Re: [ccp4bb] PDB passes 100,000 structure milestone

[David Briggs]

So, a bit like "Fold-it" but with actual data? :-D

Dr David C Briggs PhD
http://about.me/david_briggs
On 16 May 2014 06:19, "Pavel Afonine"  wrote:

>
> What about structures that are obviously wrong based on inspection of the
>> density, but no one has bothered to challenge yet?  The TWILIGHT database
>> helps some, if that counts, but it doesn't catch everything.
>>
>
> How about this utopia.. Imagine PDB has two versions: one is the original
> data and model deposited as is, and never ever changed no matter what.
> Another version is a curated one obtained in a quest-like way: anyone can
> take an original entry, improve it and deposit (into the curated version)
> with his/her name tag on it. And of course anyone can take and update that
> improved entry and re-deposit it again with his/her name tag, etc. If
> desired one could keep track of all the revisions, like in svn or so.
> Sounds like a sport with an element of public service that might yield
> crowd-perfected models -:) !
>
> Pavel
>

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Pavel Afonine]

> What about structures that are obviously wrong based on inspection of the
> density, but no one has bothered to challenge yet?  The TWILIGHT database
> helps some, if that counts, but it doesn't catch everything.
>

How about this utopia.. Imagine PDB has two versions: one is the original
data and model deposited as is, and never ever changed no matter what.
Another version is a curated one obtained in a quest-like way: anyone can
take an original entry, improve it and deposit (into the curated version)
with his/her name tag on it. And of course anyone can take and update that
improved entry and re-deposit it again with his/her name tag, etc. If
desired one could keep track of all the revisions, like in svn or so.
Sounds like a sport with an element of public service that might yield
crowd-perfected models -:) !

Pavel

Re: [ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular Replacement

[Roger Rowlett]

For P212121, I would put money on something divisible by 2 for the total 
molecules per asu. Anything from 6-12 might be likely. One of the early 
structures I worked on had 6 molecules per asu, which was darn near 
impossible to find using momomers (at the time). The way it was 
eventually solved was by finding a reasonable tetramer solution, then 
looking at the packing of that model to see what was missing and 
determine how much more would fit into the asu. Turned out to be another 
(obvious) dimer, which did the trick. The Matthews coefficient predicted 
something like 9 molecules per asu, which was not close to the actual 
answer. When n=large number, the Matthews coefficient does not easily 
identify a unique, most likely solution, but a range of reasonable 
solutions.


One possible strategy would be to look for some partial solutions to 
give you a better clue of the actual packing in the asu. If you find 
there is a reasonable looking dimer pair, try searching with multiple 
dimers, etc.

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu


On 5/15/2014 8:29 PM, Toth, Eric wrote:

Have you tried fixing the molecule that looks correct and searching for others? 
You might have greater than one but less than 9 molecules per ASU.

When you do this, try imposing severe restraints on the packing function. This 
worked for me in Phaser with a difficult case. My anecdotal experience is that, 
when you have lots of molecules per asu, the correct solution gets swamped by 
poorly-packed solutions if the default packing penalties are used.

Good luck.

Sent from my iPhone


On May 15, 2014, at 6:50 PM, "Matthew Bratkowski"  wrote:

Hello all,


I am working on the structure of a small protein in space group P212121.  The 
protein is monomeric in solution based on gel filtration analysis.  The 
Matthews Coefficeint program indicates that 9-10 molecules per asymmetric unit 
results in ~50% solvent content, while 1 molecule per asymmetric unit results 
in ~95% solvent.

  I tried molecular replacement with a search model which is essentially 
identical in sequence to my protein, and searched for 9 or 10 molecules/asu.  
Using MolRep with 9 or 10 molecules/asu, I get poor contrast scores around 
1-1.5.  However, when using Phaser, I get a solution with one molecules/asu.  
Likewise, when I went back and tried MolRep with 1 molecule/asu, I got a 
contrast score of 3.12.  This model still has some issues, but looks more 
correct compaired to models created with 9 or 10  molecules/asu.

It seems highly unlikely that a crystal would contain 95% solvent, but is there 
any possiblility that this could be the case?  Assuming that the Matthews 
coefficient is correct, does anyone have an idea why MR seems to work better 
for 1 molecule/asu with 95% solvent content compared to 9-10 molecules with 50% 
solvent content? Alternatively, is there any reason why the Matthews 
coefficient could be calculating incorrectly?  Any suggestions would be helpful.

Thanks,
Matt

Re: [ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular Replacement

[Toth, Eric]

Have you tried fixing the molecule that looks correct and searching for others? 
You might have greater than one but less than 9 molecules per ASU.

When you do this, try imposing severe restraints on the packing function. This 
worked for me in Phaser with a difficult case. My anecdotal experience is that, 
when you have lots of molecules per asu, the correct solution gets swamped by 
poorly-packed solutions if the default packing penalties are used.

Good luck.

Sent from my iPhone

> On May 15, 2014, at 6:50 PM, "Matthew Bratkowski"  wrote:
> 
> Hello all,
> 
> 
> I am working on the structure of a small protein in space group P212121.  The 
> protein is monomeric in solution based on gel filtration analysis.  The 
> Matthews Coefficeint program indicates that 9-10 molecules per asymmetric 
> unit results in ~50% solvent content, while 1 molecule per asymmetric unit 
> results in ~95% solvent. 
> 
>  I tried molecular replacement with a search model which is essentially 
> identical in sequence to my protein, and searched for 9 or 10 molecules/asu.  
> Using MolRep with 9 or 10 molecules/asu, I get poor contrast scores around 
> 1-1.5.  However, when using Phaser, I get a solution with one molecules/asu.  
> Likewise, when I went back and tried MolRep with 1 molecule/asu, I got a 
> contrast score of 3.12.  This model still has some issues, but looks more 
> correct compaired to models created with 9 or 10  molecules/asu. 
> 
> It seems highly unlikely that a crystal would contain 95% solvent, but is 
> there any possiblility that this could be the case?  Assuming that the 
> Matthews coefficient is correct, does anyone have an idea why MR seems to 
> work better for 1 molecule/asu with 95% solvent content compared to 9-10 
> molecules with 50% solvent content? Alternatively, is there any reason why 
> the Matthews coefficient could be calculating incorrectly?  Any suggestions 
> would be helpful.
> 
> Thanks,
> Matt  

[ccp4bb] report mosaicity

[hongshi WANG]

Hello everyone,

I am gonna report the mosaicity of my data set as required by the journal.
I processed the data using HKL2000. So I checked the denzo log file. I
found many different mosaicity values. The first one is default input
(0.3), the rest are corresponding to specific images. I think the mosaicity
value required should be an overall value or averaged value. Could you
please let me know how I can get it.  Or some other software can determine
it.
I really appreciate your help and response!

Hongshi

[ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular Replacement

[Matthew Bratkowski]

Hello all,


I am working on the structure of a small protein in space group P212121.
 The protein is monomeric in solution based on gel filtration analysis.
 The Matthews Coefficeint program indicates that 9-10 molecules per
asymmetric unit results in ~50% solvent content, while 1 molecule per
asymmetric unit results in ~95% solvent.

 I tried molecular replacement with a search model which is essentially
identical in sequence to my protein, and searched for 9 or 10
molecules/asu.  Using MolRep with 9 or 10 molecules/asu, I get poor
contrast scores around 1-1.5.  However, when using Phaser, I get a solution
with one molecules/asu.  Likewise, when I went back and tried MolRep with 1
molecule/asu, I got a contrast score of 3.12.  This model still has some
issues, but looks more correct compaired to models created with 9 or 10
 molecules/asu.

It seems highly unlikely that a crystal would contain 95% solvent, but is
there any possiblility that this could be the case?  Assuming that the
Matthews coefficient is correct, does anyone have an idea why MR seems to
work better for 1 molecule/asu with 95% solvent content compared to 9-10
molecules with 50% solvent content? Alternatively, is there any reason why
the Matthews coefficient could be calculating incorrectly?  Any suggestions
would be helpful.

Thanks,
Matt

[ccp4bb] Seeking postdoctoral candidate

[Reza Khayat]

Hi,

The research group of Dr. Reza Khayat at the City College of 
New York (www.khayatlab.org) is seeking candidate postdoctoral 
fellows to study host pathogen interaction using a combination 
of cryo-electron microscopy (cryo-EM), X-ray crystallography, 
biophysics and biochemistry. The research group is 
particularly interested in elucidating the structural 
mechanism by which enveloped and nonenveloped viruses and 
bacteriophages interact with their hosts to: acquire cellular 
entry, hijack cellular machinery, disassemble, replicate, 
assemble and egress. The group is also interested in 
determining the mechanism by which host antibodies and 
synthetic DNA aptamers neutralize the viruses.

The group has dedicated access to a JEOL 2100 and Zeiss EM902 
for grid preparation and screening, and to the resources at 
the New York Structural Biology Center (NYSBC) that include 
facilities for cryo-EM grid and sample preparation, JEOL 
3200FSC, Tecnai F20, JEOL 2100F, JEOL 1230 and a FEI Helios 
650. The group also has dedicated access to state-of-art 
instrumentation to be housed at the Advanced Science and 
Research Center (ASRC). Both NYSBC and ASRC are located in 
adjacent buildings and within five minute walking distance 
from the laboratory (GPS: 40.815927, -73.951201).

The group has open access to multiple Gryphon LCP robots for 
conducting crystallization experiments at multiple 
temperatures, Alchemist DT for screen optimization, and 
Minstrel HT for crystal imaging and data storage. The group 
shares the following instrumentation: microplate readers, ITC, 
DLS, CD, and bioreactors.

Candidates must have a Ph.D., be highly motivated, exhibit 
independence, and have experience with protein purification. 
Salary will be competitive for the NYC area and be 
commensurate with experience and prior success. Please send a 
cover letter, CV, and the names with contact information for 
three references to rkha...@ccny.cuny.edu.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY  10031
Tel. (212) 650-6070
www.khayatlab.org

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Pavel Afonine]

TWILIGHT database, PDBREDO database, ... what else I forgot to name? I
wonder why it should be under different brands and names, and not just be
where it belongs to - the PDB?!

Back in 2005 when I (and colleagues) started re-refining the entire PDB (to
test phenix.refine, mostly) and seeing oddities (by now well documented in
the above mentioned debases and related publications) I felt very excited
about starting a databases of curated structures, but thinking a bit it
appeared strange and unnatural to have a "parallel" version of PDB.

Pavel


On Thu, May 15, 2014 at 11:23 AM, Nat Echols wrote:

> That is an extraordinary case, and it certainly took a huge amount of
> work.  What about structures that are obviously wrong based on inspection
> of the density, but no one has bothered to challenge yet?  The TWILIGHT
> database helps some, if that counts, but it doesn't catch everything.
>
> -Nat
>
>
>
> On Thu, May 15, 2014 at 10:48 AM, Patrick Shaw Stewart <
> patr...@douglas.co.uk> wrote:
>
>>
>> I may be missing something here, but I don't think you have to rebut
>> anything.  You simply report that someone else has rebutted it.  Along the
>> lines of
>>
>> Many scientists regard this published structure as unreliable since a
>> misconduct investigation by the University of Alabama at Birmingham has
>> concluded that it
>> was, "more likely than not", faked [1]
>>
>> [1] http://www.nature.com/news/2009/091222/full/462970a.html
>>
>>
>>
>>
>>
>>
>> On 15 May 2014 18:00, Nat Echols  wrote:
>>
>>> On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart <
>>> patr...@douglas.co.uk> wrote:
>>>
 It seems to me that the Wikipedia mechanism works wonderfully well.
  One rule is that you can't make assertions yourself, only report
 pre-existing material that is attributable to a "reliable published
 source".

>>>
>>> This rule would be a little problematic for annotating the PDB.  It
>>> requires a significant amount of effort to publish a peer-reviewed article
>>> or even just a letter to the editor, and none of us are being paid to write
>>> rebuttals to dodgy structures.
>>>
>>> -Nat
>>>
>>
>>
>>
>> --
>>  patr...@douglas.co.ukDouglas Instruments Ltd.
>>  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
>>  Directors: Peter Baldock, Patrick Shaw Stewart
>>
>>  http://www.douglas.co.uk
>>  Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
>>  Regd. England 2177994, VAT Reg. GB 480 7371 36
>>
>
>

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Duarte Gamero Jose Manuel]

If one limits such a comment system to authors of PDB structures then you are 
closing the door to a lot of potentially good contributors: anyone involved in 
analysing protein structures. For instance that can be anyone in the fields of 
structural bioinformatics, molecular dynamics, computational crystallography 
etc. Those people can have quite a say in these discussions and are even very 
likely to find issues since they write tools to automatically analyse PDB 
structures. 

As I said, I'd go for a system totally open for anyone who wants to register. 
Modern tools to allow scoring of the feedback by the rest of the community 
would sort all problems out, provided there is enough participation.

Jose


-Original Message-
From: CCP4 bulletin board on behalf of Zachary Wood
Sent: Thu 5/15/2014 7:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
 
I agree with Nat. If you think a structure has a problem area, it is much 
easier to point it out to the users than to publish a rebuttal. 

Comments are easy. Simply state your observation. If you are wrong in your 
assessment, I am sure you will receive a fine education from the more learned 
individuals in our community. And since this pertains to the entire PDB, I do 
not see a lot spam/noise being produced on a single structure. I would suspect 
almost nothing will be said regarding the majority of the 100,000 structures. I 
am not aware of a ton of spam being produced on the publications in the Pubmed 
Commons. In fact, it saddens me that no one has said anything significant about 
my publications.  I personally would prefer to limit the feedback to those who 
deposit structures (similar to how Pubmed Commons limits comments to authors). 
I believe that we as a community are the ones best positioned to police the 
database. 

Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor  
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***
Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor  
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***







On May 15, 2014, at 1:00 PM, Nat Echols  wrote:

> On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart  
> wrote:
> It seems to me that the Wikipedia mechanism works wonderfully well.  One rule 
> is that you can't make assertions yourself, only report pre-existing material 
> that is attributable to a "reliable published source".  
> 
> This rule would be a little problematic for annotating the PDB.  It requires 
> a significant amount of effort to publish a peer-reviewed article or even 
> just a letter to the editor, and none of us are being paid to write rebuttals 
> to dodgy structures.
> 
> -Nat

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Nat Echols]

That is an extraordinary case, and it certainly took a huge amount of
work.  What about structures that are obviously wrong based on inspection
of the density, but no one has bothered to challenge yet?  The TWILIGHT
database helps some, if that counts, but it doesn't catch everything.

-Nat



On Thu, May 15, 2014 at 10:48 AM, Patrick Shaw Stewart <
patr...@douglas.co.uk> wrote:

>
> I may be missing something here, but I don't think you have to rebut
> anything.  You simply report that someone else has rebutted it.  Along the
> lines of
>
> Many scientists regard this published structure as unreliable since a
> misconduct investigation by the University of Alabama at Birmingham has
> concluded that it
> was, "more likely than not", faked [1]
>
> [1] http://www.nature.com/news/2009/091222/full/462970a.html
>
>
>
>
>
>
> On 15 May 2014 18:00, Nat Echols  wrote:
>
>> On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart <
>> patr...@douglas.co.uk> wrote:
>>
>>> It seems to me that the Wikipedia mechanism works wonderfully well.  One
>>> rule is that you can't make assertions yourself, only report pre-existing
>>> material that is attributable to a "reliable published source".
>>>
>>
>> This rule would be a little problematic for annotating the PDB.  It
>> requires a significant amount of effort to publish a peer-reviewed article
>> or even just a letter to the editor, and none of us are being paid to write
>> rebuttals to dodgy structures.
>>
>> -Nat
>>
>
>
>
> --
>  patr...@douglas.co.ukDouglas Instruments Ltd.
>  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
>  Directors: Peter Baldock, Patrick Shaw Stewart
>
>  http://www.douglas.co.uk
>  Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
>  Regd. England 2177994, VAT Reg. GB 480 7371 36
>

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Patrick Shaw Stewart]

I may be missing something here, but I don't think you have to rebut
anything.  You simply report that someone else has rebutted it.  Along the
lines of

Many scientists regard this published structure as unreliable since a
misconduct investigation by the University of Alabama at Birmingham has
concluded that it
was, "more likely than not", faked [1]

[1] http://www.nature.com/news/2009/091222/full/462970a.html






On 15 May 2014 18:00, Nat Echols  wrote:

> On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart <
> patr...@douglas.co.uk> wrote:
>
>> It seems to me that the Wikipedia mechanism works wonderfully well.  One
>> rule is that you can't make assertions yourself, only report pre-existing
>> material that is attributable to a "reliable published source".
>>
>
> This rule would be a little problematic for annotating the PDB.  It
> requires a significant amount of effort to publish a peer-reviewed article
> or even just a letter to the editor, and none of us are being paid to write
> rebuttals to dodgy structures.
>
> -Nat
>



-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Zachary Wood]

I agree with Nat. If you think a structure has a problem area, it is much 
easier to point it out to the users than to publish a rebuttal. 

Comments are easy. Simply state your observation. If you are wrong in your 
assessment, I am sure you will receive a fine education from the more learned 
individuals in our community. And since this pertains to the entire PDB, I do 
not see a lot spam/noise being produced on a single structure. I would suspect 
almost nothing will be said regarding the majority of the 100,000 structures. I 
am not aware of a ton of spam being produced on the publications in the Pubmed 
Commons. In fact, it saddens me that no one has said anything significant about 
my publications.  I personally would prefer to limit the feedback to those who 
deposit structures (similar to how Pubmed Commons limits comments to authors). 
I believe that we as a community are the ones best positioned to police the 
database. 

Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor  
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***
Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor  
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***







On May 15, 2014, at 1:00 PM, Nat Echols  wrote:

> On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart  
> wrote:
> It seems to me that the Wikipedia mechanism works wonderfully well.  One rule 
> is that you can't make assertions yourself, only report pre-existing material 
> that is attributable to a "reliable published source".  
> 
> This rule would be a little problematic for annotating the PDB.  It requires 
> a significant amount of effort to publish a peer-reviewed article or even 
> just a letter to the editor, and none of us are being paid to write rebuttals 
> to dodgy structures.
> 
> -Nat

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Nat Echols]

On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart  wrote:

> It seems to me that the Wikipedia mechanism works wonderfully well.  One
> rule is that you can't make assertions yourself, only report pre-existing
> material that is attributable to a "reliable published source".
>

This rule would be a little problematic for annotating the PDB.  It
requires a significant amount of effort to publish a peer-reviewed article
or even just a letter to the editor, and none of us are being paid to write
rebuttals to dodgy structures.

-Nat

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Patrick Shaw Stewart]

It seems to me that the Wikipedia mechanism works wonderfully well.  One
rule is that you can't make assertions yourself, only report pre-existing
material that is attributable to a "reliable published source".

It's immediately obvious when something is controversial.  Here's the first
para of the entry on statins, which are currently being debated in the UK:

*Statins* (or *HMG-CoA reductase inhibitors*) are a class of
drugs used
to lower cholesterol  levels by
inhibiting  the enzyme HMG-CoA
reductase , which plays a
central role in the production of cholesterol in the
liver,
which produces about 70 percent of total cholesterol in the body. Increased
cholesterol levels have been associated with cardiovascular
disease
(CVD).[1]  Statins have
been found to prevent
 cardiovascular
disease in those who are at high risk. The evidence is strong that statins
are effective for treating CVD in the early stages of a disease (secondary
prevention ). The
evidence is weaker that statins are effective for those with elevated
cholesterol levels but without CVD (primary
prevention
).[2] 
[3]
[4]  Side
effects of statins include muscle pain, increased risk of
diabetes and
abnormalities in liver enzyme
tests
.[5]  Additionally,
they have rare but severe adverse effects, particularly muscle
damage.[6]
Some
doctors believe that statins are over-prescribed.

(Could Proteopedia adopt a style that is closer to that?)




On 15 May 2014 15:35, Bernhard Rupp  wrote:

> Maybe  a prominent link in the summary page of e.g. PDBe 2a01 would help.
>
> So far, you need to go there  and expand Links -> pdb_redo -> links ->
>  Proteopedia to get to the corresponding warning.
>
> http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html#
>
> http://www.cmbi.ru.nl/pdb_redo/a0/2a01/index.html
>
> http://proteopedia.org/wiki/index.php/2a01
>
>
>
> ‘More information about this (or any) entry may be available in
> Proteopedia’
>
>
>
> Best, BR
>
>
>
> Ceterum censeo structurae Murthius delendati erunt.
>
>
>
> (Marcus Tullius Raaijmakers)
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Joel
> Sussman
> *Sent:* Donnerstag, 15. Mai 2014 16:01
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
>
>
>
> 15-May-2014
>
> Dear Martyn
>
>Proteopedia's (*http://proteopedia.org *) goal
> goes well beyond just education - it is aimed at Structural Biology and non
> Structural Biology Community and it would be pleased to be a forum for
> discussion of structures that are questionable. There are now over 2,600
> registered users, who are contributing to Proteopedia, in over 50 different
> countries.
>
>*Proteopedia has a special area for discussions related to each
> structure*. *To access it, you go to the structure's page, e.g.
> http://proteopedia.org/w/2x24 * and *click
> on the 'discussion' tab* on the page's upper border. Everyone can read
> the comments there, and it will open a fully editable page for every
> registered user to add *their comments on the structure and their full
> name will be listed below their comments.*
>
>If you would like to contribute to this, we’d be pleased to welcome
> your input.
>
>Best regards,
>
>Jaime Prilusky & Joel Sussman
>
>
>
>
>
> On 15May, 2014, at 7:29, MARTYN SYMMONS <
> martainn_oshioma...@btinternet.com> wrote:
>
>
>
> I agree some forum for community annotation and commenting would be a good
> thing for users of structural data.
>
> There was an attempt to do that with the pdbwiki project which was a
> community resource for the bioinformatics community. Unfortunately pdbwiki
> has now folded (see http://pdbwiki.org/) They are now directing people to
> Proteopedia. However Proteopedia has a more educative focus I think -
> rather than capturing technical questions and input.
>
>
>
> Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a
> forum for discussing the literature, is currently under testing. Perhaps
> this is the sort of thing that could work for structural data?
>
>
>
> cheers
>
>  M

[ccp4bb] PhD studentships in tackling M. abscessus infections in Cystic Fibrosis

[Marko Hyvonen]

PhD studentships in a collaborative project "Tackling Mycobacterium abscessus 
infection in Cystic Fibrosis"


http://www.jobs.cam.ac.uk/job/3954/

(see "Position 3" for the structural biology project)

The Departments of Biochemistry and Medicine, University of Cambridge, are 
pleased to offer 3 PhD studentships, funded by a Strategic Research Centre Award 
from The Cystic Fibrosis (CF) Trust UK, to start in October 2014 or January 
2015. The area of research will be the study of the rapid growing nontuberculous 
mycobacterium (NTM) Mycobacterium abscessus, which has emerged as a major threat 
to individuals with CF, focusing on understanding pathogenesis (through cell 
biology and population-based whole genome sequencing) and developing novel 
therapeutics (through Fragment-Based Drug Development).


We invite applications from highly motivated, enthusiastic individuals for these 
studentships leading to PhDs in the University of Cambridge. We anticipate that 
the students will work closely together and have the opportunity to develop a 
broad range of expertise across the projects.


Position 1
Supervised by Dr Andres Floto, Cambridge Institute for Medical Research/ 
Department of Medicine, and Professor Julian Parkhill, Wellcome Trust Sanger 
Institute.


The student will use cell and molecular biology techniques to understand how 
macrophages interact with M. abscessus, define novel genetic determinants 
(informed through whole genome sequencing) regulating host restriction and 
mycobacterial virulence and identify novel therapeutics to stimulate autophagic 
killing.


Position 2
Supervised by Professor Julian Parkhill, Wellcome Trust Sanger Institute, and Dr 
Andres Floto, Cambridge Institute for Medical Research/ Department of Medicine


The student will use large-scale population-level genomics on local and global 
M. abscessus populations to identify emerging and transmitting clones, and 
predict determinants of virulence and transmissibility that can be tested in the 
in vitro and in vivo models. Building on our recent identification of 
patient-to-patient transmission and the emergence of dominant clones, the 
student will use phylogenetic analyses to investigate the adaption of M. 
abscessus to survival in the CF lung, and to transmission between hosts.


Position 3
Supervised by Professor Sir Tom Blundell and Dr Marko Hyvonen, Department of 
Biochemistry


The student will use fragment-based drug discovery (FBDD) approach involving (i) 
expression and characterisation of protein targets, (ii) use of a cascade of 
biophysical techniques, followed by protein X-ray crystallography to define the 
3D structures of the complexes, and (iii) knowledge of fragment binding to 
target proteins to select commercially available compounds that would likely 
give rise to higher affinities (SAR-by-catalogue). Once a sufficiently potent 
molecule has been developed, it efficacy will be tested in cellular assays.


Queries should be made to Dr Andres Floto (ar...@cam.ac.uk) (Position 1), Prof. 
Julian Parkhill (parkh...@sanger.ac.uk) (Position 2), Prof. Sir Tom Blundell 
(tl...@cam.ac.uk) and Dr Marko Hyvonen (mh...@cam.ac.uk) (Position 3).


Candidates will be expected to have a strong CV having completed, or about to 
complete, a degree relevant to cell biology, microbiology, bioinformatics or 
structural biology but we shall consider all suitably qualified applicants.


The funding for UK/EU nationals covers stipend, University Composition fees and 
College fees for 3 years, with the potential for an extension to a fourth year. 
Overseas applicants are eligible to apply, but would be required to self-fund 
the cost difference of University Composition fees for overseas students 
compared with UK/EU students (approximately £15,700 per year for 3 years).


Applications should be sent as a single pdf document and should include a 
curriculum vitae and contact details (including email addresses) of two academic 
referees, together with a single page outline of why the applicant wishes to 
apply for , this studentship programme. Applications should be sent by email to 
cf-...@bioc.cam.ac.uk, with a subject line indicating which position the 
application is for.


Application deadline: 28th June 2014. Short-listed applicants will be invited to 
interview.


PhD expected start date: 01 October 2014 or January 2015


 --

 Marko Hyvonen
 Department of Biochemistry, University of Cambridge
 mh...@cam.ac.uk
 http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
 tel:+44-(0)1223-766 044

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Zachary Wood]

Dear Jaime and Joel, 

Perhaps an easier solution would be to get the PDB to put an obvious link on 
each entry directing the user to the Proteopedia site for discussion and 
additional details.  I would personally prefer a comments/discussion section on 
the PDB page, but as long as one is easily accessible I would be happy. By the 
way, you guys are doing a great job, and I will now go officially register on 
your site so that I can be user 2,601 ;-)

Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor  
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***







On May 15, 2014, at 10:00 AM, Joel Sussman  wrote:

> 15-May-2014
> Dear Martyn
>Proteopedia's (http://proteopedia.org) goal goes well beyond just 
> education - it is aimed at Structural Biology and non Structural Biology 
> Community and it would be pleased to be a forum for discussion of structures 
> that are questionable. There are now over 2,600 registered users, who are 
> contributing to Proteopedia, in over 50 different countries. 
>Proteopedia has a special area for discussions related to each structure. 
> To access it, you go to the structure's page, e.g. 
> http://proteopedia.org/w/2x24 and click on the 'discussion' tab on the page's 
> upper border. Everyone can read the comments there, and it will open a fully 
> editable page for every registered user to add their comments on the 
> structure and their full name will be listed below their comments.
>If you would like to contribute to this, we’d be pleased to welcome your 
> input.
>Best regards,
>Jaime Prilusky & Joel Sussman 
> 
> 
> On 15May, 2014, at 7:29, MARTYN SYMMONS  
> wrote:
> 
>> I agree some forum for community annotation and commenting would be a good 
>> thing for users of structural data. 
>> There was an attempt to do that with the pdbwiki project which was a 
>> community resource for the bioinformatics community. Unfortunately pdbwiki 
>> has now folded (see http://pdbwiki.org/) They are now directing people to 
>> Proteopedia. However Proteopedia has a more educative focus I think - rather 
>> than capturing technical questions and input.
>> 
>> Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a 
>> forum for discussing the literature, is currently under testing. Perhaps 
>> this is the sort of thing that could work for structural data?
>>  
>> cheers
>>  Martyn 
>> 
>> From: Ethan A Merritt 
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Sent: Wednesday, 14 May 2014, 19:22
>> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
>> 
>> On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
>> > As long as it's just a Technical Comments section - an obvious concern 
>> > would be the signal/noise in the comments themselves.  I'm sure PDB 
>> > would not relish having to moderate that lot.
>> > 
>> > Alternatively PDB can overtly link to papers that discuss technical 
>> > issues that reference the particular structure - wrong or fraudulent 
>> > structures are often associated with refereed publications that point 
>> > that out, and structures with significant errors often show up in that 
>> > way too.  I once did a journal club on Muller (2013) Acta Cryst 
>> > F69:1071-1076 and wish that could be associated with the relevant PDB 
>> > file(s).
>> 
>> Perhaps some combination of those two ideas?
>> 
>> The PDB could associate with each deposited structure  a crowd-sourced
>> list of published articles citing it.They already make an effort to
>> attach the primary citation, but so far as I know there is currently
>> no effort to track subsequent citations.  
>> 
>> While spam comments in a free-format forum are probably inevitable,
>> spam submission of citing papers seems less likely to be a problem.
>> 
>> - Ethan
>> 
>> > > On Wed, May 14, 2014 at 12:32 PM, Zachary Wood > > > > wrote:
>> > >
>> > >Hello All,
>> > >
>> > >Instead of placing the additional burden of policing on the good
>> > >people at the PDB, perhaps the entry page for each structure could
>> > >contain a comments section. Then the community could point out
>> > >serious concerns for the less informed users. At least that will
>> > >give users some warning in the case of particularly worrisome
>> > >structures. The authors of course could still reply to defend their
>> > >structure, and it may encourage some people to even correct their
>> > >errors.
>> > >
>> -- 
>> Ethan A Merritt
>> Biomolecular Structure Center,  K-428 Health Sciences Bldg
>> MS 357742,  University of Washington, Seattle 98195-7742
>> 
>> 
> 

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Bernhard Rupp]

Maybe  a prominent link in the summary page of e.g. PDBe 2a01 would help. 

So far, you need to go there  and expand Links -> pdb_redo -> links ->
Proteopedia to get to the corresponding warning.

http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html#

http://www.cmbi.ru.nl/pdb_redo/a0/2a01/index.html

http://proteopedia.org/wiki/index.php/2a01

 

'More information about this (or any) entry may be available in Proteopedia'


 

Best, BR

 

Ceterum censeo structurae Murthius delendati erunt.

 

(Marcus Tullius Raaijmakers) 

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joel
Sussman
Sent: Donnerstag, 15. Mai 2014 16:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone

 

15-May-2014

Dear Martyn

   Proteopedia's (http://proteopedia.org) goal goes well beyond just
education - it is aimed at Structural Biology and non Structural Biology
Community and it would be pleased to be a forum for discussion of structures
that are questionable. There are now over 2,600 registered users, who are
contributing to Proteopedia, in over 50 different countries. 

   Proteopedia has a special area for discussions related to each structure.
To access it, you go to the structure's page, e.g.
http://proteopedia.org/w/2x24 and click on the 'discussion' tab on the
page's upper border. Everyone can read the comments there, and it will open
a fully editable page for every registered user to add their comments on the
structure and their full name will be listed below their comments.

   If you would like to contribute to this, we'd be pleased to welcome your
input.

   Best regards,

   Jaime Prilusky & Joel Sussman 

 

 

On 15May, 2014, at 7:29, MARTYN SYMMONS 
wrote:





I agree some forum for community annotation and commenting would be a good
thing for users of structural data. 

There was an attempt to do that with the pdbwiki project which was a
community resource for the bioinformatics community. Unfortunately pdbwiki
has now folded (see http://pdbwiki.org/) They are now directing people to
Proteopedia. However Proteopedia has a more educative focus I think - rather
than capturing technical questions and input.

 

Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a
forum for discussing the literature, is currently under testing. Perhaps
this is the sort of thing that could work for structural data?

 

cheers

 Martyn 

 

  _  

From: Ethan A Merritt 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone


On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
> As long as it's just a Technical Comments section - an obvious concern 
> would be the signal/noise in the comments themselves.  I'm sure PDB 
> would not relish having to moderate that lot.
> 
> Alternatively PDB can overtly link to papers that discuss technical 
> issues that reference the particular structure - wrong or fraudulent 
> structures are often associated with refereed publications that point 
> that out, and structures with significant errors often show up in that 
> way too.  I once did a journal club on Muller (2013) Acta Cryst 
> F69:1071-1076 and wish that could be associated with the relevant PDB 
> file(s).

Perhaps some combination of those two ideas?

The PDB could associate with each deposited structure  a crowd-sourced
list of published articles citing it.They already make an effort to
attach the primary citation, but so far as I know there is currently
no effort to track subsequent citations.  

While spam comments in a free-format forum are probably inevitable,
spam submission of citing papers seems less likely to be a problem.

- Ethan

> > On Wed, May 14, 2014 at 12:32 PM, Zachary Wood  > > wrote:
> >
> >Hello All,
> >
> >Instead of placing the additional burden of policing on the good
> >people at the PDB, perhaps the entry page for each structure could
> >contain a comments section. Then the community could point out
> >serious concerns for the less informed users. At least that will
> >give users some warning in the case of particularly worrisome
> >structures. The authors of course could still reply to defend their
> >structure, and it may encourage some people to even correct their
> >errors.
> >
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742



 

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Jose Manuel Duarte]

As one of the responsible people for the pdbwiki project I feel I should 
comment on this one. We went out of business simply for lack of 
resources, it was difficult to keep things up-to-date and specially it 
was very difficult to combat spam. So in the end we decided to shut down 
the project.


In any case we always thought of the project more as a proof-of-concept 
than anything else. We wanted to show that a community-driven feedback 
and annotation system is needed for the PDB. I personally think that if 
such a system were to be set up by the PDB, it would be a great service 
for anyone (including the PDB themselves since some of that feedback 
could eventually go back to the main database).


In my opinion the system should stay as open as possible, allowing 
anyone to comment. The community can self-moderate it and do continuous 
reviewing. This kind of system is already used in many places and works 
extremely well. See for instance stackoverflow.com for computing-related 
questions, or even biostars.org for bioinformatics-related ones. 
Upvoting/downvoting together with user-scoring mechanisms produce 
stunningly good results.


Just my 2 cents

Jose



On 15/05/14 13:29, MARTYN SYMMONS wrote:
I agree some forum for community annotation and commenting would be a 
good thing for users of structural data.
There was an attempt to do that with the pdbwiki project which was a 
community resource for the bioinformatics community. Unfortunately 
pdbwiki has now folded (see http://pdbwiki.org/) They are now 
directing people to Proteopedia. However Proteopedia has a more 
educative focus I think - rather than capturing technical questions 
and input.


Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is 
a forum for discussing the literature, is currently under testing. 
Perhaps this is the sort of thing that could work for structural data?

cheers
 Martyn


*From:* Ethan A Merritt 
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Wednesday, 14 May 2014, 19:22
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone

On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
> As long as it's just a Technical Comments section - an obvious concern
> would be the signal/noise in the comments themselves.  I'm sure PDB
> would not relish having to moderate that lot.
>
> Alternatively PDB can overtly link to papers that discuss technical
> issues that reference the particular structure - wrong or fraudulent
> structures are often associated with refereed publications that point
> that out, and structures with significant errors often show up in that
> way too.  I once did a journal club on Muller (2013) Acta Cryst
> F69:1071-1076 and wish that could be associated with the relevant PDB
> file(s).

Perhaps some combination of those two ideas?

The PDB could associate with each deposited structure  a crowd-sourced
list of published articles citing it.They already make an effort to
attach the primary citation, but so far as I know there is currently
no effort to track subsequent citations.

While spam comments in a free-format forum are probably inevitable,
spam submission of citing papers seems less likely to be a problem.

- Ethan

> > On Wed, May 14, 2014 at 12:32 PM, Zachary Wood 

> > >> wrote:
> >
> >Hello All,
> >
> >Instead of placing the additional burden of policing on the good
> >people at the PDB, perhaps the entry page for each structure could
> >contain a comments section. Then the community could point out
> >serious concerns for the less informed users. At least that will
> >give users some warning in the case of particularly worrisome
> >structures. The authors of course could still reply to defend their
> >structure, and it may encourage some people to even correct their
> >errors.
> >
--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742

Re: [ccp4bb] PDB passes 100,000 structure milestone

[MARTYN SYMMONS]

Dear Zachary
I once suggested this sort of discussion forum to a PDB PI as a possible 
service that could be a ' validation fight-club '  - which suggestion was not 
well received ;) But as you say it is down to setting the correct professional 
tone. 

One thing that would allow a visual discussion would be the possibility to 
share molecular representations - similar to the way Proteopedia uses Jmol 
scripting to drive the graphics from the webpages. In this way commentators 
could share viewpoint and representations to make their points. This would make 
it most useful to the wider biological community. 

all the best
 Martyn 

  



 From: Zachary Wood 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Thursday, 15 May 2014, 14:47
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
 



Adding to Tim’s comment, I would not expect a tremendous amount of spurious 
comments about a single PDB out of 100,000 unless there was a problem. 
Especially if the Pubmed Commons model was applied, and only depositors could 
comment. I would assume this would be very beneficial, given that we are 
conscientious professionals.  Could actually be a great forum for authors to go 
a little deeper into specific approaches or problems that they had with a 
structure. Not all interesting details make it to the pub.  



Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor                      
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:    706-583-0303
FAX: 706-542-1738
***







On May 15, 2014, at 9:39 AM, Tim Gruene  wrote:

-BEGIN PGP SIGNED MESSAGE-
>Hash: SHA1
>
>Dear all,
>
>isn't the ccp4bb a very good example that spam may not be such an
>issue for a discussion platform on structures in the PDB? There is a
>great variety of opinions, some to agree with, some to disagree, but
>all of them interesting and contributing, and I hardly remember a
>message I would classify as spam. And it all works without restraints.
>
>Best,
>Tim
>
>
>On 05/15/2014 03:21 PM, Zachary Wood wrote:
>
>I agree with Martyn,
>>
>>Pubmed Commons could be a great model. I believe you have to be a
>>published author to obtain an account. It might cut down on some of
>>the spam/noise if the PDB adopted such a model for depositors.
>>
>>Best regards,
>>
>>Z
>>
>>
>>*** Zachary A. Wood,
>>Ph.D. Associate Professor Department of Biochemistry & Molecular
>>Biology University of Georgia Life Sciences Building, Rm A426B 120
>>Green Street Athens, GA  30602-7229 Office: 706-583-0304 Lab:
>>706-583-0303 FAX: 706-542-1738 
>>***
>>
>>
>>
>>
>>
>>
>>
>>On May 15, 2014, at 7:29 AM, MARTYN SYMMONS
>> wrote:
>>
>>
>>I agree some forum for community annotation and commenting would
>>>be a good thing for users of structural data. There was an
>>>attempt to do that with the pdbwiki project which was a community
>>>resource for the bioinformatics community. Unfortunately pdbwiki
>>>has now folded (see http://pdbwiki.org/) They are now directing
>>>people to Proteopedia. However Proteopedia has a more educative
>>>focus I think - rather than capturing technical questions and
>>>input.
>>>
>>>Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/),
>>>which is a forum for discussing the literature, is currently
>>>under testing. Perhaps this is the sort of thing that could work
>>>for structural data?
>>>
>>>cheers Martyn
>>>
>>>From: Ethan A Merritt  To:
>>>CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 
>>>Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
>>>
>>>On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
>>>
>>>As long as it's just a Technical Comments section - an obvious
concern would be the signal/noise in the comments themselves.
I'm sure PDB would not relish having to moderate that lot.

Alternatively PDB can overtly link to papers that discuss
technical issues that reference the particular structure -
wrong or fraudulent structures are often associated with
refereed publications that point that out, and structures with
significant errors often show up in that way too.  I once did a
journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish
that could be associated with the relevant PDB file(s).

>>>Perhaps some combination of those two ideas?
>>>
>>>The PDB could associate with each deposited structure  a
>>>crowd-sourced list of published articles citing it.    They
>>>already make an effort to attach the primary citation, but so far
>>>as I know there is currently no effort to track subsequent
>>>citations.
>>>
>>>While spam comments in a free-format forum are probably
>>>inevitable, spam submission of citing papers seems less lik

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Joel Sussman]

15-May-2014
Dear Martyn
   Proteopedia's (http://proteopedia.org) goal goes well beyond just education 
- it is aimed at Structural Biology and non Structural Biology Community and it 
would be pleased to be a forum for discussion of structures that are 
questionable. There are now over 2,600 registered users, who are contributing 
to Proteopedia, in over 50 different countries.
   Proteopedia has a special area for discussions related to each structure. To 
access it, you go to the structure's page, e.g. http://proteopedia.org/w/2x24 
and click on the 'discussion' tab on the page's upper border. Everyone can read 
the comments there, and it will open a fully editable page for every registered 
user to add their comments on the structure and their full name will be listed 
below their comments.
   If you would like to contribute to this, we’d be pleased to welcome your 
input.
   Best regards,
   Jaime Prilusky & Joel Sussman


On 15May, 2014, at 7:29, MARTYN SYMMONS 
mailto:martainn_oshioma...@btinternet.com>> 
wrote:

I agree some forum for community annotation and commenting would be a good 
thing for users of structural data.
There was an attempt to do that with the pdbwiki project which was a community 
resource for the bioinformatics community. Unfortunately pdbwiki has now folded 
(see http://pdbwiki.org/) They are now directing people to Proteopedia. However 
Proteopedia has a more educative focus I think - rather than capturing 
technical questions and input.

Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum 
for discussing the literature, is currently under testing. Perhaps this is the 
sort of thing that could work for structural data?

cheers
 Martyn


From: Ethan A Merritt 
mailto:merr...@u.washington.edu>>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone

On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
> As long as it's just a Technical Comments section - an obvious concern
> would be the signal/noise in the comments themselves.  I'm sure PDB
> would not relish having to moderate that lot.
>
> Alternatively PDB can overtly link to papers that discuss technical
> issues that reference the particular structure - wrong or fraudulent
> structures are often associated with refereed publications that point
> that out, and structures with significant errors often show up in that
> way too.  I once did a journal club on Muller (2013) Acta Cryst
> F69:1071-1076 and wish that could be associated with the relevant PDB
> file(s).

Perhaps some combination of those two ideas?

The PDB could associate with each deposited structure  a crowd-sourced
list of published articles citing it.They already make an effort to
attach the primary citation, but so far as I know there is currently
no effort to track subsequent citations.

While spam comments in a free-format forum are probably inevitable,
spam submission of citing papers seems less likely to be a problem.

- Ethan

> > On Wed, May 14, 2014 at 12:32 PM, Zachary Wood 
> > mailto:z...@bmb.uga.edu>
> > >> wrote:
> >
> >Hello All,
> >
> >Instead of placing the additional burden of policing on the good
> >people at the PDB, perhaps the entry page for each structure could
> >contain a comments section. Then the community could point out
> >serious concerns for the less informed users. At least that will
> >give users some warning in the case of particularly worrisome
> >structures. The authors of course could still reply to defend their
> >structure, and it may encourage some people to even correct their
> >errors.
> >
--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Zachary Wood]

Adding to Tim’s comment, I would not expect a tremendous amount of spurious 
comments about a single PDB out of 100,000 unless there was a problem. 
Especially if the Pubmed Commons model was applied, and only depositors could 
comment. I would assume this would be very beneficial, given that we are 
conscientious professionals.  Could actually be a great forum for authors to go 
a little deeper into specific approaches or problems that they had with a 
structure. Not all interesting details make it to the pub.  

Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor  
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***







On May 15, 2014, at 9:39 AM, Tim Gruene  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear all,
> 
> isn't the ccp4bb a very good example that spam may not be such an
> issue for a discussion platform on structures in the PDB? There is a
> great variety of opinions, some to agree with, some to disagree, but
> all of them interesting and contributing, and I hardly remember a
> message I would classify as spam. And it all works without restraints.
> 
> Best,
> Tim
> 
> 
> On 05/15/2014 03:21 PM, Zachary Wood wrote:
>> I agree with Martyn,
>> 
>> Pubmed Commons could be a great model. I believe you have to be a
>> published author to obtain an account. It might cut down on some of
>> the spam/noise if the PDB adopted such a model for depositors.
>> 
>> Best regards,
>> 
>> Z
>> 
>> 
>> *** Zachary A. Wood,
>> Ph.D. Associate Professor Department of Biochemistry & Molecular
>> Biology University of Georgia Life Sciences Building, Rm A426B 120
>> Green Street Athens, GA  30602-7229 Office: 706-583-0304 Lab:
>> 706-583-0303 FAX: 706-542-1738 
>> ***
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On May 15, 2014, at 7:29 AM, MARTYN SYMMONS
>>  wrote:
>> 
>>> I agree some forum for community annotation and commenting would
>>> be a good thing for users of structural data. There was an
>>> attempt to do that with the pdbwiki project which was a community
>>> resource for the bioinformatics community. Unfortunately pdbwiki
>>> has now folded (see http://pdbwiki.org/) They are now directing
>>> people to Proteopedia. However Proteopedia has a more educative
>>> focus I think - rather than capturing technical questions and
>>> input.
>>> 
>>> Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/),
>>> which is a forum for discussing the literature, is currently
>>> under testing. Perhaps this is the sort of thing that could work
>>> for structural data?
>>> 
>>> cheers Martyn
>>> 
>>> From: Ethan A Merritt  To:
>>> CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 
>>> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
>>> 
>>> On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
 As long as it's just a Technical Comments section - an obvious
 concern would be the signal/noise in the comments themselves.
 I'm sure PDB would not relish having to moderate that lot.
 
 Alternatively PDB can overtly link to papers that discuss
 technical issues that reference the particular structure -
 wrong or fraudulent structures are often associated with
 refereed publications that point that out, and structures with
 significant errors often show up in that way too.  I once did a
 journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish
 that could be associated with the relevant PDB file(s).
>>> 
>>> Perhaps some combination of those two ideas?
>>> 
>>> The PDB could associate with each deposited structure  a
>>> crowd-sourced list of published articles citing it.They
>>> already make an effort to attach the primary citation, but so far
>>> as I know there is currently no effort to track subsequent
>>> citations.
>>> 
>>> While spam comments in a free-format forum are probably
>>> inevitable, spam submission of citing papers seems less likely to
>>> be a problem.
>>> 
>>> - Ethan
>>> 
> On Wed, May 14, 2014 at 12:32 PM, Zachary Wood
> mailto:z...@bmb.uga.edu>> wrote:
> 
> Hello All,
> 
> Instead of placing the additional burden of policing on the
> good people at the PDB, perhaps the entry page for each
> structure could contain a comments section. Then the
> community could point out serious concerns for the less
> informed users. At least that will give users some warning in
> the case of particularly worrisome structures. The authors of
> course could still reply to defend their structure, and it
> may encourage some people to even correct their errors.
> 
>>> -- Ethan A Merritt Biomolecular Structure Center,  K-4

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

isn't the ccp4bb a very good example that spam may not be such an
issue for a discussion platform on structures in the PDB? There is a
great variety of opinions, some to agree with, some to disagree, but
all of them interesting and contributing, and I hardly remember a
message I would classify as spam. And it all works without restraints.

Best,
Tim


On 05/15/2014 03:21 PM, Zachary Wood wrote:
> I agree with Martyn,
> 
> Pubmed Commons could be a great model. I believe you have to be a
> published author to obtain an account. It might cut down on some of
> the spam/noise if the PDB adopted such a model for depositors.
> 
> Best regards,
> 
> Z
> 
> 
> *** Zachary A. Wood,
> Ph.D. Associate Professor Department of Biochemistry & Molecular
> Biology University of Georgia Life Sciences Building, Rm A426B 120
> Green Street Athens, GA  30602-7229 Office: 706-583-0304 Lab:
> 706-583-0303 FAX: 706-542-1738 
> ***
> 
> 
> 
> 
> 
> 
> 
> On May 15, 2014, at 7:29 AM, MARTYN SYMMONS
>  wrote:
> 
>> I agree some forum for community annotation and commenting would
>> be a good thing for users of structural data. There was an
>> attempt to do that with the pdbwiki project which was a community
>> resource for the bioinformatics community. Unfortunately pdbwiki
>> has now folded (see http://pdbwiki.org/) They are now directing
>> people to Proteopedia. However Proteopedia has a more educative
>> focus I think - rather than capturing technical questions and
>> input.
>> 
>> Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/),
>> which is a forum for discussing the literature, is currently
>> under testing. Perhaps this is the sort of thing that could work
>> for structural data?
>> 
>> cheers Martyn
>> 
>> From: Ethan A Merritt  To:
>> CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 
>> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
>> 
>> On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
>>> As long as it's just a Technical Comments section - an obvious
>>> concern would be the signal/noise in the comments themselves.
>>> I'm sure PDB would not relish having to moderate that lot.
>>> 
>>> Alternatively PDB can overtly link to papers that discuss
>>> technical issues that reference the particular structure -
>>> wrong or fraudulent structures are often associated with
>>> refereed publications that point that out, and structures with
>>> significant errors often show up in that way too.  I once did a
>>> journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish
>>> that could be associated with the relevant PDB file(s).
>> 
>> Perhaps some combination of those two ideas?
>> 
>> The PDB could associate with each deposited structure  a
>> crowd-sourced list of published articles citing it.They
>> already make an effort to attach the primary citation, but so far
>> as I know there is currently no effort to track subsequent
>> citations.
>> 
>> While spam comments in a free-format forum are probably
>> inevitable, spam submission of citing papers seems less likely to
>> be a problem.
>> 
>> - Ethan
>> 
 On Wed, May 14, 2014 at 12:32 PM, Zachary Wood
 mailto:z...@bmb.uga.edu>> wrote:
 
 Hello All,
 
 Instead of placing the additional burden of policing on the
 good people at the PDB, perhaps the entry page for each
 structure could contain a comments section. Then the
 community could point out serious concerns for the less
 informed users. At least that will give users some warning in
 the case of particularly worrisome structures. The authors of
 course could still reply to defend their structure, and it
 may encourage some people to even correct their errors.
 
>> -- Ethan A Merritt Biomolecular Structure Center,  K-428 Health
>> Sciences Bldg MS 357742,  University of Washington, Seattle
>> 98195-7742
>> 
>> 
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFTdMOTUxlJ7aRr7hoRAinqAJ9tAzMX6DSeFO7hiyEEqFhCPV7IxQCgg0Ay
Ya6HwJD/ugPU1dwGHNAJfkQ=
=JABI
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Re: [ccp4bb] PDB passes 100,000 structure milestone

[Zachary Wood]

I agree with Martyn,

 Pubmed Commons could be a great model. I believe you have to be a published 
author to obtain an account. It might cut down on some of the spam/noise if the 
PDB adopted such a model for depositors. 

Best regards,

Z


***
Zachary A. Wood, Ph.D.
Associate Professor  
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***







On May 15, 2014, at 7:29 AM, MARTYN SYMMONS 
 wrote:

> I agree some forum for community annotation and commenting would be a good 
> thing for users of structural data. 
> There was an attempt to do that with the pdbwiki project which was a 
> community resource for the bioinformatics community. Unfortunately pdbwiki 
> has now folded (see http://pdbwiki.org/) They are now directing people to 
> Proteopedia. However Proteopedia has a more educative focus I think - rather 
> than capturing technical questions and input.
> 
> Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum 
> for discussing the literature, is currently under testing. Perhaps this is 
> the sort of thing that could work for structural data?
>  
> cheers
>  Martyn 
> 
> From: Ethan A Merritt 
> To: CCP4BB@JISCMAIL.AC.UK 
> Sent: Wednesday, 14 May 2014, 19:22
> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
> 
> On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
> > As long as it's just a Technical Comments section - an obvious concern 
> > would be the signal/noise in the comments themselves.  I'm sure PDB 
> > would not relish having to moderate that lot.
> > 
> > Alternatively PDB can overtly link to papers that discuss technical 
> > issues that reference the particular structure - wrong or fraudulent 
> > structures are often associated with refereed publications that point 
> > that out, and structures with significant errors often show up in that 
> > way too.  I once did a journal club on Muller (2013) Acta Cryst 
> > F69:1071-1076 and wish that could be associated with the relevant PDB 
> > file(s).
> 
> Perhaps some combination of those two ideas?
> 
> The PDB could associate with each deposited structure  a crowd-sourced
> list of published articles citing it.They already make an effort to
> attach the primary citation, but so far as I know there is currently
> no effort to track subsequent citations.  
> 
> While spam comments in a free-format forum are probably inevitable,
> spam submission of citing papers seems less likely to be a problem.
> 
> - Ethan
> 
> > > On Wed, May 14, 2014 at 12:32 PM, Zachary Wood  > > > wrote:
> > >
> > >Hello All,
> > >
> > >Instead of placing the additional burden of policing on the good
> > >people at the PDB, perhaps the entry page for each structure could
> > >contain a comments section. Then the community could point out
> > >serious concerns for the less informed users. At least that will
> > >give users some warning in the case of particularly worrisome
> > >structures. The authors of course could still reply to defend their
> > >structure, and it may encourage some people to even correct their
> > >errors.
> > >
> -- 
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,  University of Washington, Seattle 98195-7742
> 
> 

[ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone

[Colin Nave]

Roger
Thanks for this reply. Sometime in the next millennium I guess.

I did get replies from several well wishers implying that it would be a good 
idea if I retired as soon as possible.

More usefully, Marjolein Thunnissen reminded me of the article 
http://www.uic.edu/labs/caz/downloads/Abad-Zapatero-PDB-rates-Acta-Cryst2012t.pdf.
 This gives a comprehensive analysis of growth rates.

Of course exponential growth can’t go on forever – the hidden point behind my 
question.

Regards
Colin



From: Roger Rowlett [mailto:rrowl...@colgate.edu]
Sent: 15 May 2014 12:36
To: ccp4bb
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone


A logarithmic plot of cumulative entries to the PDB is approximately linear and 
shows a growth rate of about 15% per year. That means it doubles in size about 
every 5 years at current growth rate.

Roger Rowlett
On May 15, 2014 4:23 AM, "Colin Nave" 
mailto:colin.n...@diamond.ac.uk>> wrote:
From James's figure, assuming perfect lossless compression, the information 
content of the PDB is 20GB or about 2X10**11 bits
The information content of the universe has been estimated to be 2**305 bits or 
10**92 bits (this might or might not be changing).
The PDB is said to be growing exponentially. If we know the coefficients, we 
can work out when the PDB takes over the present universe. This would be time 
to retire.
Can anyone do this?
Thanks
  Colin


From: James Holton [mailto:jmhol...@lbl.gov]
Sent: 14 May 2014 16:19
To: ccp4bb
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone


I think 249 GB is uncompressed.  My local copy of the PDB only takes up 20 GB, 
or one Blu-Ray.

I can remember a time when the whole of the PDB fit onto a single CD-ROM.  The 
PDB booth at the ACA meeting would hand them out for free!  That was impressive 
to me because CD-R disks were really expensive (to an undergraduate like me 
anyway), and I had to figure out how to do "multi-session" writes so I could 
back up my whole hard drive 2 or 3 times before I filled one up.  And, of 
course, I had to take out my hard drive and go over to that really wealthy lab 
that had a "CD writer" to do that.  Each write took about an hour, and didn't 
always work.  Ah, those were the days.

But yes, it is impressive how so much effort by so many people over so many 
years can be compressed into such a tiny space.  "Is it not a strange fate that 
we should suffer so much fear and doubt for so small a thing?"

-James Holton
MAD Scientist



On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote:
I reckon it's two box sets of 25 discs each  - am I calculating that wrong? 
Maybe room for a 'making of' feature

;)


From: Jon Agirre 
mailto:jon.agi...@york.ac.uk>>>
To: 
CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, 14 May 2014, 14:28
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone

249GB? That's a whole lot of DVDs!

On 14 May 2014 14:08, MARTYN SYMMONS 
mailto:martainn_oshioma...@btinternet.com>>>
 wrote:
Although the line boasting that the PDB adds up to 'more than 249 GBbytes (sic) 
of storage' was obviously written by someone from a pre i-tunes generation
http://www.wwpdb.org/news/news_2014.html#13-May-2014
;)

-M.


From: mesters 
mailto:mest...@biochem.uni-luebeck.de>>>
To: 
CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, 14 May 2014, 13:41
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone

Amazing, great!

And, which structure ended up as number 100.000?

- J. -


Am 14.05.14 10:42, schrieb battle:
The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that 
the Protein Data Bank archive now contains more than 100,000 entries.

Established in 1971, this central, public archive of experimentally-determined 
protein and nucleic acid structures has reached a critical milestone thanks to 
the efforts of structural biologists throughout the world.

Read the full story at:
http://www.wwpdb.org/news/news_2014.html#13-May-2014

--
Gary Battle
on behalf on the wwPDB

--
Dr. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer

Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany

phone: +49-451-5004065 (secretariate 5004061)
fax: +49-451-5004068

http://www.biochem.uni-luebeck.de
http://www.iobcr.org
[cid:image001.png@01CF701D.0C132EE0]  [cid:image002.jpg@01CF701D.0C132EE0]
--
If you can look into the seeds of time and tell which grain will grow and which 
will not, speak then to me who neither beg nor 

[ccp4bb] Crymon

[Hargreaves, David]

Dear CCP4bb,

Does anyone know who (if anyone) supports Crystal Miner (Emerald / Decode).

Kind Regards,

David

David Hargreaves
Associate Principal Scientist
_
AstraZeneca
Discovery Sciences, Structure & Biophysics
Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF
Tel +44 (0)01625 518521  Fax +44 (0) 1625 232693
David.Hargreaves @astrazeneca.com

Please consider the environment before printing this e-mail


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Re: [ccp4bb] PDB passes 100,000 structure milestone

[MARTYN SYMMONS]

I agree some forum for community annotation and commenting would be a good 
thing for users of structural data. 
There was an attempt to do that with the pdbwiki project which was a community 
resource for the bioinformatics community. Unfortunately pdbwiki has now folded 
(see http://pdbwiki.org/) They are now directing people to Proteopedia. However 
Proteopedia has a more educative focus I think - rather than capturing 
technical questions and input.

Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum 
for discussing the literature, is currently under testing. Perhaps this is the 
sort of thing that could work for structural data?
 
cheers
 Martyn 



 From: Ethan A Merritt 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
 

On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
> As long as it's just a Technical Comments section - an obvious concern 
> would be the signal/noise in the comments themselves.  I'm sure PDB 
> would not relish having to moderate that lot.
> 
> Alternatively PDB can overtly link to papers that discuss technical 
> issues that reference the particular structure - wrong or fraudulent 
> structures are often associated with refereed publications that point 
> that out, and structures with significant errors often show up in that 
> way too.  I once did a journal club on Muller (2013) Acta Cryst 
> F69:1071-1076 and wish that could be associated with the relevant PDB 
> file(s).

Perhaps some combination of those two ideas?

The PDB could associate with each deposited structure  a crowd-sourced
list of published articles citing it.     They already make an effort to
attach the primary citation, but so far as I know there is currently
no effort to track subsequent citations.  

While spam comments in a free-format forum are probably inevitable,
spam submission of citing papers seems less likely to be a problem.

    - Ethan

> > On Wed, May 14, 2014 at 12:32 PM, Zachary Wood  > > wrote:
> >
> >     Hello All,
> >
> >     Instead of placing the additional burden of policing on the good
> >     people at the PDB, perhaps the entry page for each structure could
> >     contain a comments section. Then the community could point out
> >     serious concerns for the less informed users. At least that will
> >     give users some warning in the case of particularly worrisome
> >     structures. The authors of course could still reply to defend their
> >     structure, and it may encourage some people to even correct their
> >     errors.
> >
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Roger Rowlett]

A logarithmic plot of cumulative entries to the PDB is approximately linear
and shows a growth rate of about 15% per year. That means it doubles in
size about every 5 years at current growth rate.

Roger Rowlett
On May 15, 2014 4:23 AM, "Colin Nave"  wrote:

> From James's figure, assuming perfect lossless compression, the
> information content of the PDB is 20GB or about 2X10**11 bits
> The information content of the universe has been estimated to be 2**305
> bits or 10**92 bits (this might or might not be changing).
> The PDB is said to be growing exponentially. If we know the coefficients,
> we can work out when the PDB takes over the present universe. This would be
> time to retire.
> Can anyone do this?
> Thanks
>   Colin
>
>
> From: James Holton [mailto:jmhol...@lbl.gov]
> Sent: 14 May 2014 16:19
> To: ccp4bb
> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
>
>
> I think 249 GB is uncompressed.  My local copy of the PDB only takes up 20
> GB, or one Blu-Ray.
>
> I can remember a time when the whole of the PDB fit onto a single CD-ROM.
>  The PDB booth at the ACA meeting would hand them out for free!  That was
> impressive to me because CD-R disks were really expensive (to an
> undergraduate like me anyway), and I had to figure out how to do
> "multi-session" writes so I could back up my whole hard drive 2 or 3 times
> before I filled one up.  And, of course, I had to take out my hard drive
> and go over to that really wealthy lab that had a "CD writer" to do that.
>  Each write took about an hour, and didn't always work.  Ah, those were the
> days.
>
> But yes, it is impressive how so much effort by so many people over so
> many years can be compressed into such a tiny space.  "Is it not a strange
> fate that we should suffer so much fear and doubt for so small a thing?"
>
> -James Holton
> MAD Scientist
>
>
>
> On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote:
> I reckon it's two box sets of 25 discs each  - am I calculating that
> wrong? Maybe room for a 'making of' feature
>
> ;)
>
> 
> From: Jon Agirre 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Wednesday, 14 May 2014, 14:28
> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
>
> 249GB? That's a whole lot of DVDs!
>
> On 14 May 2014 14:08, MARTYN SYMMONS  > wrote:
> Although the line boasting that the PDB adds up to 'more than 249 GBbytes
> (sic) of storage' was obviously written by someone from a pre i-tunes
> generation
> http://www.wwpdb.org/news/news_2014.html#13-May-2014
> ;)
>
> -M.
>
> 
> From: mesters  mest...@biochem.uni-luebeck.de>>
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Wednesday, 14 May 2014, 13:41
> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
>
> Amazing, great!
>
> And, which structure ended up as number 100.000?
>
> - J. -
>
>
> Am 14.05.14 10:42, schrieb battle:
> The Worldwide Protein Data Bank (wwPDB) organization is proud to announce
> that the Protein Data Bank archive now contains more than 100,000 entries.
>
> Established in 1971, this central, public archive of
> experimentally-determined protein and nucleic acid structures has reached a
> critical milestone thanks to the efforts of structural biologists
> throughout the world.
>
> Read the full story at:
> http://www.wwpdb.org/news/news_2014.html#13-May-2014
>
> --
> Gary Battle
> on behalf on the wwPDB
>
> --
> Dr. Jeroen R. Mesters
> Deputy, Senior Researcher & Lecturer
>
> Institute of Biochemistry, University of Lübeck
> Ratzeburger Allee 160, 23538 Lübeck, Germany
>
> phone: +49-451-5004065 (secretariate 5004061)
> fax: +49-451-5004068
>
> http://www.biochem.uni-luebeck.de
> http://www.iobcr.org
> [cid:image001.png@01CF701D.0C132EE0]
>  [cid:image002.jpg@01CF701D.0C132EE0]
> --
> If you can look into the seeds of time and tell which grain will grow and
> which will not, speak then to me who neither beg nor fear (Shakespeare's
> Macbeth, Act I, Scene 3)
> --
> Disclaimer
> * This message contains confidential information and is intended only for
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Re: [ccp4bb] PDB passes 100,000 structure milestone

[Bärbel Blaum]

Hello,

I also agree that the right order of things would be the journals  
taking action (i.e. retracting and commenting on why), then informing  
the pdb which structures are associated with a retraction - for the  
simple reason that very likely many readers take conclusions in  
made-up publications for granted even if they do not directly work  
with the fraudent models that are deposited, i.e. the publications do  
even more harm to the research community than the associated fraud  
structures.


Because the case of Murthy came up I would like to mention that the US  
Office of Research Integrity (http://ori.hhs.gov/) is still reviewing  
the case (at least they told me so in Nov 2013), and I hope their  
final conclusion will result in more comprehensive action against ALL  
structures in question, not just 2hr0 (by the University of Birmingham  
and the journals). So while it may be frustratingly slow, there is  
actually an institution that does take care of such issues (at least  
in the US).


Bärbel


Quoting Mark Wilson :


Hi Nat,
I agree that journals should be doing the heavy lifting here, for the
reasons that you note. I also want to be clear that I believe the PDB is a
crowning achievement of transparency and open access in the sciences,
which is one reason that I am so concerned about this issue.  I am in no
way trying to impugn the hard and superb work that they have done over
many decades.  I still contend, however, that having models whose
integrity is highly suspect lurking in the PDB with no indications of
problems beyond a dodgy validation report is a non-optimal outcome.  As
for the meaning of integrity, I'm using this word in place of others that
might be considered more legally actionable.  A franker conversation would
likely more clearly draw the line that we're wrestling with here.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu






On 5/14/14 12:41 PM, "Nat Echols"  wrote:


On Wed, May 14, 2014 at 10:26 AM, Mark Wilson  wrote:

Getting to Eric's point about an impasse, if the PDB will not claim the
authority to safeguard the integrity of their holdings (as per their
quoted statement in Bernhard's message below), then who can?



I think this may in part boil down to a semantic dispute over the meaning
of "integrity".  I interpreted it to mean "integrity (and public
availability) of the data as deposited by the authors", which by itself
is quite a lot of work.  Safeguarding
the integrity of the peer-review process is supposed to be the job of
the journals, some of which - unlike the PDB - are making a tidy profit
from our efforts.  Since they justify this profit based on the value they
supposedly add as gatekeepers, I don't think
it's unreasonable for us to expect them to do their job, rather than
leave it to the PDB annotators, who surely have enough to deal with.


I do share some of the concern about 2hr0, but I am curious where the
line should be drawn.  This is an extraordinary case where the
researcher's institution requested retraction, but I think everyone who's
been in this field for a while has
a list of dodgy structures that they think should be retracted - not
always with justification.


-Nat










--
Bärbel Blaum, Ph.D.
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Re: [ccp4bb] PDB passes 100,000 structure milestone

[Colin Nave]

>From James's figure, assuming perfect lossless compression, the information 
>content of the PDB is 20GB or about 2X10**11 bits
The information content of the universe has been estimated to be 2**305 bits or 
10**92 bits (this might or might not be changing).
The PDB is said to be growing exponentially. If we know the coefficients, we 
can work out when the PDB takes over the present universe. This would be time 
to retire.
Can anyone do this?
Thanks
  Colin


From: James Holton [mailto:jmhol...@lbl.gov]
Sent: 14 May 2014 16:19
To: ccp4bb
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone


I think 249 GB is uncompressed.  My local copy of the PDB only takes up 20 GB, 
or one Blu-Ray.

I can remember a time when the whole of the PDB fit onto a single CD-ROM.  The 
PDB booth at the ACA meeting would hand them out for free!  That was impressive 
to me because CD-R disks were really expensive (to an undergraduate like me 
anyway), and I had to figure out how to do "multi-session" writes so I could 
back up my whole hard drive 2 or 3 times before I filled one up.  And, of 
course, I had to take out my hard drive and go over to that really wealthy lab 
that had a "CD writer" to do that.  Each write took about an hour, and didn't 
always work.  Ah, those were the days.

But yes, it is impressive how so much effort by so many people over so many 
years can be compressed into such a tiny space.  "Is it not a strange fate that 
we should suffer so much fear and doubt for so small a thing?"

-James Holton
MAD Scientist



On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote:
I reckon it's two box sets of 25 discs each  - am I calculating that wrong? 
Maybe room for a 'making of' feature

;)


From: Jon Agirre 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 14:28
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone

249GB? That's a whole lot of DVDs!

On 14 May 2014 14:08, MARTYN SYMMONS 
mailto:martainn_oshioma...@btinternet.com>> 
wrote:
Although the line boasting that the PDB adds up to 'more than 249 GBbytes (sic) 
of storage' was obviously written by someone from a pre i-tunes generation
http://www.wwpdb.org/news/news_2014.html#13-May-2014
;)

-M.


From: mesters 
mailto:mest...@biochem.uni-luebeck.de>>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 13:41
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone

Amazing, great!

And, which structure ended up as number 100.000?

- J. -


Am 14.05.14 10:42, schrieb battle:
The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that 
the Protein Data Bank archive now contains more than 100,000 entries.

Established in 1971, this central, public archive of experimentally-determined 
protein and nucleic acid structures has reached a critical milestone thanks to 
the efforts of structural biologists throughout the world.

Read the full story at:
http://www.wwpdb.org/news/news_2014.html#13-May-2014

--
Gary Battle
on behalf on the wwPDB

--
Dr. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer

Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany

phone: +49-451-5004065 (secretariate 5004061)
fax: +49-451-5004068

http://www.biochem.uni-luebeck.de
http://www.iobcr.org
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