Re: [ccp4bb] self-rotation interpretation, 5 minutes

[Wim Burmeister]

Yanming Zhang a écrit :

Hi,

Would some experts help me to interpretate the attached self rotation 
function ps graph? The cell: 84.847 84.847 172.485 P4 indexing. In 
perticular, I was puzzled by:


1,Does the peak (90 45 180) a crystallographic 2-fold or 
non-crystallographic 2-fold?
2,Why there is no crystallographic peak on the section kappa=90? 
Giving P4 space group, there should be some high crystallographic 
4-fold peaks appear on the section.


It probably takes you only 5 minutes. Your help is greatly appreciated.

Yanming

Deqr Yanming
The north pole of the diagramm corresponds to the direction of the z 
axis. There is well a crystallographic 4-fold (and automatically 2- 
fold) peak in this direction. Then there are non-crystallographic 2-fold 
axes in the x,y plane, spaced by 45 degrees, as all the peaks appear to 
have the same height.




Greetings

Wim Burmeister

--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro
***

Re: [ccp4bb] self-rotation interpretation, 5 minutes

[Miguel Ortiz-Lombardía]

Unless there is pseudo-symmetry, I would say that the self-rotation
indicates that crystal point group is 422... Did the indexing program
suggested something with this symmetry?

Cheers,

Miguel

2007/8/20, Wim Burmeister <[EMAIL PROTECTED]>:
>
> Yanming Zhang a écrit :
> > Hi,
> >
> > Would some experts help me to interpretate the attached self rotation
> > function ps graph? The cell: 84.847 84.847 172.485 P4 indexing. In
> > perticular, I was puzzled by:
> >
> > 1,Does the peak (90 45 180) a crystallographic 2-fold or
> > non-crystallographic 2-fold?
> > 2,Why there is no crystallographic peak on the section kappa=90?
> > Giving P4 space group, there should be some high crystallographic
> > 4-fold peaks appear on the section.
> >
> > It probably takes you only 5 minutes. Your help is greatly appreciated.
> >
> > Yanming
> Deqr Yanming
> The north pole of the diagramm corresponds to the direction of the z
> axis. There is well a crystallographic 4-fold (and automatically 2-
> fold) peak in this direction. Then there are non-crystallographic 2-fold
> axes in the x,y plane, spaced by 45 degrees, as all the peaks appear to
> have the same height.
>
>
>
> Greetings
>
> Wim Burmeister
>
> --
>
> ***
> Wim Burmeister
> Professeur, Membre de l'Institut Universitaire de France
> Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
> 6 rue Jules Horowitz
> B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
> E-mail: [EMAIL PROTECTED]
> Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
> http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro
>
> ***
>



-- 
correo-e: [EMAIL PROTECTED]
~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!

Georges Brassens

Re: [ccp4bb] The importance of USING our validation tools

[George M. Sheldrick]

Dear Alex,

Of course a simplified one page summary would not be the last word, but I 
think that it would be a big step in the right direction. For example a 
value of Rfree that is 'too good' because the reflection set for it has 
been chosen wrongly can be detected statistically (Tickle et al., Acta 
D56 (2000) 443-450). And it would be not be too difficult to distinguish 
between three possible causes of incomplete data: (a) there is a dead 
cone of data because it was a single scan of a low symmetry crystal, 
(b) a large number of 'overloads' were rejected (they would all have 
fairly low resolution and high Fc values) or (c) the missing reflections 
are fairly randomly distributed because they have been removed by hand to 
improve the R-values. I think that there is a very good case for making 
this Rinformation available to referees in an easily comprehensible form.

George 

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Sun, 19 Aug 2007, Alexander Aleshin wrote:

> I do not think the small molecule approach proposed by George Sheldrick
> is sufficient for validation of protein structures, as misrepresentation
> of experimental statistics/resolution is hard to detect with it, and
> these factors appear to play crucial role in defining the fate of many
> hot structures. 
> 
> The bad statistics hurts publication more than mistakes in a model, and
> improving the experiment is often too hard. "I know my structure is
> right. Why should I spend another year growing better crystals only to
> make the statistics look right?" - sounds as a strong argument for a
> desperate researcher. Making up an artificial data set overkills the
> task. There are easier and "less amoral" ways such as rejection of
> outliers and incorrect assignment of the Rfree test set. Ironically, an
> undereducated crystallographer may not recognize wrongdoing in such data
> treatment, which makes it even more likely to occur. 
> 
> Do I sound paranoid? And please do not suggest that I have shared
> personal experiences.
> 
> 
> Alex Aleshin
> 
> 
> On Sat, 18 Aug 2007, George M. Sheldrick wrote:
> 
> > There are good reasons for preserving frames, but most of all for the 
> > crystals that appeared to diffract but did not lead to a successful 
> > structure solution, publication, and PDB deposition. Maybe in the
> future 
> > there will be improved data processing software (for example to
> integrate 
> > non-merohedral twins) that will enable good structures to be obtained
> from 
> > such data. At the moment most such data is thrown away. However,
> forcing 
> > everyone to deposit their frames each time they deposit a structure
> with 
> > the PDB would be a thorough nuisance and major logistic hassle.
> > 
> > It is also a complete illusion to believe that the reviewers for
> Nature 
> > etc. would process or even look at frames, even if they could download
> 
> > them with the manuscript. 
> > 
> > For small molecules, many journals require an 'ORTEP plot' to be
> submitted 
> > with the paper. As older readers who have experienced Dick Harlow's
> 'ORTEP 
> > of the year' competition at ACA Meetings will remember, even a viewer 
> > with little experience of small-molecule crystallography can see from
> the 
> > ORTEP plot within seconds if something is seriously wrong, and many 
> > non-crystallographic referees for e.g. the journal Inorganic Chemistry
> 
> > can even make a good guess as to what is wrong (e.g wrong element
> assigned 
> > to an atom). It would be nice if we could find something similar for 
> > macromolecules that the author would have to submit with the paper.
> One 
> > immediate bonus is that the authors would look at it carefully 
> > themselves before submitting, which could lead to an improvement of
> the 
> > quality of structures being submitted. My suggestion is that the wwPDB
> 
> > might provide say a one-page diagnostic summary when they allocate
> each 
> > PDB ID that could be used for this purpose.
> > 
> > A good first pass at this would be the output that the MolProbity
> server 
> > http://molprobity.biochem.duke.edu/ sends when is given a PDB file. It
> 
> > starts with a few lines of summary in which bad things are marked red 
> > and the structure is assigned to a pecentile: a percentile of 6% means
> 
> > that 93% of the sturcture in the PDB with a similar resolution are 
> > 'better' and 5% are 'worse'. This summary can be understood with very 
> > little crystallographic background and a similar summary can 
> > of course be produced for NMR structures. The summary is followed by 
> > diagnostics for each residue, normally if the summary looks good it 
> > would not be necessary for the editor or referee to look at the rest.
> > 
> > Although this server was intended to help us to improve our structures
> 
> > rather than detect manipulated or fabrica

Re: [ccp4bb] self-rotation interpretation, 5 minutes

[Wim Burmeister]

Dear Yanming
My previous message only holds if there is no sign of twinning. 
Alternatively, you may have a near perfect-twinning with a twin 
operation corresponding to an rotation around the xy-diagonal and a 
crystallographic or non-crystallographic 2-fold axis around x and y.


Wim Burmeister

--
***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED]
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro
***

Re: [ccp4bb] diffraction images images/jpeg2000

[Winter, G (Graeme)]

Hi,

I looked at jpeg2000 as a compression for diffraction images for
archiving purposes - it works well but is *SLOW*. It's designed with the
idea in mind of compressing a single image, not the several hundred
typical for our work. There is also no place to put the header.

Bzip2 works pretty much as well and is standard, but again slow. This is
what people mostly seem to use for putting diffraction images on the
web, particularly the JCSG.

The ccp4 "pack" format which has been around for a very long time works
very well and is jolly quick, and is supported in a number of data
processing packages natively (Mosflm, XDS). Likewise there is a new
compression being used for the Pilatus detector which is quicker again.
These two have the advantage of being designed for diffraction images
and with speed in mind.

So there are plenty of good compression schemes out there - and if you
use CBF these can be supported natively in the image standard... So you
don't even need to know or care...

Just my 2c on this one.

Cheers,

Graeme

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Maneesh Yadav
Sent: 18 August 2007 00:02
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] diffraction images images/jpeg2000

FWIW, I don't agree with storing image data, I don't think they justify
the cost of storage even remotely (some people debate the value of the
structures themselves)...but if you want to do it anyway, maybe we
should use a format like jpeg2000.

Last time I checked, none of the major image processing suites used it,
but it is a very impressive and mature format that (I think) would be
suitable for diffraction images.  If anyone is up for experimenting, you
can get a nice suite of tools from kakadu (just google kakdu +
jpeg2000).

Re: [ccp4bb] diffraction images images/jpeg2000

[Harry Powell]

Hi

Just to add to this. imgCIF (or CBF, which amounts to pretty well the same 
thing) has fast and efficient compression built in, and has been developed 
with protein crystallography (particularly) in mind. There are even (a 
few) detectors out there which will write these instead of (or as well as) 
the manufacturer's native format, saving the user the trouble of 
conversion.


If you're looking for a standard format for storing image data in, I 
wouldn't look any further, since (in principle) imgCIF/CBF can store all 
the image information you (or a fussy^H^H^H^H^H conscientious reviewer who 
could be bothered to re-process your dataset) would want about your data 
collection and you wouldn't need to come up with inventive tags for data 
items that might be required for other (general purpose) image formats.


There are even conversion programs available to convert to imgCIF/CBF 
files from some native formats - if your favourite detector isn't one of 
these, drop Herb Bernstein a line and ask for support ;-)



I looked at jpeg2000 as a compression for diffraction images for
archiving purposes - it works well but is *SLOW*. It's designed with the
idea in mind of compressing a single image, not the several hundred
typical for our work. There is also no place to put the header.

Bzip2 works pretty much as well and is standard, but again slow. This is
what people mostly seem to use for putting diffraction images on the
web, particularly the JCSG.

The ccp4 "pack" format which has been around for a very long time works
very well and is jolly quick, and is supported in a number of data
processing packages natively (Mosflm, XDS). Likewise there is a new
compression being used for the Pilatus detector which is quicker again.
These two have the advantage of being designed for diffraction images
and with speed in mind.

So there are plenty of good compression schemes out there - and if you
use CBF these can be supported natively in the image standard... So you
don't even need to know or care...

Just my 2c on this one.

Cheers,

Graeme

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Maneesh Yadav
Sent: 18 August 2007 00:02
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] diffraction images images/jpeg2000

FWIW, I don't agree with storing image data, I don't think they justify
the cost of storage even remotely (some people debate the value of the
structures themselves)...but if you want to do it anyway, maybe we
should use a format like jpeg2000.

Last time I checked, none of the major image processing suites used it,
but it is a very impressive and mature format that (I think) would be
suitable for diffraction images.  If anyone is up for experimenting, you
can get a nice suite of tools from kakadu (just google kakdu +
jpeg2000).



Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

Re: [ccp4bb] The importance of USING our validation tools

[Phil Evans]

I worry a bit about some of this discussion, in that I wouldn't like  
the free-R-factor police to get too powerful. I imagine that many of  
us have struggled with datasets which are  sub-optimal for all sorts  
of reasons (all crystals are multiple/split/twinned; substantial  
disordered regions; low resolution, etc) - and it is not possible to  
get better data. I have certainly fought hard to get free-R below  
(the magic) 30%, when I know the structure is _essentially_ right,  
but the details are a little blurred in places, even when I have done  
the best I can. Anyway the important things are not the statistics,  
but the maps.


Does this make the structure unpublishable? No, provided that we  
remember a basic tenet of science, that the conclusions drawn should  
be supported by the evidence available. With limited data, the  
conclusions may be more limited, but still often illuminate the  
biology, which is the reason for solving the structure in the first  
place.


The evidence should be available to readers & referees, so deposition  
at least structure factors should be compulsory (why isn't it  
already?). Unmerged data or images would be nice, but I doubt that  
many people would use them (great for developers though)


Phil

On 20 Aug 2007, at 08:24, George M. Sheldrick wrote:


Dear Alex,

Of course a simplified one page summary would not be the last word,  
but I
think that it would be a big step in the right direction. For  
example a
value of Rfree that is 'too good' because the reflection set for it  
has

been chosen wrongly can be detected statistically (Tickle et al., Acta
D56 (2000) 443-450). And it would be not be too difficult to  
distinguish

between three possible causes of incomplete data: (a) there is a dead
cone of data because it was a single scan of a low symmetry crystal,
(b) a large number of 'overloads' were rejected (they would all have
fairly low resolution and high Fc values) or (c) the missing  
reflections
are fairly randomly distributed because they have been removed by  
hand to
improve the R-values. I think that there is a very good case for  
making
this Rinformation available to referees in an easily comprehensible  
form.


George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Sun, 19 Aug 2007, Alexander Aleshin wrote:

I do not think the small molecule approach proposed by George  
Sheldrick
is sufficient for validation of protein structures, as  
misrepresentation

of experimental statistics/resolution is hard to detect with it, and
these factors appear to play crucial role in defining the fate of  
many

hot structures.

The bad statistics hurts publication more than mistakes in a  
model, and

improving the experiment is often too hard. "I know my structure is
right. Why should I spend another year growing better crystals  
only to

make the statistics look right?" - sounds as a strong argument for a
desperate researcher. Making up an artificial data set overkills the
task. There are easier and "less amoral" ways such as rejection of
outliers and incorrect assignment of the Rfree test set.  
Ironically, an
undereducated crystallographer may not recognize wrongdoing in  
such data

treatment, which makes it even more likely to occur.

Do I sound paranoid? And please do not suggest that I have shared
personal experiences.


Alex Aleshin


On Sat, 18 Aug 2007, George M. Sheldrick wrote:

There are good reasons for preserving frames, but most of all for  
the

crystals that appeared to diffract but did not lead to a successful
structure solution, publication, and PDB deposition. Maybe in the

future

there will be improved data processing software (for example to

integrate
non-merohedral twins) that will enable good structures to be  
obtained

from

such data. At the moment most such data is thrown away. However,

forcing

everyone to deposit their frames each time they deposit a structure

with

the PDB would be a thorough nuisance and major logistic hassle.

It is also a complete illusion to believe that the reviewers for

Nature
etc. would process or even look at frames, even if they could  
download



them with the manuscript.

For small molecules, many journals require an 'ORTEP plot' to be

submitted

with the paper. As older readers who have experienced Dick Harlow's

'ORTEP
of the year' competition at ACA Meetings will remember, even a  
viewer
with little experience of small-molecule crystallography can see  
from

the

ORTEP plot within seconds if something is seriously wrong, and many
non-crystallographic referees for e.g. the journal Inorganic  
Chemistry



can even make a good guess as to what is wrong (e.g wrong element

assigned

to an atom). It would be nice if we could find something similar for
macromolecules that the author would have to submit with the paper.

One

immediate bonus is that the autho

[ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?

[Juergen J. Mueller]

Dear all,
using refmac5 to provide H-atoms for a known protein structure the
distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif.

This distance has been critisiced by a non-CCP4 program
by
* Poor covalent bond length of 1.33954 for hydrogen atom HG.

In an other library-file CSH.cif the same distance is defined to 1.1 Ang.
WHATIF uses 1.0 Ang. What is the most correct one?
Could the CCP4-people comment on this?

(Of course I know hydrogens will not be refined but they are neccessary 
for some

modeling programs).

Thank you,
Juergen

Re: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?

[Eleanor Dodson]

I think Garib or Alexei must answer this and they are both on holiday 
till the end of August


Eleanor
juergen J. Mueller wrote:

Dear all,
using refmac5 to provide H-atoms for a known protein structure the
distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif.

This distance has been critisiced by a non-CCP4 program
by
* Poor covalent bond length of 1.33954 for hydrogen atom HG.

In an other library-file CSH.cif the same distance is defined to 1.1 Ang.
WHATIF uses 1.0 Ang. What is the most correct one?
Could the CCP4-people comment on this?

(Of course I know hydrogens will not be refined but they are 
neccessary for some

modeling programs).

Thank you,
Juergen

[ccp4bb] AW: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?

[Herman . Schreuder]

Dear Juergen,
I did a quick check in the CSD and found SG-H bondlengths between 0.587 and 
1.338 Ang. for various cysteine derivatives. The most common values where 
around 1.33 Ang. but the average may be around 1.1 or 1.2 Ang. I did not work 
out any statistics. It seems that the SG-H distance is either experimentally 
not very well defined (there were quite a few entries with this hydrogen 
missing) or it might be very sensitive to e.g. (ionization).

I hope this helps.
Best regards,
Herman  



-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von Juergen J. 
Mueller
Gesendet: Montag, 20. August 2007 15:31
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library 
correct?

Dear all,
using refmac5 to provide H-atoms for a known protein structure the distance 
between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif.

This distance has been critisiced by a non-CCP4 program by
* Poor covalent bond length of 1.33954 for hydrogen atom HG.

In an other library-file CSH.cif the same distance is defined to 1.1 Ang.
WHATIF uses 1.0 Ang. What is the most correct one?
Could the CCP4-people comment on this?

(Of course I know hydrogens will not be refined but they are neccessary for 
some modeling programs).

Thank you,
Juergen

Re: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?

[George M. Sheldrick]

For what it is worth, SHELXL sets the S-H distance to 1.20A. As with other 
bonds to hydrogen, this allows for apparent shortening to fit the electron 
distribution and also librational effects. An S-H distance determined by 
neutron diffraction would be longer.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 20 Aug 2007, Juergen J. Mueller wrote:

> Dear all,
> using refmac5 to provide H-atoms for a known protein structure the
> distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif.
> 
> This distance has been critisiced by a non-CCP4 program
> by
> * Poor covalent bond length of 1.33954 for hydrogen atom HG.
> 
> In an other library-file CSH.cif the same distance is defined to 1.1 Ang.
> WHATIF uses 1.0 Ang. What is the most correct one?
> Could the CCP4-people comment on this?
> 
> (Of course I know hydrogens will not be refined but they are neccessary for
> some
> modeling programs).
> 
> Thank you,
> Juergen
> 
> 

Re: [ccp4bb] The importance of USING our validation tools

[Miller, Mitchell D.]

Hi Boaz,
  We were informed by an RCSB annotator in April 2006 that the
RCSB had suspended including REMARK 42 records in PDB files
pending the review of the process by the wwPDB.

  In looking at the new annotation guidelines, it looks
like the result of that review was to reject the REMARK 42 
record and the listing of additional validation items.  
See page 23 of the July 2007 "wwPDB Processing Procedures 
and Policies Document"
http://www.wwpdb.org/documentation/wwPDB-A-20070712.pdf

"REMARK 42 and use of other programs for validation Use of REMARK 42 is
discontinued.

If authors wish to indicate presubmission validation and other programs used 
before
deposition, the programs may be listed in a new remark, REMARK 40. This remark 
will
list the software name, authors and function of the program. Results of the 
software will
not be listed. Use of this remark is voluntary."

It seems that the wwPDB only allows the inclusion of validation 
statistics output by the refinement program but not from additional 
validation programs. So for additional statistics to be included 
in the PDB header, they will either need to be implemented by the 
refinement package or the wwPDB annotators.

Regards,
Mitch 



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Boaz Shaanan
Sent: Sunday, August 19, 2007 2:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools


Curiously enough, when I've recently submitted a coordinates file to RCSB with 
this Molprobity summary (as remark 42; it is added onto the analyzed file by 
the Molprobity program) it was deleted by the RCSB team.
 
  Boaz

- Original Message -
From: "George M. Sheldrick" <[EMAIL PROTECTED]>
Date: Saturday, August 18, 2007 15:27
Subject: Re: [ccp4bb] The importance of USING our validation tools
To: CCP4BB@JISCMAIL.AC.UK

> There are good reasons for preserving frames, but most of all for the 
> crystals that appeared to diffract but did not lead to a successful 
> structure solution, publication, and PDB deposition. Maybe in the future 
> there will be improved data processing software (for example to integrate 
> non-merohedral twins) that will enable good structures to be obtained from 
> such data. At the moment most such data is thrown away. However, forcing 
> everyone to deposit their frames each time they deposit a structure with 
> the PDB would be a thorough nuisance and major logistic hassle.
> 
> It is also a complete illusion to believe that the reviewers for Nature 
> etc. would process or even look at frames, even if they could download 
> them with the manuscript. 
> 
> For small molecules, many journals require an 'ORTEP plot' to be submitted 
> with the paper. As older readers who have experienced Dick Harlow's 'ORTEP 
> of the year' competition at ACA Meetings will remember, even a viewer 
> with little experience of small-molecule crystallography can see from the 
> ORTEP plot within seconds if something is seriously wrong, and many 
> non-crystallographic referees for e.g. the journal Inorganic Chemistry 
> can even make a good guess as to what is wrong (e.g wrong element assigned 
> to an atom). It would be nice if we could find something similar for 
> macromolecules that the author would have to submit with the paper. One 
> immediate bonus is that the authors would look at it carefully 
> themselves before submitting, which could lead to an improvement of the 
> quality of structures being submitted. My suggestion is that the wwPDB 
> might provide say a one-page diagnostic summary when they allocate each 
> PDB ID that could be used for this purpose.
> 
> A good first pass at this would be the output that the MolProbity server 
> http://molprobity.biochem.duke.edu/ sends when is given a PDB file. It 
> starts with a few lines of summary in which bad things are marked red 
> and the structure is assigned to a pecentile: a percentile of 6% means 
> that 93% of the sturcture in the PDB with a similar resolution are 
> 'better' and 5% are 'worse'. This summary can be understood with very 
> little crystallographic background and a similar summary can 
> of course be produced for NMR structures. The summary is followed by 
> diagnostics for each residue, normally if the summary looks good it 
> would not be necessary for the editor or referee to look at the rest.
> 
> Although this server was intended to help us to improve our structures 
> rather than detect manipulated or fabricated data, I asked it for a 
> report on 2HR0 to see what it would do (probably many other people were 
> trying to do exactly the same, the server was slower than usual). 
> Although the structure got poor marks on most tests, MolProbity 
> generously assigned it overall to the 6th pecentile, I suppose that 
> this is about par for structures submitted to Nature (!). However there 
> was one feature that was unlike anything I have ever seen before 
> althou

Re: [ccp4bb] self-rotation interpretation, 5 minutes

[Alejandro Buschiazzo]

I'd rather agree with Miguel.
You certainly have evidence telling your 4-fold is crystallographic 
(indexing, cell, ), and you do see it on your k=90 section (of course 
also on your 180).


You need to check your k=180 peak heights to compare with the 4-fold 
axis: they seem to be so perfectly at 90deg to the 4-fold (and 
apparently strong enough...), really suggesting a 422 point group. They 
could of course be the result of a 2-fold NCS, "accidentally" at 90deg 
of the single 4-fold , but then they should show a significantly lower 
height wrt the xtallographic axis; how many mols/ASU are you expecting?


(if the heights are equivalent, you shouldn't automatically rule out a 
twinning phenomenon in this PG (twinning law would be kh-l): look at 
intensity distribution statistics (CCP4 TRUNCATE gives you several), at 
regular solvent fractions they are usually quite revealing...)


hth

ale

Miguel Ortiz-Lombardía wrote:
Unless there is pseudo-symmetry, I would say that the self-rotation 
indicates that crystal point group is 422... Did the indexing program 
suggested something with this symmetry?


Cheers,

Miguel

2007/8/20, Wim Burmeister <[EMAIL PROTECTED] 
>:


Yanming Zhang a écrit :
> Hi,
>
> Would some experts help me to interpretate the attached self
rotation
> function ps graph? The cell: 84.847 84.847 172.485 P4 indexing. In
> perticular, I was puzzled by:
>
> 1,Does the peak (90 45 180) a crystallographic 2-fold or
> non-crystallographic 2-fold?
> 2,Why there is no crystallographic peak on the section kappa=90?
> Giving P4 space group, there should be some high crystallographic
> 4-fold peaks appear on the section.
>
> It probably takes you only 5 minutes. Your help is greatly
appreciated.
>
> Yanming
Deqr Yanming
The north pole of the diagramm corresponds to the direction of the z
axis. There is well a crystallographic 4-fold (and automatically 2-
fold) peak in this direction. Then there are non-crystallographic
2-fold
axes in the x,y plane, spaced by 45 degrees, as all the peaks
appear to
have the same height.



Greetings

Wim Burmeister

--

***
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9  FRANCE
E-mail: [EMAIL PROTECTED] 
Tel:+33 (0) 476 20 72 82   Fax: +33 (0) 476 20 94 00
http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro

***





--
correo-e: [EMAIL PROTECTED] 
~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!
 
Georges Brassens



--
Alejandro Buschiazzo, PhD
Research Scientist
Laboratory of Structural Biology
Pasteur Institute of Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY

Phone: +5982 5220910 int. 120
Fax:   +5982 5220910 int. 111

[ccp4bb] Scientist or Senior Scientist position available in Plexxikon Inc.

[Jinyu Liu]

Department: Structural Biology
Location: Berkeley, California 
URL: www.plexxikon.com
Start Date: ASAP
Duration: Perminant
Description: Located in Berkeley, California, Plexxikon is a leader in
the discovery and development of novel small molecule pharmaceuticals to
treat human disease. Since operations commenced June 2001, Plexxikon has
applied its proprietary platform technology to identify and build a
portfolio of product opportunities for therapeutic indications in
metabolic disorders, cardiovascular disease, inflammation and oncology.
We are seeking a highly motivated and experienced X-ray protein
crystallographer in our Structural Biology Department at the level of
Scientist or Senior Scientist depending on qualifications. The
successful candidate will participate in our scaffold-based drug
discovery effort on many exciting therapeutic targets by carrying out
high throughput co-crystal structure determination, co-crystallization
and synchrotron data collection. The incumbent will also participate in
specific drug target project teams and collaborate closely with
scientists from Molecular Biology, Protein Chemistry, Assay Development,
Informatics and Chemistry in shaping the direction of our drug discovery
effort. This position requires a PhD and, for Sr. Scientist, a minimum
of five years of industry experience in drug discovery. Postdoctoral
research experience in related areas will be considered, however
preference will be given to candidates with relevant industrial
experience. Qualified candidates must possess excellent communication
skills and the ability to work in a highly collaborative and team
oriented environment. The ideal candidate will have a track record of
accomplishments demonstrating technical proficiency, independent
thinking, and scientific creativity. Extensive experience with high
throughput co-crystal structure determination and high throughput
co-crystallization are required. Experience with script writing and
programming that facilitates automatic crystallographic structure
determination and related tasks would be a plus. If you are interested
in applying for this opportunity, please submit your resume or CV, a
cover letter and salary requirements to the address below. All
submissions will be evaluated and interviews will be conducted for those
applicants who most strongly fit our needs. If you are not contacted for
an interview, your resume will remain on file and active for available
positions for a period of one year. 
Other details: Plexxikon is an equal opportunity employer.
Please submit: CV, 3 references
Person to contact: Human Resources
Surface mail address: Plexxikon Inc., 91 Bolivar Dr., Berkeley, CA
94710, USA.
Email address: [EMAIL PROTECTED]
Phone number: (510)647-4000
Fax number: (510)647-4090
Job Posted: 08/20/07
Job ID Number: 1179788911

 

Re: [ccp4bb] The importance of USING our validation tools

[Axel T. Brunger]

Phil,

A few points:


1. The recent erroneous structures that I'm aware of had either extremely
high free R values ( 40 - 45%) or unreasonably low free R values (low
twenties) despite the presence of > 80% solvent and gaps in crystal 
packing. 



2. At low resolution (3.5 A and lower) , maps can be very difficult to
interpret.  In fact, it can be impossible to correct the model based on
low resolution maps alone.  Yet, the statistics (free R value, geometry, 
...)

will ultimately tell you if you have a better model.  The problem is how
to get to the better model.  High resolution structures of fragments of the
molecule may be required to ultimately obtain a better structure of the 
full-length

molecule.


3. The journals and funding agencies should make it
the responsibility of the authors to maintain archives of
their raw diffraction images, and they should make them available upon
request as is customary with other published materials. 



Axel






Phil Evans wrote:
I worry a bit about some of this discussion, in that I wouldn't like 
the free-R-factor police to get too powerful. I imagine that many of 
us have struggled with datasets which are  sub-optimal for all sorts 
of reasons (all crystals are multiple/split/twinned; substantial 
disordered regions; low resolution, etc) - and it is not possible to 
get better data. I have certainly fought hard to get free-R below (the 
magic) 30%, when I know the structure is _essentially_ right, but the 
details are a little blurred in places, even when I have done the best 
I can. Anyway the important things are not the statistics, but the maps.


Does this make the structure unpublishable? No, provided that we 
remember a basic tenet of science, that the conclusions drawn should 
be supported by the evidence available. With limited data, the 
conclusions may be more limited, but still often illuminate the 
biology, which is the reason for solving the structure in the first 
place.


The evidence should be available to readers & referees, so deposition 
at least structure factors should be compulsory (why isn't it 
already?). Unmerged data or images would be nice, but I doubt that 
many people would use them (great for developers though)


Phil

On 20 Aug 2007, at 08:24, George M. Sheldrick wrote:


Dear Alex,

Of course a simplified one page summary would not be the last word, 
but I

think that it would be a big step in the right direction. For example a
value of Rfree that is 'too good' because the reflection set for it has
been chosen wrongly can be detected statistically (Tickle et al., Acta
D56 (2000) 443-450). And it would be not be too difficult to distinguish
between three possible causes of incomplete data: (a) there is a dead
cone of data because it was a single scan of a low symmetry crystal,
(b) a large number of 'overloads' were rejected (they would all have
fairly low resolution and high Fc values) or (c) the missing reflections
are fairly randomly distributed because they have been removed by 
hand to

improve the R-values. I think that there is a very good case for making
this Rinformation available to referees in an easily comprehensible 
form.


George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Sun, 19 Aug 2007, Alexander Aleshin wrote:


I do not think the small molecule approach proposed by George Sheldrick
is sufficient for validation of protein structures, as 
misrepresentation

of experimental statistics/resolution is hard to detect with it, and
these factors appear to play crucial role in defining the fate of many
hot structures.

The bad statistics hurts publication more than mistakes in a model, and
improving the experiment is often too hard. "I know my structure is
right. Why should I spend another year growing better crystals only to
make the statistics look right?" - sounds as a strong argument for a
desperate researcher. Making up an artificial data set overkills the
task. There are easier and "less amoral" ways such as rejection of
outliers and incorrect assignment of the Rfree test set. Ironically, an
undereducated crystallographer may not recognize wrongdoing in such 
data

treatment, which makes it even more likely to occur.

Do I sound paranoid? And please do not suggest that I have shared
personal experiences.


Alex Aleshin


On Sat, 18 Aug 2007, George M. Sheldrick wrote:


There are good reasons for preserving frames, but most of all for the
crystals that appeared to diffract but did not lead to a successful
structure solution, publication, and PDB deposition. Maybe in the

future

there will be improved data processing software (for example to

integrate

non-merohedral twins) that will enable good structures to be obtained

from

such data. At the moment most such data is thrown away. However,

forcing

everyone to deposit their frames each time they deposit a structure

with

[ccp4bb] Release of Mosflm version 7.0.1 & iMosflm 0.5.3

[Harry Powell]

Hi folks

I'm pleased to announce the release of Mosflm version 7.0.1 & iMosflm 
version 0.5.3. They can be downloaded from


http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701
and
http://www.mrc-lmb.cam.ac.uk/harry/imosflm

respectively.

Note that earlier versions of either program will not work with these 
latest releases - you will need to upgrade both.


Mosflm - changes since 6.2.6

* Many changes which allow processing information to be communicated
  between Mosflm and the new TclTk-based Graphical User Interface,
  which is now called iMosflm. Mosflm itself can be run as before as
  a standalone program, but can also be run from iMosflm. The
  original X11 GUI, based on John Campbell's XDL_VIEW libraries is
  still included and can be used if desired.
* Now checks to see if an image file is still being written
  before attempting to process it.
* More improvements to the autoindexing to make it more robust in
  cases where it failed previously.
* Build developed which will run (without the X11 graphics) on
  MS-Windows, allowing iMosflm to run properly on that operating
  system. It works on both XP and Vista, and may well work on 2000
  and 98.
* Many small bug fixes which address rare but annoying problems.

Thanks go to everyone who has contributed their comments and bug reports 
during the development stages.


iMosflm - changes since 0.5.2
=
* mostly bug fixes, e.g. filename parsing
* some user-definable locations for outputting files, e.g. the MTZ
  file
* separation of experimental parameters into two lists, for the
  detector and experimental set-up
* rudimentary command-line options (try starting with "imosflm
  --help") - the list will grow

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

Re: [ccp4bb] Release of Mosflm version 7.0.1 & iMosflm 0.5.3

[Harry Powell]

Hi folks

a sharp-eyed user has noticed a bug in the Windows version of iMosflm 
0.5.3; this does not affect any other version.


If you have already downloaded the Windows version, you should replace the 
file "imosflm.tcl" in the top-level imosflm folder with this file -


http://www.mrc-lmb.cam.ac.uk/harry/imosflm/downloads/imosflm.tcl

NOTE that this is _not_ the file of the same name in the "src" folder.

I've fixed this in the imosflm.zip file so any further downloads will not 
display this bug.


Sorry about this!

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

[ccp4bb] water water everywhere

[price]

While we're still on the subject of good model-building habits and 
reviewing pitfalls, I've been shocked to download a couple of 
structures recently that seem to have solvent channels chock full of 
allegedly ordered water (many "layers" deep, and not exactly at 0.5A 
resolution).  To any new students out there:   making Rfree go down a 
bit by putting a water in every unexplained blob is NOT the same as 
building a good model!
I'm afraid I reviewed one of these (sans coordinates) ... so sorry to 
the community ... it wasn't obvious from table 1.

Phoebe


---
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html 

Re: [ccp4bb] water water everywhere

[William Scott]

I've often wondered whether it would be more fair to report R-factors with
and without waters, since waters can be used to beautify statistics. I
also think providing pdb coordinates and Fobs with experimental phases as
supplementary information in a standard format to be supplied
automatically to all the reviewers should be required by the journals.

I actually tried to force Cell to do this in 2006, or at least provide a
link to our password-protected website, but they balked.  I did manage to
sneak in a pymol saved session with the MAD and composite omit maps, and
at least one of the referees thanked us for that.

[EMAIL PROTECTED] wrote:
> While we're still on the subject of good model-building habits and
> reviewing pitfalls, I've been shocked to download a couple of
> structures recently that seem to have solvent channels chock full of
> allegedly ordered water (many "layers" deep, and not exactly at 0.5A
> resolution).  To any new students out there:   making Rfree go down a
> bit by putting a water in every unexplained blob is NOT the same as
> building a good model!
> I'm afraid I reviewed one of these (sans coordinates) ... so sorry to
> the community ... it wasn't obvious from table 1.
>  Phoebe
>
>
> ---
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> fax 773 702 0439
> http://bmb.bsd.uchicago.edu/index.html
> http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
>

Re: [ccp4bb] self-rotation interpretation, 5 minutes

[Yanming Zhang]

Hi,

Thank you all the repliers who kindly offer their hands after my 
PREVIOUS posting message. I received around 12 messages in total and the 
concensus reply is:


P422 POINT GROUP WITH ONLY ONE MOLECULE IN ONE A.U.(peak (90 45 180) 
indicates P422 with the 2-fold crystallographic symmetry along the 
diagonal. The 4-fold symmetry is at the origin along C axis).


Hope this will help to my peers who has the similar wanderings.

Thanks you again.
Yanming

[ccp4bb] Seeking collaborators.Again.

[cry]

Dear all,

Our laboratory can undertake Academic or Commercial Project in protein
expression, crystallization of protein/nucleic acid/complex and some
functional study with considerable low cost (or you have to apply in
conjunction with us for the funding of Chinese government).

We have an independent protein crystallography laboratory, managed by an
experienced crystallographer.  Now we would like to undertake some
projects which are thought by their providers suitable for collaboration.
What we can do includes protein expression with E.coli, yeast or cell
line; crystallization of protein, DNA, RNA, protein-ligand complex or
protein-DNA/RNA complex; data collection, structure solution and
especially some related functional study including site-directed mutation,
enzyme activity assay, binding constant determination, etc. The satisfying
peripheral academic environments and facilities will favor the functional
study.
Our biggest advantage is abundance of manpower source and very low labor  
cost, the salary of common junior researcher is about $350 per month, so  
it enable us deal with some big or difficult projects with acceptable or  
even lower payout.

Because of our great advantage of comparatively low labor cost, we can
provide those services with low cost; I think generally the overall cost
of completing a common project (from protein expression to refined
structure and some functional study) is no more than one third of the
annual salary of a postdoctoral researcher; in addition, if our
collaborator would like to apply for the funding of Chinese government (in
conjunction with us), we can also share the funding. To projects
practicable or really make sense the success rate of application is fairly
acceptable.

If there is any result, our collaborator should sign the paper as
corresponding author accordingly. To the results acquired the only right
we reserve is that our crystallographer should sign the article as one of
the authors. We recommend that a contract should be signed in advance to
prevent abuse and divulgence of any sensitive information. We can from
time to time communicate with our collaborators via email or telephone.

We will apply for our own synchrotron time in Beijing Synchrotron
Radiation Laboratory, Beijing, China.

Generally we carry out the primary screening with Emerald Biostructures
Wizard I/II/III, Hampton Crystal Screen kit/Crystal Screen 2 kit, Qiagen
NeXtal Classics I / II, as well as Hampton Crystal Screen Lite,
Sigma-Aldrich Crystallization Kit for Protein-Protein Complexes, Hampton
Natrix, Sigma-Aldrich DNA Crystallization Kit and Sigma-Aldrich RNA
Crystallization Kit if needed.

Thanks!

H.Y Zhang
Professor,
Life Science School,
Shandong University of Technology,
Zibo, China, 255049
Tel/Fax:  0086-533-2780271
Email: [EMAIL PROTECTED]