PDBe launches its redesigned website (pdbe.org)
-----------------------------------------------

The Protein Data Bank in Europe (PDBe; http://pdbe.org) has launched its
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Hi, I have the some problem about creating two DNA sequence.
I want to generate the sequece of DNA duplex. And then create the extended
structure. Finally use anneal.inp which contains NOE restraints to stimulate the
structure. But I got the residue numbering problem of the second strand.

Here is the generate_seq.inp contents:
{* nucleic acid sequence file *}
{===>} nucl_sequence_infile_1="nr_a.seq";
{* segid *}
{===>} nucl_segid_1="A";
{* start residue numbering at *}
{===>} renumber_1=1;

{* nucleic acid sequence file *}
{===>} nucl_sequence_infile_2="nr_b.seq";
{* segid *}
{===>} nucl_segid_2="B";
{* start residue numbering at *}
{===>} renumber_2=13;

The second strand still start from 1

I also try generate_easy.inp to create mtf and pdb files by following the
protocol on the CNS website. And then use anneal.inp to anneal the structure.
But I got error like these:

  %NOESET-ERR: error in selection - no atoms spec.
  %NOE-ERR: problem at     1  -999.000  -999.000
  %NOESET-ERR: error in selection - no atoms spec.
  %NOE-ERR: problem at     2  -999.000  -999.000

My CNS version is 1.2
Can anyone give me some advice?
Thank you!!

My email: magic2313@...

Why don't you try generating duplex DNA in coot and then reading it into
CNS?

On Tue, 2010-07-06 at 06:03 +0000, æ„›å¿ƒé ­ wrote:
>
> Hi, I have the some problem about creating two DNA sequence.
> I want to generate the sequece of DNA duplex. And then create the
> extended structure. Finally use anneal.inp which contains NOE
> restraints to stimulate the structure. But I got the residue numbering
> problem of the second strand.
>
> Here is the generate_seq.inp contents:
> {* nucleic acid sequence file *}
> {===>} nucl_sequence_infile_1="nr_a.seq";
> {* segid *}
> {===>} nucl_segid_1="A";
> {* start residue numbering at *}
> {===>} renumber_1=1;
>
> {* nucleic acid sequence file *}
> {===>} nucl_sequence_infile_2="nr_b.seq";
> {* segid *}
> {===>} nucl_segid_2="B";
> {* start residue numbering at *}
> {===>} renumber_2=13;
>
> The second strand still start from 1
>
> I also try generate_easy.inp to create mtf and pdb files by following
> the protocol on the CNS website. And then use anneal.inp to anneal the
> structure. But I got error like these:
>
> %NOESET-ERR: error in selection - no atoms spec.
> %NOE-ERR: problem at 1 -999.000 -999.000
> %NOESET-ERR: error in selection - no atoms spec.
> %NOE-ERR: problem at 2 -999.000 -999.000
>
> My CNS version is 1.2
> Can anyone give me some advice?
> Thank you!!
>
> My email: magic2313@...
>
>
>
>
>

--
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,
I suspect that something went wrong when you generated files for cns.
You could check your pdb and mtf files in a text editor. I find it
easier to keep full control over chain id, residue id and segment id.
Besides, I would also recommend what Ed suggested: Create DNA
coordinates externally in coot (or make-na server) and then run
generate_easy to set it up for cns.

Remember that you need the 3-letter notation for DNA/RNA in cns. It
comes with a script for conversion: 'fix_dna_rna < nucleic.pdb >
nucleic_fix.pdb'. Furthermore, you need "'" instead of "*" for ribose
atoms and the base methyl of thymine is C5A instead of C5M or C7.

Cheers,
christian



Ed Pozharski wrote:
>
>
> Why don't you try generating duplex DNA in coot and then reading it into
> CNS?
>
> On Tue, 2010-07-06 at 06:03 +0000, æ„›å¿ƒé ­ wrote:
>>
>> Hi, I have the some problem about creating two DNA sequence.
>> I want to generate the sequece of DNA duplex. And then create the
>> extended structure. Finally use anneal.inp which contains NOE
>> restraints to stimulate the structure. But I got the residue numbering
>> problem of the second strand.
>>
>> Here is the generate_seq.inp contents:
>> {* nucleic acid sequence file *}
>> {===>} nucl_sequence_infile_1="nr_a.seq";
>> {* segid *}
>> {===>} nucl_segid_1="A";
>> {* start residue numbering at *}
>> {===>} renumber_1=1;
>>
>> {* nucleic acid sequence file *}
>> {===>} nucl_sequence_infile_2="nr_b.seq";
>> {* segid *}
>> {===>} nucl_segid_2="B";
>> {* start residue numbering at *}
>> {===>} renumber_2=13;
>>
>> The second strand still start from 1
>>
>> I also try generate_easy.inp to create mtf and pdb files by following
>> the protocol on the CNS website. And then use anneal.inp to anneal the
>> structure. But I got error like these:
>>
>> %NOESET-ERR: error in selection - no atoms spec.
>> %NOE-ERR: problem at 1 -999.000 -999.000
>> %NOESET-ERR: error in selection - no atoms spec.
>> %NOE-ERR: problem at 2 -999.000 -999.000
>>
>> My CNS version is 1.2
>> Can anyone give me some advice?
>> Thank you!!
>>
>> My email: magic2313@... <mailto:magic2313%40hotmail.com>
>>
>>
>>
>>
>>
>
> --
> 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 /
>
>


_______________________________________________________________________

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
_______________________________________________________________________

I am using Red hat Linux 5 and Fedora. I am trying to install CNS since last one
year. My problem is I am trying "cns_solve_1.21". But can't proceed at all. I am
new to Linux. So kindly please tell me all the procedures to install it. Please
anybody !!!!

Thanking you in advance,
Rajabrata

Traditionally, the Protein Data Bank (PDB) has been accessed mostly by PDB
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--Gerard

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

Hi,
You may try the CCPN FormatConverter.
-mandar

On 2010 July 9 Friday 06:16:13 Krisztina Varga wrote:
> Hi,
>
> I would like to use CNS for structural calculations, and I am very much a
> novice. I have problem getting my files (NMR assignments) in the right
> format for CNS. I have my peak list from Sparky in this format, and I would
> like to make a  CACB and proton chemical shift list.
>
> This
> Group   Atom  Nuc    Shift   SDev  Assignments
>
>
>    A26     CA  13C   52.237  0.019      4
>    A26     CB  13C   20.311  0.025      4
>    A26     CO  13C  176.999  0.029      3
>    A26      H   1H    8.594  0.007     12
>    A26     HA   1H    4.515  0.004      2
>    A26     HB   1H    1.411  0.006      2
>    A26      N  15N  124.243  0.038     12
>   M27     CA  13C   55.943  0.045      3
>   M27     CB  13C   33.133  0.037      4
>   M27     CG  13C   32.165  0.000      1
>   M27     CO  13C  176.382  0.003      3
>   M27      H   1H    8.443  0.003     16
>   M27     HA   1H    4.456  0.009      3
>   M27    HB2   1H    2.053  0.003      4
>   M27    HG2   1H    2.607  0.000      1
>   M27      N  15N  120.186  0.013     16
>
> How do I get it to this format? (as copied from the example
> trx_shift_c35a.tbl in CNS)
>
>  !!    v2
>  assign (resid  1  and name c ) (resid  2  and name n )
>         (resid  2  and name ca) (resid  2  and name c )
>         (resid  3  and name n )                           61.15 32.86
>   !!    k3
>  assign (resid  2  and name c ) (resid  3  and name n )
>         (resid  3  and name ca) (resid  3  and name c )
>         (resid  4  and name n )                           55.75 33.94
>   !!    q4
>  assign (resid  3  and name c ) (resid  4  and name n )
>         (resid  4  and name ca) (resid  4  and name c )
>         (resid  5  and name n )                           54.94 29.12
>   !!    i5
>
>
> Does anybody have a suggestion?
>
> thank you,
>
> Kris

If you were born before the Dutch lost their first World Cup final, you may
remember the days when "everybody" knew that PDB entry 1tim was the structure
of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was hen
egg-white lysozyme, etc. Unfortunately, life for a structural biologist is not
that simple any longer. Nevertheless, occasionally it would be very handy to
get at-a-glance information about some of the crucial details of a PDB entry
or a list of entries.

When the Protein Data Bank in Europe (PDBe; pdbe.org) launched its redesigned
website recently, we also introduced PDBlogos and PDBprints. PDBlogos are
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(e.g., the experimental technique, the source organism of the sample, or the
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PDBprints are used in a number of places already, e.g.:

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- at the top of EDS summary pages (e.g.:
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A number of other (structural) bioinformatics resources are also considering
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For a five-minute illustrated introduction to PDBprints (including
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to:

                   http://pdbe.org/pdbprints

We hope that you will find PDBprints useful and we value your feedback.


--Gerard

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

We are pleased to announce the 2010 Cryo-EM Modeling challenge and a PSB 2011
workshop, organized by Steven Ludtke, Wah Chiu, Helen Berman and Gerard
Kleywegt.

                     http://ncmi.bcm.edu/challenge

     * Modeling as a tool for interpretation of cryo-EM reconstructions *

Cryo-EM single particle analysis is a method for determining structures of
large molecules and macromolecular assemblies at resolutions ranging from 3.5
- 30 A. Interpreting the density maps produced by this technique represents an
ongoing challenge, for which molecular modeling techniques offer some unique
solutions.

Over the last five years, cryo-EM single particle analysis has begun producing
structures at resolutions better than 5 A, with subnanometer resolutions
becoming common. At resolutions between 5 and 9 A it becomes possible to move
beyond simple rigid-body docking and alter atomistic models to reposition
helices and sheets, to better fit the cryo-EM based density maps. At 3-5 A
resolution de-novo C-alpha traces and in some cases full atomistic models can
be constructed directly from the cyro-EM density without invoking x-ray
crystallography.

We call this a challenge rather than a contest because, unlike CASP, there is
no hidden answer to be revealed. In this project, we provide publicly
available cryo-EM densities for a selected set of structures at different
resolutions, and challenge those in the modeling community to apply their
tools to extract as much information as they can from each. At the end, the
results will be evaluated by comparing the results of different groups, and
validating against any other existing knowledge about each target. We hope
this will yield new insights into these published structures, and at the very
least, it will establish the capabilities of current modeling methods, and
give the cryo-EM community some guidance as to how to proceed with maps in
various resolution ranges. For modelers it provides a new area in which to
apply/develop their techniques, and demonstrating your tools' capabilities may
lead to new opportunities for collaboration.

Please see the challenge website for more details.

Dear all,

	 we are refining a structure that contains several crystal contacts
formed by metal ions that bridge the molecule in the assymmetric unit to
crystallographic symmetry mates. To improve refinement we want to
restrain the corresponding bonds, angles, etc. Does anyone know if and
if so how such patches including symmetry related protein molecules can
be applied in cns (v.1.2)?

	 Any help is appreciated.

	 Thank you very much !

	 Best, Manuel
--
**************************************************************************
PD Dr. Manuel E. Than

Protein Crystallography Group
Leibniz Institute for Age Research -
Fritz Lipmann Institute (FLI)
Beutenbergstraße 11
D-07745 Jena
Germany

Tel.: ++49 3641 65 6170
Fax.: ++49 3641 65 6335

e-mail: than@...
http://www.fli-leibniz.de/groups/than.php

You should take a look at igroup statement.  Search for "symmetry
operation" here

http://cns.csb.yale.edu/v1.2/faq/frame.html

Some information there may lead you to a solution.  I understand that
only vdw and elec terms are active for the symmetry mate interaction (as
pele and pvdw energy flags).  You want essentially covalent bonds made
by symmetry - perhaps they are implemented by default as Boaz suggested,
but manual doesn't say that.  But perhaps I am missing something.

There are few workarounds though.  You can drop the symmetry lower and
then impose strict ncs - it's not perfect but as you are lowering the
resolution, but it will work.  Another trick may be to split the metal
coordinating residues into two conformers, move one to the
symmetry-related position, impose strict NCS between them to keep them
identical, eliminate peptide bond restraints to flanking residues, and
then impose distance restraints to the metal ion.  Messy, but may work.



On Mon, 2010-07-19 at 15:21 +0200, Manuel Than wrote:
> Dear all,
>
>  we are refining a structure that contains several crystal contacts
> formed by metal ions that bridge the molecule in the assymmetric unit to
> crystallographic symmetry mates. To improve refinement we want to
> restrain the corresponding bonds, angles, etc. Does anyone know if and
> if so how such patches including symmetry related protein molecules can
> be applied in cns (v.1.2)?
>
>  Any help is appreciated.
>
>  Thank you very much !
>
>  Best, Manuel

--
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 /

Introducing one-click access to PDB data at PDBe
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For the following, first throw your browser at: http://pdbe.org/

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

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

There is an EMBL Interdisciplinary Post-doc ("EIPOD") position available to
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--Gerard

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

As part of the recent Midsummer Make-over of the Protein Data Bank in Europe
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--Gerard

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

As part of the recent Midsummer Make-over of the Protein Data Bank in Europe
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gerard@... ..................... pdbe.org
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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard@... ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin@...

Grouped B-factor refinement doesn't work well because it is unrestrained
in nature and allows for discontinuites in B-factors of covalently
bonded atoms.  Just avoid it and you will be fine.  Properly restrained
individual B-factor refinement works better (at all resolutions).

On Wed, 2010-08-11 at 17:19 -0400, Rongjin Guan wrote:
>
>
>
> Dear CNS users,
>
> I am refining a 3.1 A structure (from Molecular Replacement) with CNS
> 1.3, and after
> rigid-body and annealing, I wanted to do group B refinement first.
>
> When I tried to do group b-factor refinement, I got very strange B
> factors:
>  Atom type          Number  Average B  Maximum B  Average Q
>  Protein main chain   9044    103.607    539.300      1.000
>  Protein side chain   6762    113.419    463.420      1.000
>
> then I tried individual B factor refinement, which gave very
> reasonable B factors:
>  Atom type          Number  Average B  Maximum B  Average Q
>  Protein main chain   9044     89.426    120.750      1.000
>  Protein side chain   6762     87.788    120.880      1.000
>
> This is my first time encountering such strange phenomenon. Can anyone
> give me some
> hints what caused this problem?
>
> Thanks
>
> Rongjin Guan
>
> PS: below is part of the bgroup.pdb:
>
> ATOM   5790  C   LYS C 169      22.830  39.494  -5.364  1.00142.68
> C
> ATOM   5791  O   LYS C 169      22.114  38.919  -4.547  1.00142.68
> C
> ATOM   5792  N   THR C 170      23.126  40.788  -5.284  1.00 88.73
> C
> ATOM   5793  CA  THR C 170      22.550  41.691  -4.299  1.00 88.73
> C
> ATOM   5794  CB  THR C 170      23.485  41.792  -3.092  1.00 82.04
> C
> ATOM   5795  OG1 THR C 170      24.838  41.844  -3.546  1.00 82.04
> C
> ATOM   5796  CG2 THR C 170      23.372  40.558  -2.273  1.00 82.04
> C
> ATOM   5797  C   THR C 170      22.298  43.058  -5.014  1.00 88.73
> C
> ATOM   5798  O   THR C 170      22.525  44.152  -4.481  1.00 88.73
> C
> ATOM   5799  N   GLY C 171      21.822  42.952  -6.256  1.00135.54
> C
> ATOM   5800  CA  GLY C 171      21.671  44.075  -7.189  1.00135.54
> C
> ATOM   5801  C   GLY C 171      21.535  43.644  -8.673  1.00135.54
> C
> ATOM   5802  O   GLY C 171      22.110  44.268  -9.583  1.00135.54
> C
> ATOM   5803  N   LEU C 172      20.741  42.588  -8.894  1.00539.30
> C
> ATOM   5804  CA  LEU C 172      20.656  41.836 -10.170  1.00539.30
> C
> ATOM   5805  CB  LEU C 172      20.702  40.303  -9.904  1.00281.84
> C
> ATOM   5806  CG  LEU C 172      20.760  39.337 -11.122  1.00281.84
> C
> ATOM   5807  CD1 LEU C 172      21.886  38.257 -11.029  1.00281.84
> C
> ATOM   5808  CD2 LEU C 172      19.381  38.715 -11.488  1.00281.84
> C
> ATOM   5809  C   LEU C 172      19.430  42.158 -11.086  1.00539.30
> C
> ATOM   5810  O   LEU C 172      19.492  42.001 -12.320  1.00539.30
> C
> ATOM   5811  N   ILE C 173      18.304  42.542 -10.479  1.00352.48
> C
> ATOM   5812  CA  ILE C 173      17.210  43.145 -11.233  1.00352.48
> C
> ATOM   5813  CB  ILE C 173      15.805  42.684 -10.729  1.00273.67
> C
> ATOM   5814  CG2 ILE C 173      14.688  43.325 -11.547  1.00273.67
> C
> ATOM   5815  CG1 ILE C 173      15.664  41.151 -10.811  1.00273.67
> C
> ATOM   5816  CD1 ILE C 173      16.573  40.336  -9.870  1.00273.67
> C
> ATOM   5817  C   ILE C 173      17.484  44.643 -11.069  1.00352.48
> C
> ATOM   5818  O   ILE C 173      16.850  45.493 -11.703  1.00352.48
> C
> ATOM   5819  N   ASP C 174      18.470  44.936 -10.211  1.00135.52
> C
> ATOM   5820  CA  ASP C 174      19.097  46.250 -10.137  1.00135.52
> C
> ATOM   5821  CB  ASP C 174      19.413  46.601  -8.685  1.00245.49
> C
>
>
>

--
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
I do have heterocomplex in the structure and wants to do ncs constrain for
individual complex.

For example, I do have complex A (segid a) and B (segid b). I wants to do ncs
constraint for a1, a2, a3 and b1 , b2 and b3.


I do have combine A and B as one chain A ?

Ncs def did not give me more option for different chains?

How can  I do that ncs by keeping both A and B as  protomer?

Thanks

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--Gerard

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

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DATA ACCESS
-----------

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--Gerard

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

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

It is great that the new CNS is now using the PDB format for DNA but it would be
even better if it could read its on old DNA coordinates and convert them to the
new format.
Is there a conversion tool?
Also, generate.inp has no DNA to RNA conversion option anymore and it turns DNA
into RNA.
Why was that taken out?

Thanks,

Eva Vanamee