[ccp4bb] Error in CAD during ARP/wWARP run in sharp/autoSHARP - also posted in sharp discuss

[Narayanan Ramasubbu]

Hi:
Sorry for the same posting in here as well but I thought may be some of 
you might have encountered the same problem but may not be subscribing 
to sharp list.


I am trying run sharp/autoSHARP on a mac (os x 10.4) using the guven 
example file: krel1-SAD.0

I am getting an error at the CAD as provided below
++
The parameter file is: 
/Users/subbu/sharp/sharpfiles/logfiles_local/krel-SAD.1/wARP_49.4pc/20091213_080749/arp_warp_tracing.par 



Entering warp_tracing.sh from the command line
The working directory is: 
/Users/subbu/sharp/sharpfiles/logfiles_local/krel-SAD.1/wARP_49.4pc/20091213_080749 



ARP/wARP will run in the subdirectory: temp_tracing

Building free atoms model

Initial map will be calculated with pre-weighted amplitudes ...
CAD:  Error in label assignments in LKYSET

QUITTING ... ARP/wARP module stopped with an error message:
CAD
++

The relevant CAD log file is also attached below


Chosen Asymmetric unit of reciprocal space:
[mmm] hkl:h>=0, k>=0, l>=0


** "Missing" flag set in HKLIN1 to Nan:


** "Missing" entries LISTED as   -999.000
Data line--- LABIN  E1=FBshasol E2
MtzParseLabin: run out of labels trying to match "E2"
CAD:  Error in label assignments in LKYSET

++

This happened on another dataset so I wanted to see whether the example 
file runs ok.


Please help

Subbu

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

[Nicholas M Glykos]

Dear Robbie, List,

This thread is steadily diverging. Apologies for my contribution to its 
diversification.


> Who knows what they did to the maps in terms of (unwarrented) density 
> modefication to make them look cleaner?
>
> The advantage of the EDS is that it is impartial and
> uniform. The maps are generated in a clear and well-described way.


I agree with you that map deposition is probably a waste of resources. 

I strongly disagree, though, with the existence of validation tools that 
have strong views about how best I should do science. For example, your 
sentence above imply that the validation tool is more fit (than myself) to 
decide which maps I should be looking at. Which means that if I chose to 
calculate (and view) not the simple FFT-derived map, but its maximum 
entropy estimate, I am in danger of being accused that 'I did something to 
the maps to make them look cleaner', where in fact, I'm just doing a 
better job out of the existing data than the validation tool (which 
probably generate maps in a clear, well-described and wrong way :-) 

The take home message of what I'm saying is this: We should not be 
deterred from practising our craft as best as we could, even if that 
implies that our models contain information that a validation tool can not 
reproduce. It is only fair that a well-informed and well-educated human 
being can do a better job than a fixed-frozen automated procedure. Fraud 
is a moral issue, and can not (and should not) be used as an excuse for 
converting validation tools to the sacred holders of scientific standards.


My twocents,
Nicholas


-- 


  Dr Nicholas M. Glykos, Department of Molecular Biology
 and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

[ccp4bb] Validation and maps (was: Retraction of 12 Structures...)

[Robbie Joosten]

Dear Nicholas,

Yes we are diverging, but you make a few important and valid points. So
let's diverge some more...

I fully agree that validation tools should not tell people how to do
science. That would kill free thought and lead to circularity in the
results. A typical example is the question what the RMSD from E&H bond
lengths should be at a given resolution. If a popular validation tool
would give a specific value and everyone would stick to that, then
eventually the PDB would reflect that even if there was no proof for the
initially claimed target value.

If you run into the problem you describe, that is, if a validation program
says there is something wrong with your structure because it fails to
recognise the cool stuff you did with your model, please complain. That is
by far the best way to ensure validation software gets better. You won't
just help yourself but the entire community.

As for the maps, I'll happily trust the maps of a good flesh-and-blood
crystallographer. But the avarage PDB user does not know who are the good
crystallographers and who are not. It also happens that crystallographers
make gross errors without realising it (the penta-retraction for
instance). I agree that a good flesh and blood person can get (much)
better results than an automatated procedure. But errors happen and we
should keep that in mind.

An example (not naming names here) is a structure I recently saw with a
large loop half a residue out-of-register. All the side chain density was
filled with water. It was an error of the type "How can anybody miss
that?". Their maps would certainly be very interesting. But I will put
more faith in the ones generated by the EDS. I hope you agree.

Cheers,
Robbie


> Date: Sun, 13 Dec 2009 17:20:04 +0200
> From: gly...@mbg.duth.gr
> Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...
> To: CCP4BB@JISCMAIL.AC.UK
>
> Dear Robbie, List,
>
> This thread is steadily diverging. Apologies for my contribution to its
> diversification.
>
>
> > Who knows what they did to the maps in terms of (unwarrented) density
> > modefication to make them look cleaner?
> >
> > The advantage of the EDS is that it is impartial and
> > uniform. The maps are generated in a clear and well-described way.
>
>
> I agree with you that map deposition is probably a waste of resources.
>
> I strongly disagree, though, with the existence of validation tools that
> have strong views about how best I should do science. For example, your
> sentence above imply that the validation tool is more fit (than myself) to
> decide which maps I should be looking at. Which means that if I chose to
> calculate (and view) not the simple FFT-derived map, but its maximum
> entropy estimate, I am in danger of being accused that 'I did something to
> the maps to make them look cleaner', where in fact, I'm just doing a
> better job out of the existing data than the validation tool (which
> probably generate maps in a clear, well-described and wrong way :-)
>
> The take home message of what I'm saying is this: We should not be
> deterred from practising our craft as best as we could, even if that
> implies that our models contain information that a validation tool can not
> reproduce. It is only fair that a well-informed and well-educated human
> being can do a better job than a fixed-frozen automated procedure. Fraud
> is a moral issue, and can not (and should not) be used as an excuse for
> converting validation tools to the sacred holders of scientific standards.
>
>
> My twocents,
> Nicholas
>
>
> --
>
>
> Dr Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

[Anastassis Perrakis]

I just scrapped most of my answer, Robbie was quicker, and I guess  
Gerard is on holiday ;-)

As 'honorary Dutch' though here are my two cents.


 It is only fair that a well-informed and well-educated human
being can do a better job than a fixed-frozen automated procedure.


This is exactly the whole problem Niko.

I must say that a certain proportion of the PDB depositors, are  
neither well-informed nor well-educated.
Else, I cannot see why anyone in his right mind would put 'waters'   
1.8 A from a Ca in 2009 (see Robbie's email) or
create O-O clashes of 2.4 A in 2008 (where a simple peptide flip would  
make two perfect hydrogen bonds), etc etc.


Would be easy to blame it to students that spend three or four years  
cloning before they get a structure
that ends up with many mistakes in the PDB. PIs here carry most (if  
not all) of the blame: many are simply not
competent to supervise crystallographic projects (see some CCP4  
questions to see what I mean ...),
a few are too busy (thus they should not be supervising PhD students  
if they lack the time), some make
honest mistakes (ehm ... just in case somebody finds any errors in my  
lab's structures ...), and many do a

good job and educate good students. But errors in the PDB accumulate.

Recently, I had a look, together with Robbie, at my good-old chitinase  
(1994). Thats a pre-likelihood structure.
Simple re-refinement with Robbie's tools (and some new tricks, also  
automated) and the script does in this 2.3 A
structure a better job than I did as a PhD student, pushing it from  
the 48% of MolProbity to 98%.
And I dont think that me or my supervisors could had done a better job  
at that time,
sharing night shifts in an Indy and an ESV, with PROLSQ/PROTIN. So, I  
am more than happy
if an automated procedure in 2009 can tell me that this job can be  
done better with new tools.


Finally, validation tools are not there to pass judgement. They are  
tools to be used by depositors, referees, and users
alike, to help them make a better informed interpretation of  
crystallographic *models*. Servers like EDS and PDB_REDO

must be seen in that light,

Take care -

A.

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

[Nicholas M Glykos]

Those Greeks again ...

> Finally, validation tools are not there to pass judgement. They are 
> tools to be used by depositors, referees, and users alike, to help them 
> make a better informed interpretation of crystallographic *models*. 
> Servers like EDS and PDB_REDO must be seen in that light,

Validation tools are programs written by crystallographers and structural 
biologists. As it happens, most crystallographers that write programs, 
have the neurotic belief that they can treat others' people data better 
than those other people. And, I share that neurosis ;-))



-- 


  Dr Nicholas M. Glykos, Department of Molecular Biology
 and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

[Jürgen Bosch]

Not sure if in any of the 112 posts regarding either the retraction  
theme or 'was 12 retraction' theme did mention, that after all despite  
good or as good as possible refinement of the structure, the goal is  
still to describe as accurately as possible the biological system  
using crystallography as a tool.


If you can't confirm your structure by solid biochemical or  
biophysical methods what conclusions should you draw ?
Sure faking data is not the default and looking at the ratio of  
suspected faked structures / deposited structures I do believe we are  
doing much better than other researchers e.g. in medical science.


I agree that validation tools are very helpful and everybody should  
use them prior to deposition of your structure to ensure good  
standards and if you are not happy with the result of those validation  
tools e.g. Procheck, Molprobity well then change something - re-refine  
your structure and fix it prior to deposition.


Regarding paper submissions, I think it would be a good idea to  
include e.g. the Molprobity Ramachandran plot & the summary attached  
to the cover letter when submitting - additional to the table 1 of  
course. Bill Scott once mentioned that he provides a Pymol scene file  
with PDB coordinates & electron density map to reviewers, if one could  
ensure that the coordinates can not be extracted from this file, I  
would be willing to do the same, but it's to easy to extract the  
coordinates and save them for 'other purposes'.


My 2.5 cents,

Jürgen

On Dec 13, 2009, at 1:35 PM, Nicholas M Glykos wrote:


Those Greeks again ...


Finally, validation tools are not there to pass judgement. They are
tools to be used by depositors, referees, and users alike, to help  
them

make a better informed interpretation of crystallographic *models*.
Servers like EDS and PDB_REDO must be seen in that light,


Validation tools are programs written by crystallographers and  
structural

biologists. As it happens, most crystallographers that write programs,
have the neurotic belief that they can treat others' people data  
better

than those other people. And, I share that neurosis ;-))



--


 Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
 Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)  
+302551030620,

   Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/


-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

[James Stroud]

On Dec 13, 2009, at 11:00 AM, Jürgen Bosch wrote:

If you can't confirm your structure by solid biochemical or  
biophysical methods what conclusions should you draw ?


Don't you wish it worked the other way in that every time someone had  
a biochemical, physiological, or genetic result, they would be  
required to get a structure before they published in a good journal.


That would even the playing field a bit.

[ccp4bb] Post Doctoral Position at UCLA. Membrane Protein Complexes.

[Pascal Egea]

*Post-Doctoral Researcher. Structure and Function of Membrane Protein
Complexes*.

We seek a motivated individual to join our laboratory in the Department of
Biological Chemistry at the University of California in Los Angeles. We are
interested in studying the mechanisms of protein folding/translocation and
organelle biogenesis in diverse systems. Research projects involve the study
of various multi-subunits membrane protein complexes using X-ray
crystallography and cryoEM. State-of-the-art equipment is available in a
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*Qualifications. *Applicants should have received a Ph.D degree in a field
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*Contact.* To apply please email the following to pe...@mednet.ucla.edu: a
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Assistant Professor
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Department of Biological Chemistry
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lab (310)-983-3516
email pe...@mednet.ucla.edu

[ccp4bb] MR question

[Sylvia Fanucchi]

  

Morning all

Apologies for the simple question. I have a structure I would like to
solve using molecular replacement. I am a bit confused by the patterson
peaks. There appears to be a large non-origin peak (although it is
apparently symmetry-related to the origin?). Does this mean that there
is some translation occurring in the asymmetric unit? Or is there
non-crystallographic symmetry? Does anyone know what I should do to
address this? I have continued with the molecular replacement as normal
and did not get a solution with Phaser. Molrep gives a solution that
appears correct based on the maps and refines reasonably well.

Count Site HeightGrid Fractional coordinates
Orthogonal coordinates

 

   11100.00 0   0   0   0.  0.  0. 0.00
0.00   0.00

   21 67.1633   0   0   0.9706  0.  0.41.11
0.00   0.00

   32 16.5910   0   2   0.3070  0.  0.030413.00
0.00   2.51

   43 16.5424   0   2   0.6920  0.  0.031729.30
0.00   2.63

   54 14.2417   0   3   0.5034  0.  0.044721.31
0.00   3.70

   65 14.1920   0   3   0.5763  0.  0.050724.40
0.00   4.20   

 

Best regards

Sylvia Fanucchi Ph.D

Protein Structure-Function Research Unit
East Campus, Gate House Room 416
School of Molecular and Cell Biology
University of the Witwatersrand
Johannesburg 2050
South Africa

Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 
E-mail: sylvia.fanuc...@wits.ac.za   

 


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