CNS actually calculate these values (and yes, the flag
> for elec is on), or maybe some multiplicative constant is zero.
>
> Can anybody help?
>
> thanks,
>
> Kay

thanks to Fred Dyda, I inspected my parameter files and found a nbonds
repel statement - this prevents the electrostatics from being calculated.

Thanks to all who responded!

Kay
--
Kay Diederichs                 http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@...     Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

Hi,
Is there anyway to do molecular simulation using cns both by fixing main chain
and flexible side chain and both flexible.

Also how can I get a final energy values for the simulation using cns.

Let me know if there is any other program that could be useful to do this
(especially free for academic).

thanks
venk

hi all
I am trying to minimize the model with chain ID as A and residues are 100-200 ,
300-400, 500-600. I did generate pdb and mtf seems fine and takes the same chain
ID 'A" but after minimization it only give the segid ID and changed to B and C.

It is kind of frustrating, I want the same chain and segid ID as input
not sure I am missing any thing in the input file.

Appreciate if anyone knows how can I handle this problem?


thanks
venkt

{===>} atom_fixed=(name c or name n or name ca or name o or name ot+);

to fix the backbone.

To get energy values:

energy end

See here for more details and/or unearth an X-PLOR manual

http://cns.csb.yale.edu/v1.2/syntax_manual/html/cns-energy.html

If you are looking for free software to do molecular dynamics, take a
look at Gromacs.

Ed.

On Tue, 2009-12-29 at 16:57 +0000, Venkataraman wrote:
>
> Hi,
> Is there anyway to do molecular simulation using cns both by fixing
> main chain and flexible side chain and both flexible.
>
> Also how can I get a final energy values for the simulation using cns.
>
> Let me know if there is any other program that could be useful to do
> this (especially free for academic).
>
> thanks
> venk
>
>
>
>
>


--
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 /

We are offering RapiData 2010, the twelfth 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 11-16 April 2010.  Students could be at any level from
advanced undergraduate to full professor.  The course should accommodate 48
students total. All students are encouraged 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 eighth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 11 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,

Bob Sweet, Sal Sclafani, 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

I wanted to do ncs restrain for only main chain. I do have six monomer
and wanted to do the ncs restrain for main chain.

I mutated many residues to alanine cause of lack of density, so again
if I wanted to ncs restrain, I do have to mutate back all to keep the same in
order ncs to work in cns.

Please let me know what is the syntax for mentioning segid ID and atom name.

Thanks

venakt

http://cns.csb.yale.edu/v1.2/tutorial/language/atom_sele_basic/text.html

http://cns.csb.yale.edu/v1.2/tutorial/language/atom_sele/text.html

These parts of tutorial may be helpful.

On Mon, 2010-01-04 at 23:14 +0000, Venkataraman wrote:
>
> Hi
>
> I wanted to do ncs restrain for only main chain. I do have six monomer
> and wanted to do the ncs restrain for main chain.
>
> I mutated many residues to alanine cause of lack of density, so again
> if I wanted to ncs restrain, I do have to mutate back all to keep the
> same in order ncs to work in cns.
>
> Please let me know what is the syntax for mentioning segid ID and atom
> name.
>
> Thanks
>
> venakt
>
>
>
>
>


--
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 /

We are offering RapiData 2010, the twelfth 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 11-16 April 2010.  Students could be at any level from
advanced undergraduate to full professor.  The course should accommodate 48
students total. All students are encouraged 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 eighth time we will hold a short lecture course on the fundamentals of
crystallography for roughly five hours on Sunday 11 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,

Bob Sweet, Sal Sclafani, 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)
=========================================================================

Dear all,
I am refining a crystal structure with a modified DNA base. I tried to
input the modification via a patch in cns (1.2). So, I modified
generate.inp, dna-rna.top, dna-rna.param and dna-rna.link accordingly
(see below). When I generate pdb/mtf files and refine in cns I do not
get any errors in the logs. However, all residues of the DNA have broken
bonds between P and O3' (distance is 1.8 instead of 1.6 A; everywhere
not only where the modified base is). Can anybody point me to settings I
can check or things I might have overlooked? Is the link definition correct?

Of course, I am also trying to define the modification with a
non-standard residue but a patch would be the easiest solution for my case.

Thank you,
christian


>> in generate.inp:

patch PCH
   reference=1=(segid A and resid 6)
   reference=2=(segid A and resid 7)
end

>> in dna-rna.top:

PRESidue PCH
  GROUp
    MODIFY ATOM ...  TYPE=...   END
  ADD BOND ...
  ADD ANGLe  ...
  ADD DIHEdral  ...
  ADD IMPRoper  ...
END {PCH}

>> in dna-rna.param

bond ...
angle ...
dihedral ...
improper ...
nonbonded ...

>> in dna-rna.link:

link  nuc  head - pch  tail + * end
link  pch  head - nuc  tail + * end


_______________________________________________________________________

Dr. Christian Biertümpfel
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
_______________________________________________________________________

Hey,

How do I type the logic AND operator? I tried '&&' and '&' and 'and' and nothing
works. Can you help me understand how to put 'and' 'or' and 'not' in if/while
conditions?

if ($expr1="one" AND $expr2 = 2) then
   if true
   if true

end if


Thanks!
Josh.

Simple, yet interesting.  It may be described somewhere in the XPLOR
manual, but a quick look at the .inp files reveals no examples of what
you are trying to do.  I guess you should consider using nested if
operators, as in

if ($expr1 = "one") then
   if ($expr2 = 2) then
     ...

On Wed, 2010-01-27 at 15:51 +0000, stan_124 wrote:
>
> Hey,
>
> How do I type the logic AND operator? I tried '&&' and '&' and 'and'
> and nothing works. Can you help me understand how to put 'and' 'or'
> and 'not' in if/while conditions?
>
> if ($expr1="one" AND $expr2 = 2) then
> if true
> if true
>
> end if
>
>
> Thanks!
> Josh.
>
>
>
>
>


--
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 /

Hello everybody,
                 When using refine.inp of CNS ver 1.2 the rsmd bonds and angles
outputs are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly.
Using optimize_wa.inp gives wa=0.0 for all the cycles and optimize_rweight.inp
gives 0.2 as best value. I recreated a new refine.inp and ran it but I get the
same result. The R- and R-free are near 20%. There are a few anions and metal
ions (but used as neutral) along with waters and protein chain in the input pdb.
I had refined with only protein and waters, with and without the ions but with
no luck. Fixing the wa= 0.3 to 1.5 increases the R- to very high values.
I would appreciate any help to get proper rsmds and wa values.
Thanks in advance,
Amit Das.

Just to verify, you are using the *latest* version, 1.21 (not 1.2)?

This is really strange.  Do both R and Rfree go up when you weaken
restraints?  And how high they go?  You see, normally you would expect
that with weaker restraints Rfree may go up, but R should go down.
What's the resolution?

How do the maps look?  Can you get anything else refined (which would
indicate that the issue is this particular dataset).  If you try other
refinement programs (refmac, phenix), do you still have the problem?

On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
>
> Hello everybody,
> When using refine.inp of CNS ver 1.2 the rsmd bonds and angles outputs
> are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly.
> Using optimize_wa.inp gives wa=0.0 for all the cycles and
> optimize_rweight.inp gives 0.2 as best value. I recreated a new
> refine.inp and ran it but I get the same result. The R- and R-free are
> near 20%. There are a few anions and metal ions (but used as neutral)
> along with waters and protein chain in the input pdb.
> I had refined with only protein and waters, with and without the ions
> but with no luck. Fixing the wa= 0.3 to 1.5 increases the R- to very
> high values.
> I would appreciate any help to get proper rsmds and wa values.
> Thanks in advance,
> Amit Das.
>
>
>
>
>
--
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 /

Yes I am using 1.21 version. Forcing the wa to higher than automatic value of
wa= 7.230911E-02, increases the r and rfree to above 50!

The opt_rweight output is :
------> initial rweight estimate=   0.1000

rweight=   0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)=   3.8780 rms B(angle)=  
4.7275
rweight=   0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)=   3.8205 rms B(angle)=  
4.6736
rweight=   0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)=   3.5794 rms B(angle)=  
4.4422
rweight=   0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)=   3.4538 rms B(angle)=  
4.3251
rweight=   0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)=   3.0403 rms B(angle)=  
3.9464
rweight=   0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)=   2.5454 rms B(angle)=  
3.4242
rweight=   1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)=   1.9617 rms B(angle)=  
2.7739
rweight=   2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)=   1.5863 rms B(angle)=  
2.3047
rweight=   5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)=   1.0437 rms B(angle)=  
1.5197

------> lowest free_r for target "mlf" with rweight=   0.2000 (with wa= 4.41916)

The opt_wa output is:
------> initial wa estimate= 0

wa=          0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000  rmsd angles= 
0.00000
wa=          0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000  rmsd angles= 
0.00000

------> lowest free_r for target mlf with wa= 0

------> The best value for wa is one that produces a low
         free_r value and also good model geometry. As a general
         guide, good geometry is indicated by rms deviations from
         ideal values of less than:
              bonds -> 0.01 A
              angles -> 2.00 degrees

The rsmds are bad since the planarity of the rings are distorted although R and
Rfree are good.
Thanks
Amit.


--- In cnsbb@yahoogroups.com, Ed Pozharski <epozh001@...> wrote:
>
> Just to verify, you are using the *latest* version, 1.21 (not 1.2)?
>
> This is really strange.  Do both R and Rfree go up when you weaken
> restraints?  And how high they go?  You see, normally you would expect
> that with weaker restraints Rfree may go up, but R should go down.
> What's the resolution?
>
> How do the maps look?  Can you get anything else refined (which would
> indicate that the issue is this particular dataset).  If you try other
> refinement programs (refmac, phenix), do you still have the problem?
>
> On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
> >
> > Hello everybody,
> > When using refine.inp of CNS ver 1.2 the rsmd bonds and angles outputs
> > are 0.000 and very low values of wa=2x10-2 and rweight= 0.02 resptly.
> > Using optimize_wa.inp gives wa=0.0 for all the cycles and
> > optimize_rweight.inp gives 0.2 as best value. I recreated a new
> > refine.inp and ran it but I get the same result. The R- and R-free are
> > near 20%. There are a few anions and metal ions (but used as neutral)
> > along with waters and protein chain in the input pdb.
> > I had refined with only protein and waters, with and without the ions
> > but with no luck. Fixing the wa= 0.3 to 1.5 increases the R- to very
> > high values.
> > I would appreciate any help to get proper rsmds and wa values.
> > Thanks in advance,
> > Amit Das.
> >
> >
> >
> >
> >
> --
> 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 /
>

Did you try the Windows executables from CNS website?  If that doesn't
work, consider running linux version in a virtual machine.  Or break
with the dark side and move to linux :)

On Tue, 2010-02-09 at 11:24 +0530, Satyabrata Das wrote:
>
>
>
> Dear All,
>         I want to install CNS in a PC running on Windows-Vista
> (32bit).
> Is it possible? if yes, How to do it? Ideal thing if executable file
> is
> available.
>
> Thank you,
> With regards,
>
> Satyabrata Das
>
> ======================================================
> Satyabrata Das, Ph.D.
> Scientist
> Central Salt & Marine Chemicals Research Institute,
> Gijubhai Badheka Marg, Bhavnagar,
> Gujarat - 364 002 (INDIA)
>
> Phone(off): +91-0278-2567760 (extn. 662/669)
> mobile:        +91-9275174842
>
> FAX: 0278-2567562 / 2566970 / 2572354
> e-mail: satya@...; satyabratadas@...
> ======================================================
>
--
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 /

OK, this clearly indicates that there is something wrong with the CNS
1.21 binaries that you use.  Where did you get them and what OS you are
running?

On Thu, 2010-02-11 at 13:53 +0530, AMIT wrote:
> Yes I was puzzled. I tried the same refinements using CNS 1.1 (I
> switched to this version now) which works fine gives following pdb
> output file:
>
> REMARK starting r= 0.1854 free_r= 0.2018
> REMARK final    r= 0.1830 free_r= 0.2026
> REMARK rmsd bonds= 0.008089  rmsd angles=  1.45742 ..........
> REMARK target= mlf  final wa= 0.6668
> REMARK final rweight=  0.1204 (with wa= 0.6668)
>
> Actually the refine.out used earlier says CNS ver 1.2. I assume that
> refine.inp works for both 1.2 and 1.21 because I created a fresh
> refine.inp for 1.21 from web and ran but the rsmds are still become
> 0.000.
> Actually the same input pdb in refmac 5.5 gives proper rsmds as is now
> given by CNS 1.1.
>
> Regards
> Amit Das.
>
>
>
> On Mon, Feb 8, 2010 at 8:29 PM, Ed Pozharski <epozh001@...>
> wrote:
>         This is obviously abnormal.  It's hard to diagnose what the
>         problem is
>         without further details.  I assume that your installation of
>         CNS works
>         with other datasets/models, so it's something with the data.
>          If you can
>         send me the data/model I will take a look and will treat this
>         confidentially.  Otherwise, consider trying other refinement
>         programs
>         and checking the original data for signs of twinning (although
>         I don't
>         see how twinning can produce this behavior)
>
>         Ed.
>
>
>         On Mon, 2010-02-08 at 04:30 +0000, amitd_01 wrote:
>         >
>         > Yes I am using 1.21 version. Forcing the wa to higher than
>         automatic
>         > value of wa= 7.230911E-02, increases the r and rfree to
>         above 50!
>         >
>         > The opt_rweight output is :
>         > ------> initial rweight estimate= 0.1000
>         >
>         > rweight= 0.0100 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8780
>         rms
>         > B(angle)= 4.7275
>         > rweight= 0.0200 r= 0.1685 free_r= 0.2128 rms B(bond)= 3.8205
>         rms
>         > B(angle)= 4.6736
>         > rweight= 0.0500 r= 0.1687 free_r= 0.2127 rms B(bond)= 3.5794
>         rms
>         > B(angle)= 4.4422
>         > rweight= 0.1000 r= 0.1688 free_r= 0.2126 rms B(bond)= 3.4538
>         rms
>         > B(angle)= 4.3251
>         > rweight= 0.2000 r= 0.1691 free_r= 0.2121 rms B(bond)= 3.0403
>         rms
>         > B(angle)= 3.9464
>         > rweight= 0.5000 r= 0.1699 free_r= 0.2123 rms B(bond)= 2.5454
>         rms
>         > B(angle)= 3.4242
>         > rweight= 1.0000 r= 0.1716 free_r= 0.2127 rms B(bond)= 1.9617
>         rms
>         > B(angle)= 2.7739
>         > rweight= 2.0000 r= 0.1734 free_r= 0.2135 rms B(bond)= 1.5863
>         rms
>         > B(angle)= 2.3047
>         > rweight= 5.0000 r= 0.1781 free_r= 0.2169 rms B(bond)= 1.0437
>         rms
>         > B(angle)= 1.5197
>         >
>         > ------> lowest free_r for target "mlf" with rweight= 0.2000
>         (with wa=
>         > 4.41916)
>         >
>         > The opt_wa output is:
>         > ------> initial wa estimate= 0
>         >
>         > wa= 0.0000 r= 0.1689 free_r= 0.2126 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1688 free_r= 0.2126 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1687 free_r= 0.2126 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1686 free_r= 0.2127 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1684 free_r= 0.2128 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1680 free_r= 0.2129 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1675 free_r= 0.2129 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         > wa= 0.0000 r= 0.1666 free_r= 0.2131 rmsd bonds= 0.000000
>         rmsd angles=
>         > 0.00000
>         >
>         > ------> lowest free_r for target mlf with wa= 0
>         >
>         > ------> The best value for wa is one that produces a low
>         > free_r value and also good model geometry. As a general
>         > guide, good geometry is indicated by rms deviations from
>         > ideal values of less than:
>         > bonds -> 0.01 A
>         > angles -> 2.00 degrees
>         >
>         > The rsmds are bad since the planarity of the rings are
>         distorted
>         > although R and Rfree are good.
>         > Thanks
>         > Amit.
>         >
>         > --- In cnsbb@yahoogroups.com, Ed Pozharski <epozh001@...>
>         wrote:
>         > >
>         > > Just to verify, you are using the *latest* version, 1.21
>         (not 1.2)?
>         > >
>         > > This is really strange. Do both R and Rfree go up when you
>         weaken
>         > > restraints? And how high they go? You see, normally you
>         would expect
>         > > that with weaker restraints Rfree may go up, but R should
>         go down.
>         > > What's the resolution?
>         > >
>         > > How do the maps look? Can you get anything else refined
>         (which would
>         > > indicate that the issue is this particular dataset). If
>         you try
>         > other
>         > > refinement programs (refmac, phenix), do you still have
>         the problem?
>         > >
>         > > On Fri, 2010-02-05 at 07:42 +0000, amitd_01 wrote:
>         > > >
>         > > > Hello everybody,
>         > > > When using refine.inp of CNS ver 1.2 the rsmd bonds and
>         angles
>         > outputs
>         > > > are 0.000 and very low values of wa=2x10-2 and rweight=
>         0.02
>         > resptly.
>         > > > Using optimize_wa.inp gives wa=0.0 for all the cycles
>         and
>         > > > optimize_rweight.inp gives 0.2 as best value. I
>         recreated a new
>         > > > refine.inp and ran it but I get the same result. The R-
>         and R-free
>         > are
>         > > > near 20%. There are a few anions and metal ions (but
>         used as
>         > neutral)
>         > > > along with waters and protein chain in the input pdb.
>         > > > I had refined with only protein and waters, with and
>         without the
>         > ions
>         > > > but with no luck. Fixing the wa= 0.3 to 1.5 increases
>         the R- to
>         > very
>         > > > high values.
>         > > > I would appreciate any help to get proper rsmds and wa
>         values.
>         > > > Thanks in advance,
>         > > > Amit Das.
>         > > >
>         > > >
>         > > >
>         > > >
>         > > >
>         > > --
>         > > 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 /
>         > >
>         >
>         >
>         >
>         >
>         >
>
>
>
>
>         --
>         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 /
>
>
>
>
>
>
> --
> AMIT DAS,
> PROTEIN CRYSTALLOGRAPHY SECTION,
> SOLID STATE PHYSICS DIVISION, BARC, TROMBAY,
> MUMBAI-400085.
> INDIA.
> Alt E-mail:amitdas@...
> PHONE:+91-22-25594688/4063
> FAX:+91-22-25505151


--
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 /