Hello All:

I am having a problem with refine.inp.  Actually, it
is the map building part that is causing the problem.
The refinement is carried out and .pdb files are
generated but I get no maps due to the following
error:

CNSsolve> xray
  XRAY>   declare name=dtarg domain=reciprocal
type=complex end
  XDECLARE: Object DTARG has been declared.
  XRAY>   declare name=total domain=reciprocal
type=complex end
  XDECLARE: Object TOTAL has been declared.
  XRAY>   declare name=fmap domain=reciprocal
type=complex end
  XDECLARE: Object FMAP has been declared.
  XRAY> end
  CNSsolve>
  CNSsolve> xray
  XRAY>   predict
  PREDict>     mode=dtarget(fcalc)
  PREDict>     to=dtarg
  PREDict>     selection=(ref_active=1)
  Total of      3797 structure factor elements were
selected.
  PREDict>     atomselection=( &atom_select )
  SELRPN:   1947 atoms have been selected out of   1947
  PREDict>   end
  FCALC: #scatt.= 1947 #anomalous=  0 #special pos.=  0
occupancies=1
  XSFAL: allocating space for complex reciprocal space
object.
  XFFT: using grid [  20,  54,  72] and sublattice [
20(  21),  54(  55),  72]
  XRAY> end
  CNSsolve>
  CNSsolve> xray
  XRAY>   predict
  PREDict>     mode=reciprocal
  PREDict>     to=fcalc
  PREDict>     selection=(all)
  Total of     15699 structure factor elements were
selected.
  PREDict>     atomselection=( &atom_select )
  SELRPN:   1947 atoms have been selected out of   1947
  PREDict>   end
  FCALC: #scatt.= 1947 #anomalous=  0 #special pos.=  0
occupancies=1
  %XFGRCHK error encountered: Grid in x-direction too
coarse (FFT GRID or MAPRes).
    (CNS is in mode: SET ABORT=NORMal END)
  *****************************************************
  ABORT mode will terminate program execution.
  *****************************************************
  Program will stop immediately.

============================================================
            Maximum dynamic memory allocation:
7034000 bytes
            Maximum dynamic memory overhead:
1000 bytes
            Program started at: 11:03:18 on 02-Feb-2004
            Program stopped at: 11:15:28 on 02-Feb-2004
            CPU time used:     361.6100 seconds

============================================================

Any suggestions would be helpful.  I have varied the
grid size from 0.2 to 0.4 with no successs.

Alex


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> %XFGRCHK error encountered: Grid in x-direction too coarse (FFT GRID or
> MAPRes).

the combination of your a-axis length, the resolution and the map grid makes
that cns feels that the grid along x is too coarse. in the refine.inp file
look for the line:

   {===>} grid=0.33;

and change the number 0.33, e.g. to 0.25 (or even smaller if you still get the
same error message)

of course, you don't need to re-run the entire refine.inp job since you
already have the new pdb file. so just run the model_map.inp (and don't forget
to change the number 0.33 there as well !) job instead to just do the map
calculations

--gerard

******************************************************************
                         Gerard J.  Kleywegt
     [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                 Biomedical Centre  Box 596
                 SE-751 24 Uppsala  SWEDEN

     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.
******************************************************************

hi,
i am trying to calculate certain stats about my structures and print
them out in a separate file, not in the main output stream.

i would appreciate if anybody could give a hint how to do that.

thanks!
evgeny.

PhD student
Princeton University

Use STDERR. You can send the STDOUT of "command" to one file ("file1")
and STDERR to another ("file2") with this construct:

( command > file1 ) >& file2

On Feb 2, 2004, at 5:38 PM, Zhenya wrote:

> hi,
> i am trying to calculate certain stats about my structures and print
> them out in a separate file, not in the main output stream.
>
> i would appreciate if anybody could give a hint how to do that.
>
> thanks!
> evgeny.
>
> PhD student
> Princeton University
>
>
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On Tue, 3 Feb 2004, Zhenya wrote:
> i am trying to calculate certain stats about my structures and print
> them out in a separate file, not in the main output stream.
>
> i would appreciate if anybody could give a hint how to do that.

You want something like:

set print_file filename end

and to return to the stdout:

set print_file=OUTPUT end

----
b.smith at bio.gla.ac.uk

also if you need to link this group in a special way different from
peptide links,
you'll need to build a patch residue (topology presidue)
similar to PEPT (in parallhdg.pro) but serving your 'custom' needs

and then when you build up the sequence you will need to specify which
patch to apply when linking in your custom residue.
within your

segment ... chain ... sequence ... end end end
statement

in the case if your new residue is not in the main chain, but is sort
of a side chain modification, then you will need to apply a separate patch

<create a separate segment for the formyl before this patch>
patch <your linking presidue name>
         reference 1 ( <selection statement for your methionine> )
         reference 2 ( <selection statement for formyl group> )
end



evgeny.
--- In cnsbb@yahoogroups.com, "Nuno S.L.S. Ferreira" <nunolf2003@y...>
wrote:
> Hi all
>
> Does anibody have a .top and .par files already built for group formyl?
>
> Never built a residue before. I'm trying to build this residue
> following the cns manual, but I am having some problems about the H
> (which atom type?). And then to assign the proper values to the
> geometric properties involving this H. The C and O are easy (similar
> to C,O of the peptide link).
> Any hints about this?
>
> Kind regards,
> NUno

i think it is not too important how you'd define the formyl proton.
if you look into parallhdg.pro file you will see that almost all
the parameters are the same that's because the older version of charmm
force field is not too fussy about parameters

type H for formyl hydrogen should work

look at how a small residue like GLY is built in parallhdg.pro and
topallhdg.pro
and build the formyl the same way. it should be even simpler since
there's fewer number of atoms.

for the charges, you can ignore them (setting them to 0.0) if you do
not use electrostatic term in the structure caclulations as it is
commonly done in NMR solution structures. or if you really need them,
you could calculate them ab-initio in gaussian.

evgeny.

--- In cnsbb@yahoogroups.com, "Nuno S.L.S. Ferreira" <nunolf2003@y...>
wrote:
> Hi all
>
> Does anibody have a .top and .par files already built for group formyl?
>
> Never built a residue before. I'm trying to build this residue
> following the cns manual, but I am having some problems about the H
> (which atom type?). And then to assign the proper values to the
> geometric properties involving this H. The C and O are easy (similar
> to C,O of the peptide link).
> Any hints about this?
>
> Kind regards,
> NUno

set display=file end works!
thanks for your responses!
evgeny
--- In cnsbb@yahoogroups.com, brian.o.smith@e... wrote:
> On Tue, 3 Feb 2004, Zhenya wrote:
> > i am trying to calculate certain stats about my structures and print
> > them out in a separate file, not in the main output stream.
> >
> > i would appreciate if anybody could give a hint how to do that.
>
> You want something like:
>
> set print_file filename end
>
> and to return to the stdout:
>
> set print_file=OUTPUT end
>
> ----
> b.smith at bio.gla.ac.uk

Dear all,
Hereby i am inviting for the 8th World
Multi-Conference on Systemics, Cybernetics and
Informatics 2004 (SCI-2004) from July 18-21, 2004 at
Orlando, Florida, USA  is organizing special technical
sessions on Nanotechnology on behalf of the my head of
division dr. lalit m bharadwaj. See attached file for
detail of the conference.
With Best regards
rakesh dabas
scientist
BEND, CSIO, Chandigarh
India

________________________________________________________________________
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I've been using NOE distance restraints (based on biochemical data) in CNS
to try and dock an RNA structure onto a protein structure.

I would like to try adding random rotations and translations between
cycles of rigid body docking in an attempt to minimize bias of the initial
RNA starting position. Currently, the program is just trying to bash the
RNA onto the protein. If I move the RNA on the side opposite the binding
site I get very high E(NOE) but the program seems to converge and
terminate with this high energy without doing much rot or trans. It won't
push the RNA onto the proper side of the protein. If anyone has an idea of
how to do this, I'd love some input. Also, if anyone knows of a program
that would be better suited for this, let me know.

Thanks.

-------------------------------------------------------------------------------
Paul Paukstelis
Institute for Cellular and Molecular Biology
University of Texas at Austin
(512) 471-4778
paul@...

Sorry folks, I figured out how to do this, minus one little thing. How do
I call random numbers in CNS?

On Fri, 6 Feb 2004, Paul Paukstelis wrote:

> I've been using NOE distance restraints (based on biochemical data) in CNS
> to try and dock an RNA structure onto a protein structure.
>
> I would like to try adding random rotations and translations between
> cycles of rigid body docking in an attempt to minimize bias of the initial
> RNA starting position. Currently, the program is just trying to bash the
> RNA onto the protein. If I move the RNA on the side opposite the binding
> site I get very high E(NOE) but the program seems to converge and
> terminate with this high energy without doing much rot or trans. It won't
> push the RNA onto the proper side of the protein. If anyone has an idea of
> how to do this, I'd love some input. Also, if anyone knows of a program
> that would be better suited for this, let me know.
>
> Thanks.
>
>
-------------------------------------------------------------------------------
> Paul Paukstelis
> Institute for Cellular and Molecular Biology
> University of Texas at Austin
> (512) 471-4778
> paul@...
>
>
>
> --------------------------------------------------------
> List information at http://groups.yahoo.com/group/cnsbb.
> Posting is only allowed for members of this list.
>
>
> Yahoo! Groups Links
>
>
>
>
>
>

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either way would work, but i think presidue is more
economical in terms of typing(in addition you might
need to define some parameters for the formyl; xplor
will stop executing if any parameters are missing upon
first call to energy calculation and tell about it in
the output, so you can just determine which parameters
are still needed from the output and then plug them
in)

you can construct a presidue
and then apply a patch with it onto the otherwise
assembled molecule

for example you can take PEPT presidue defined in
toppar/topallhdg.pro as a starting point and make the
formyl out of it (you will need some 'add atom' 'add
bond' and 'add angle' statements to add formyl's atoms
and remove some angles that dont apply to the formyl (
also ic statements are not needed and you won't need
+/- signs by the atom symbols).it may be convinient if
you do it in a separate file for example mylib.inp
and then include it with @mylib.inp in your main file

then after assembing the rest of the peptide use

patch FORM
       reference=nil=(segidentifier PEP and residue N)
end

nil is used because you only use one piece as the
patching point (i.e. your peptide segment PEP)
for the same reason you dont need +/- signs in the
presidue definition. + and - signs are used in linear
chain construction to understand which residue is
upsetream/downstream. in some special case you might
need to connect more then two residues by a single
patch, then other single character symbols can be used
to refer to different residues

for example:
topology
presidue FERR
     add atom 1FE type=FE charge=0.0 end
     add bond 1Fe 1O
     add bond 1Fe 2O
     ...
     add bond 1Fe 6O
     add angle ...
     add improper ...
end

patch FERR
     reference=1=(<residue with O1>
     ...
     reference=6=(<residue with O6>)
end

end

would insert iron and bind six residues to it throug
their oxygens

or

construct a residue
then include it in the
segment
      chain
      end
end
statement

i think you would still need a separate presidue to
attach the formyl to the chain because PEPT presidue
used for linking the aminoacids might not work here as
it will try to create the angle
(N(term)-C(formyl)-CA(formyl)) and should fail because
formyl does not have the CA atom, it has H there

so this method would take more typing then just
presidue and patch combination

--- "Nuno S.L.S. Ferreira" <nunolf2003@...>
wrote:
> --- In cnsbb@yahoogroups.com, "Zhenya" <fadeev@r...>
> wrote:
> > also if you need to link this group in a special
> way different from
> > peptide links,
> > you'll need to build a patch residue (topology
> presidue)
> > similar to PEPT (in parallhdg.pro) but serving
> your 'custom' needs
> >
>
> So if I understood correctly I'm going to build a
> residue, and not a
> patchRES.
> Formyl is going to be attached to the N of the
> Nterminal MET residue.
>
>  O=C-->
>    |
>    H
>
> Thanks evgeny
>
> Kind regards
> NUno
>
>


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to get random number use

evaluate ($a=random())

that will set $a to a number within (0;1) interval

you can also use

set seed=$n end

to use a different random seed

evgeny.


--- In cnsbb@yahoogroups.com, Paul Paukstelis <paul@i...> wrote:
> Sorry folks, I figured out how to do this, minus one little thing.
How do
> I call random numbers in CNS?
>
> On Fri, 6 Feb 2004, Paul Paukstelis wrote:
>
> > I've been using NOE distance restraints (based on biochemical
data) in CNS
> > to try and dock an RNA structure onto a protein structure.
> >
> > I would like to try adding random rotations and translations between
> > cycles of rigid body docking in an attempt to minimize bias of the
initial
> > RNA starting position. Currently, the program is just trying to
bash the
> > RNA onto the protein. If I move the RNA on the side opposite the
binding
> > site I get very high E(NOE) but the program seems to converge and
> > terminate with this high energy without doing much rot or trans.
It won't
> > push the RNA onto the proper side of the protein. If anyone has an
idea of
> > how to do this, I'd love some input. Also, if anyone knows of a
program
> > that would be better suited for this, let me know.
> >
> > Thanks.
> >
> >
-------------------------------------------------------------------------------
> > Paul Paukstelis
> > Institute for Cellular and Molecular Biology
> > University of Texas at Austin
> > (512) 471-4778
> > paul@i...
> >
> >
> >
> > --------------------------------------------------------
> > List information at http://groups.yahoo.com/group/cnsbb.
> > Posting is only allowed for members of this list.
> >
> >
> > Yahoo! Groups Links
> >
> >
> >
> >
> >
> >

Hi,
i just have a small question about the use of
<R-3> noe distance averaging option.

i understand that this option calculates
the distance between a proton and another *one* that
is jumping through several sites a lot faster then overall tumbling.
(i emphasised *one* because that follows from description of analogous
<R-6> option in the manual
http://atb.slac.stanford.edu/xplor/manual/node358.html#noeaveraging
)

now if i have a methyl group that is rotating through its three
minimum energy sites i have three such protons. should i therefore use
scaled distance restraint

d_scaled = d_raw * N^(-1/6), with N=3 for the three methyl protons.

where d_raw = (cal_const/Intensity)^(-1/6)
(or in other words use scaled noe signal to get a contribution from an
individual 'jumping' atom)

or XPLOR does that scaling automatically and i could just use "d_raw"
for the distance restraint?

Thank you.
Evgeny.

There are still positions available, especially for Experimenters.

If some who applied as Observers would like to apply also as
Experimenters, please do so, and we'll try to find the best place for you
in the course.

=========================================================================

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The course will be held 25-30 April 2004.  Students could be at any level
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and find the application materials there.  The application deadline is 18
Feb 2004.

For the second time we will hold a short lecture course on the
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Dear PX beamline users,

Here at APS, as most probably at other synchrotrons as well, attempts
will be made to standardize the user software for beamline control and
data collection.

Standardization of low level software is difficult due to vastly
different hardware at different beamlines and it is not the priority at
this point. Instead, effort will be made to make top level software be
user-friendly and as much standardized as possible.

We would appreciate if user community could assist us by indicating
their favorite software package which should serve as a base for this
effort. Please reply by sending a one line message, stating the

Name of the software  Beamline Synchrotron

Thank you for your contribution,
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Hi everybody,

  I need to use the cross-validation method to evaluate the degree of
conformational variability of my structures and I am trying to use the script
".inp" from CNS_solve. Has anybody done this before? Is there any sequence of
events to be followed?
Thank you very much!

Lenize
--
Lenize Fernandes Maia, Ph.D.
Centro Nacional de Ressonancia Magnetica Nuclear - CNRMN
Universidade Federal do Rio de Janeiro
http://cnrmn.bioqmed.ufrj.br
Phone/FAX  +5521-2562-6756
lenize@...

hi, all,
I am refining a structure whose lattice packing is very tight. Automatic water
picking run in CNS yielded waters around one molecule but also many around
adjacent symmetry-related molecule. Although they are not redundant, the latter
part make visual inspection very tough. The problem is that how can I distribute
them on surface of only one molecule in a layer, say thickness of 4.0 angstrom.

Thanks a lot!

Yadong Yu
Ph.D student
Institute of Biochemistry and Cell Biology, Shanghai Institute for Life
Sciences, CAS
Room 144, Shanghai Institute of Biochemistry
320 Yue-Yang Road
Shanghai, 200031
P.R. China

> I am refining a structure whose lattice packing is very tight. Automatic
> water picking run in CNS yielded waters around one molecule but also many
> around adjacent symmetry-related molecule. Although they are not redundant,
> the latter part make visual inspection very tough. The problem is that how
> can I distribute them on surface of only one molecule in a layer, say
> thickness of 4.0 angstrom.

if you run what_check you will find that this is one of the tests
it carries out. it will identify such waters and provide you with
the new coordinates. you can get what_check from:

   http://www.cmbi.kun.nl/gv/whatcheck/

--gerard

******************************************************************
                         Gerard J.  Kleywegt
     [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                 Biomedical Centre  Box 596
                 SE-751 24 Uppsala  SWEDEN

     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.
******************************************************************

Has anybody tried this in Xplor? I am documenting Xplor-NIh and I
would like to add an example like this to the standard examples.

Sincerely,
Kirsten Frank

Dear structural(-ly interested) biologist !

HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and
now contains information on 4,669 (up from 4,511) hetero-entities that have
been taken from the PDB (see http://xray.bmc.uu.se/hicup/release.html for
details).

HIC-Up is also available for local mirroring (follow the instructions in
http://xray.bmc.uu.se/hicup/mirror.html). You can also download a single PDB
file (ftp://xray.bmc.uu.se/pub/gerard/extras/hetero/hetero.pdb) that contains
coordinates for all the compounds.

The URL for HIC-Up is:                http://xray.bmc.uu.se/hicup

The following changes and improvements have been implemented compared to the
previous release (7.3):

1. For every hetero-compound that occurs at least once in any entry in EDS
(the Uppsala Electron Density Server), a separate page is generated with
statistics concerning the real-space R-values (RSR), real-space correlation
coefficients (RSCC), and occupancy-weighted average B-factors (OWAB) for that
compound in a number of resolution shells. The average and standard deviation
of these statistics are listed as well as the minimum and maximum observed
values in each resolution shell, with pointers back to EDS.
   This information can be used, e.g.:
   - to select the copy of the compound that lies in the highest resolution
     shell, but in addition has the lowest RSR or OWAB, or the highest RSCC
   - to locate examples of good and poor fit to the density for that compound at
     a given resolution (e.g., to decide if a density feature can reasonably be
     interpreted as being due to the compound in question)
   - to assess whether a certain observed RSR, RSCC or OWAB value for that
     compound in a certain structure is reasonable for the given resolution
   Of course, many compounds only occur in one or two PDB entries, so the
statistics are not much use, but as the PDB grows (and structure factors
continue to be deposited) this facility will become more and more useful. At
the moment, statistics for all resolution shells are available for the
following compounds: ACT ADP FAD FS4 GLC GNP GOL HEC HEM MAN MES MSE NAD NAG
NDP NH2 PCA PO4 SAH SO4 TRS CA CD CL CO FE HG MG MN NA ZN K

2. The TNT dictionaries for every compound have been improved. They now
contain BCORREL restraints, and problems with the CHIRAL restraints have been
fixed

3. For every entry, there is now a link to Google to search on the (first)
name of the compound

4. For every entry, there is now a link to the Ligand Depot at RCSB

5. For every entry, there is now a link to KEGG-LIGAND to search on the
(first) name of the compound

6. If there are more than 15 PDB entries that contain a certain compound, the
summary at the top of the page will contain a link to the PDB that will
produce an up-to-date listing of all those entries

7. The LIGPLOT figures are back

8. The problems with the generation of the connection tables and listings of
super-structures have been fixed

9. All links related to EDS now point to the new (definitive) home of the EDS
server (http://eds.bmc.uu.se/)

10. The compound pages are now rendered in spring-green :-)

--dvd

******************************************************************
                         Gerard J.  Kleywegt
     [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                 Biomedical Centre  Box 596
                 SE-751 24 Uppsala  SWEDEN

     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.
******************************************************************

Hi all

I've read in the Xplor-NIH homepage (did not knew this soft, till
yesterday; ups, not doing my everyday search :), that:

"CNS is no longer under development, and its NMR facilities are dated.
Use Xplor-NIH for NMR structure determination". They also say that CNS
X-ray facilities are more up-to-date.

Well, I'm just starting the process of determining the "structure" of
a small peptide (26 aa), with restraints coming from NMR. BTW, thanks
Evgeny, formyl-MET is done.

I was preparing myself for this challenge under CNS, but now I'm a bit
confused. Took already a look at the *inp files of Xplor-NIH, and they
are "similar" to CNS.

Can somebody comment this, cause I really want to start, but, with the
right pack.

Thanks.
Regards,

NUno

Hello all-

This might be a very FAQ!

Is there a way to refine over-oxidized cysteines in CNS?

Any help is appreciated.

Thanks,
Sarma.

--------------------------------------------------------------
Ganapathy Sarma
Department of Biochemistry and Biophysics,
2011 ALS, Oregon State University,
Corvallis, OR 97331. USA.
Tel. no. : 541-737-3196
--------------------------------------------------------------

-----Message d'origine-----
De : Nuno S.L.S. Ferreira [mailto:nunolf2003@...]
Envoyé : vendredi 20 février 2004 21:36
À : cnsbb@yahoogroups.com
Objet : [cnsbb] Which one? CNS or Xplor-NIH

Hi all

I've read in the Xplor-NIH homepage (did not knew this soft, till
yesterday; ups, not doing my everyday search :), that:

"CNS is no longer under development, and its NMR facilities are dated.
Use Xplor-NIH for NMR structure determination". They also say that CNS
X-ray facilities are more up-to-date.

Well, I'm just starting the process of determining the "structure" of
a small peptide (26 aa), with restraints coming from NMR. BTW, thanks
Evgeny, formyl-MET is done.

I was preparing myself for this challenge under CNS, but now I'm a bit
confused. Took already a look at the *inp files of Xplor-NIH, and they
are "similar" to CNS.

Can somebody comment this, cause I really want to start, but, with the
right pack.

Thanks.
Regards,

NUno





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> Is there a way to refine over-oxidized cysteines in CNS?

i assume you mean things like S-hydroxycysteine
(http://xray.bmc.uu.se/hicup/CSO) etc. ?

you can either define them as new residue types, or (probably
easier) apply a patch to add the oxygen(s)

--gerard

******************************************************************
                         Gerard J.  Kleywegt
     [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                 Biomedical Centre  Box 596
                 SE-751 24 Uppsala  SWEDEN

     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.
******************************************************************

Hi guys,

although the torsion angle dynamics protocols for both Xplor-NIH and CNS
are the same (the original TAD/Cartesian Stein, Rice and Brunger
protocol), a major advantage for Xplor-NIH is the Internal Variable
Dynamics module (quite similar to the TAD engine in DYANA/CYANA).  This
simulated annealing protocol is quite efficient, and most importantly
allows one to "fix" the tetra-atomic coordinate system for RDCs such
that no distortion of its tetrahedral geometry occurs.  Xplor-NIH is
very well maintained and updated, including the most recent database
potentials for Ca Cb shift refinement and ramachandran potential terms.
I find it very easy to modify both input and output in Xplor-NIH as
modifications can all be made in the annealing script without having to
dive into modules.  Hope this helps.

All the best,

Haydyn


On Mon, 2004-02-23 at 19:34, florent.barbault wrote:
> Hi all
>
> Personally I tried XPLOR-NIH and CNS for NMR structure determination. There
> is no real difference for me. In fact, it is the same Torsion Angle
> Molecular Dynamics for simulated annealing and, in my opinion, all
> restraints options are identical. To be sure, I did a structure elucidation
> of a DNA with Xplor-NIH and also with CNS using classical nmr data (noe,
> dihedral and planarity restraints). The structure was identical (of course)
> and the convergence rate too. Finally I choosed CNS for two reasons : the
> parameters for DNA/RNA are better defined in CNS and I like its html
> interface.
> Regards
> Florent
> --------------------------------------------------------------------
> Dr Florent Barbault
> Maitre de conférence Université Paris7
> ITODYS (Interface Traitement Organisation et DYnamique des Systèmes)
> 1 rue Guy de la Brosse
> 75005 Paris
> tel  : 01 44 27 68 21

--
--
--------------------
Haydyn Mertens
PhD student
Dept. Biochemistry
University of Melbourne
Victoria
Australia, 3010
--------------------

Hi guys,

although the torsion angle dynamics protocols for both Xplor-NIH and CNS
are the same (the original TAD/Cartesian Stein, Rice and Brunger
protocol), a major advantage for Xplor-NIH is the Internal Variable
Dynamics module (quite similar to the TAD engine in DYANA/CYANA).  This
simulated annealing protocol is quite efficient, and most importantly
allows one to "fix" the tetra-atomic coordinate system for RDCs such
that no distortion of its tetrahedral geometry occurs.  Xplor-NIH is
very well maintained and updated, including the most recent database
potentials for Ca Cb shift refinement and ramachandran potential terms.
I find it very easy to modify both input and output in Xplor-NIH as
modifications can all be made in the annealing script without having to
dive into modules.  Hope this helps.

All the best,

Haydyn   


On Mon, 2004-02-23 at 19:34, florent.barbault wrote:
> Hi all
>
> Personally I tried XPLOR-NIH and CNS for NMR structure determination. There
> is no real difference for me. In fact, it is the same Torsion Angle
> Molecular Dynamics for simulated annealing and, in my opinion, all
> restraints options are identical. To be sure, I did a structure elucidation
> of a DNA with Xplor-NIH and also with CNS using classical nmr data (noe,
> dihedral and planarity restraints). The structure was identical (of course)
> and the convergence rate too. Finally I choosed CNS for two reasons : the
> parameters for DNA/RNA are better defined in CNS and I like its html
> interface.
> Regards
> Florent
> --------------------------------------------------------------------
> Dr Florent Barbault
> Maitre de conférence Université Paris7
> ITODYS (Interface Traitement Organisation et DYnamique des Systèmes)
> 1 rue Guy de la Brosse
> 75005 Paris
> tel  : 01 44 27 68 21

--
--
--------------------
Haydyn Mertens
PhD student
Dept. Biochemistry
University of Melbourne
Victoria
Australia, 3010
--------------------



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On 15 March there will be a workshop to discuss the possibilities for a
new synchrotron radiation source at Brookhaven National Laboratory.  This
is the same workshop that was scheduled then postponed for last December.

There will be a description of the proposed source and its capabilities
for various disciplines, discussion of possibilities for funding, and
finally open discussion about facilities.  It will be VERY USEFUL for you
to attend, please, to begin to talk about the sort of facilites we'd like,
and to show support for the concept.  Your attendance will be a strong
message to the funding agencies.

To register, visit http://www.nsls2.bnl.gov -->

http://www.nsls2.bnl.gov/newsroom/workshops/2003/NSLS-II/ -->

http://www.nsls2.bnl.gov/newsroom/workshops/2003/NSLS-II/registration/register.a\
sp


Here is more information, taken from the web site:

Description

NSLS-II is a proposed new state-of-the-art, medium-energy storage ring
designed to deliver world-leading brightness and flux with top-off
operation for constant output. The superlative character and combination
of capabilities will have profound impact on a wide range of scientific
disciplines and initiatives in the coming decades.

Who Should Attend

All members of the scientific community, including participants from
universities, other research institutions, and commercial, governmental
and industrial organizations, who wish to provide input and feedback on
the design and direction of NSLS-II, its beamlines and instrumentation.
Workshop Program

     * Overview of NSLS-II
     * Perspectives by representatives from DOE, New York State, and BNL.
     * Keynote address by Congressman Sherwood Boehlert, Chairman, House
Science Committee.
     * Plenary lectures by Professor Roderick MacKinnon, Rockefeller
University, and a distinguished nanoscience researcher
     * Breakout sessions featuring presentations on science and
instrumentation as well as open discussion. These will provide
participants an opportunity for input and feedback on NSLS-II design
features, beamline characteristics, and instrumentation concepts.
     * An evening poster session and dinner will conclude the workshop.

For Additional Information

Phone: 631-344-2297
Email: nslsinfo@...

=========================================================================
	 Robert M. Sweet 	 E-Dress: sweet@...
	 Biology Dept. 				 ^ (that's L
	 Brookhaven Nat'l Lab.  Phones: 	     not 1)
	 Upton, NY  11973  631 344 3401  (Office)
	 U.S.A. 		 631 344 2741  (Facsimile)
=========================================================================

On the CNS web site (http://cns.csb.yale.edu/v1.1/), they have a
poorly detailed "syntax manual". Under which there is a description
of:

topology <topology-statement> end Residue and patch topology database

in particular:

donor [<reference>]<atom> [<reference>]<atom>
    Define a hydrogen bond donor. Hydrogen atom followed by connected
heavy atom.
acceptor [<reference>]<atom> [<reference>]<atom>|none
    Define a hydrogen bond acceptor. Bond acceptor followed by
optional connected heavy atom.

Does anyone have any experience using the "donor" and "acceptor"
definitions in their dictionary files? If so, could you please
include an example of how one would use them in a minimization of a
protein ligand complex?