[ccp4bb] Help EMBL-EBI maintain its services: articulating the value of open data

[Gerard DVD Kleywegt]

Dear colleagues,

As a community of structural molecular (and, increasingly, cellular) biologists 
we are fortunate to have a large collection of well-established, well-managed 
and open data resources at our disposal. (Physicists are often impressed when 
they learn that a protein structure deposited in the PDB in the mid-1970s can 
still be loaded into any molecular viewer and analysed and used as if it was 
determined yesterday.) You may have used (or deposited) structural data from 
archives such as the PDB, EMDB, EMPIAR, BMRB or SASBDB, but perhaps also 
sequence data from UniProt, chemical activity data from ChEMBL or maybe 
discovered relevant literature in PubMed or Europe PMC.


EMBL-EBI is involved in operating many of these public data resources (in many 
cases, together with international partners and as part of global 
collaborations). The institute is currently running a survey that aims to 
assess the worldwide value of the bioinformatics resources it offers.


I would like to invite all of you, as well as any other data users in your 
organisation, to participate in this survey. Your input is extremely important 
and will help EMBL-EBI maintain and develop its resources for the global 
scientific community. It would obviously be helpful to have a good 
representation of the structural biology community providing input into this 
process.


The survey can be accessed here:

 https://www.surveymonkey.co.uk/r/EMBL-EBI_Impact_PE

It takes around 15 minutes and closes on 31 March 2021. The results of the 
survey will be anonymised and all personal data treated as confidential.


I recognise there are many demands on your time so I would like to thank you in 
advance for your participation and input.


If you have any questions or comments about the survey please contact 
impactsur...@ebi.ac.uk.


Many thanks and best wishes,

--Gerard

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Roisin Dunloppdbe_ad...@ebi.ac.uk



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Re: [ccp4bb] Pymol Map range

[Gerard DVD Kleywegt]

Hi all,

Following up on this: some time ago, Martyn Winn was kind enough to put the 
source of a bunch of old Uppsala Software Factory programs in GitHub:


   https://github.com/martynwinn/Uppsala-Software-Factory

It's all unsupported now (I haven't compiled anything in 12 years...) but free 
to do with whatever you like.


(The website in Uppsala has unfortunately not been accessible for several 
months already. This means that the manuals are not online. If there is 
interest I could post a tgz file with -as far as I can determine- the latest 
version of all manuals in HTML format (0.8 MB total).)


--Gerard


On Wed, 3 Mar 2021, James Holton wrote:


Yes, I stand corrected. "mapmask" is the CCP4 program.

mapman is still around.  I even found a way to get it to work on 64-bit!
https://git.bl831.als.lbl.gov/jamesh/map-bender/-/blob/master/mapman_regression_test.csh

-James Holton
MAD Scientist


On 3/3/2021 9:10 AM, Jon Cooper wrote:

 For old-schoolers, mapmask (once known as extend) in ccp4 does this.
 Mapman was from the Upsala suite and became XDLmapman in ccp4, but then
 became unusable and disappeared. I liked the original mapman as you had to
 actually give a name for your map, like 'jim' or 'jon'.

 Best wishes, Jon Cooper


 Sent from ProtonMail mobile



  Original Message 
 On 1 Mar 2021, 21:19, James Holton < jmhol...@lbl.gov> wrote:


 The CCP4 program you are looking for is called "mapman", and the
 option you need is "border".

 -James Holton
 MAD Scientist


 On 2/26/2021 8:07 AM, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:


 Hello BB,

 I’m trying to make an image of some electron density in pymol but
 am running into a problem, my atoms are half in and half out of
 the unit cell so I only get half the density.

 Has anyone ran into this problem previously, and if so, is there
 a way to shift the origin, extend the map, or something so
 everything is covered?

 I realise this is not a ccp4 problem exactly, so I am ready for
 the inevitable replies, but I imagine a program in ccp4 might be
 the answer.

 Cheers,

 Sam

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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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[ccp4bb] In situ Structural Biology Conference (fwd)

[Gerard DVD Kleywegt]

Dear all,

Cross-posting this on behalf of Julia Mahamid.

--Gerard

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Roisin Dunloppdbe_ad...@ebi.ac.uk

-- Forwarded message --
Date: Mon, 28 Sep 2020 08:53:30 +0200
From: Julia Mahamid 
To: 3...@ncmir.ucsd.edu
Subject: [3dem] In situ Structural Biology Conference

Dear colleagues, 

I want to bring to your attention the EMBO workshop on In situ Structural
Biology - From Cryo-EM to Integrative Modelling, that will be held virtually on
Dec. 6-8, 2020:
https://www.embl.de/training/events/2020/ISS20-01/index.html?ct=t%28ISS20-abstract+reminder_COPY_01%29

The abstract submission deadline has been extended to Oct. 12, 2020. Don’t miss
the chance to present your work in this unique setup, and have the chance to win
a poster award.

Cheers, Julia


Julia Mahamid
Structural and Computational Biology Unit
European Molecular Biology Laboratory
Meyerhofstrasse 1
69117 Heidelberg
Germany
Phone: +49 (0)6221 387 8451
julia.maha...@embl.de
https://www.embl.de/research/units/scb/mahamid/



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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

Hi Frances,

I'm not surprised. Just correcting (from old orthogonal via fractional to new 
orthogonal) will "stretch" bonds ever so slightly. I would have done 
rigid-body followed by some all-atom refinement and maybe checked the map and 
model fit afterwards (esp. at crystal contacts), and if necessary rebuilt some 
residues followed by more refinement.


--Gerard



On Thu, 16 Jul 2020, Frances C. Bernstein wrote:


I do not remember the date or the PDB entry but it was during
the time that the PDB at BNL was including distance and angle
outliers in the checking report sent back to the depositor.
It was a not-too-large protein and there were perhaps half a
dozen outliers each on distances and angles which was typical of
an entry without 'problems'.  So I sent the proposed entry to the
depositor and got a panicked call that something was wrong based
on the depositor looking at a display of the entry.  By the next
day the depositor had figured out that s/he had decided to convert
to orthogonal for deposition and mistyped one of the cell dimensions
by 1 Angstrom.  That length was about 135 so the error was less than
1% in one direction and I was very impressed that the depositor had
spotted it graphically.

After I did the appropriate linear algebra to correct the coordinates
I took a look at the distance and angle outliers.  Of course they
were different but to my great surprise there were about the same
number of outliers for the 'bad' and the corrected entries.  So based
on the checking at that time we could not tell the bad from the good.

I would be interested to know what would happen now with all the
additional checking that is available.  Perhaps someone should do
that experiment.

Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
 *   ***  f...@bernstein-plus-sons.com
 *** *
 *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:


 There was a case a few years ago (not too many though) where a 1.6 ?
 structure had been solved using an incorrect value for the wavelength (~5%
 too low, leading to a cell that was slightly too small for its contents to
 be comfortable). It was later corrected so we could compare their
 validation statistics. Some interesting observations:

 - the geometry had been very tightly restrained so that didn't give a clue
  about the cell error (WhatCheck only suggested a very small change)

 - somewhat surprisingly (I thought) the Ramachandran plot did not improve
 in
  the correct model (0.3% outliers in the wwPDB validation report), and the
  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)

 - the map looked surprisingly good for the incorrect cell

 - however, RSR-Z told clearly that the map was not good enough for the
 claimed
  resolution - the model had 24% outliers! (3% in the corrected model which
  still only put it at the ~50th percentile)

 - another good indicator was the clashscore (went from 44 to 7)

 - the original model did not include an Rfree, but the R-value (>0.3 at
 1.6?
  resolution) ought to have provided a clue to the crystallographers and
  reviewers one would think

 It would be interesting to see what would happen if the wavelength would
 be set 5% too high.

 --Gerard



 On Thu, 16 Jul 2020, Clemens Vonrhein wrote:


 Hi Robbie,

 On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:

 At the same time if you have a a more relaxed approach to restraints
 than you might find systematic deviations in bond lengths. A test
 for that has been in WHAT_CHECK for decades and it actually works
 surprisingly well to detect cell dimension problems.


 Indeed.


 That said, the problem is uncommon now.


 Not so sure about that: we all rely on an accurate value of the
 energy/wavelength from the instrument/beamline - and if that is off
 (for whatever reasons) it will result in incorrect cell dimensions and
 a systematic deviation from the various restraints.

 This would even affect the best experiment done on the best crystal
 ... so fairly easy to spot at the refinement stage, especially if such
 an energy/wavelength offset is constant over a long period of time on
 a given instrument. To spot this at the data collection stage one
 would hope that at some point a crystal with very pronounced ice-rings
 will be looked at properly (and the fact these are not where we expect
 them to should cause some head-scratching).

 Cheers

 Clemens

 

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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

No, I only wore Dutch clogs :-) Uppsala was an observer I think so Alwyn and I 
could attend the meetings, but we couldn't hire anyone.


--G


On Thu, 16 Jul 2020, Eleanor Dodson wrote:


Well - it was Hamburg high resolution data - I guess we all had a stake in
it.. Good meetings but You were part of them? Did you wear a Dutch hat?
E

On Thu, 16 Jul 2020 at 12:07, Gerard DVD Kleywegt 
wrote:


Hi Eleanor,

Yes, I remember those meetings, when the UK was still an EU member and
Sweden
not yet (so Uppsala couldn't be formally involved) :-)

Did Victor look into this too? I remember Gert doing it. And maybe Tom
Oldfield?

Best wishes,

--Gerard



On Thu, 16 Jul 2020, Eleanor Dodson wrote:


Hmm - remember Gerard, the EU Validation initiative in the 1990s? We
analysed these effects, or at least Victor Lamsin did, and we applauded

him.

Cheers Eleanor

On Thu, 16 Jul 2020 at 11:52, Clemens Vonrhein <

vonrh...@globalphasing.com>

wrote:


Hi Robbie,

On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:

At the same time if you have a a more relaxed approach to restraints
than you might find systematic deviations in bond lengths. A test
for that has been in WHAT_CHECK for decades and it actually works
surprisingly well to detect cell dimension problems.


Indeed.


That said, the problem is uncommon now.


Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



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Best wishes,

--Gerard

**
Gerard J. Kleywegt

   http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
The opinions in this message are fictional.  Any similarity
to actual opinions, living or dead, is purely coincidental.
**
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
 of that pizza is equal to pi*z*z*a !
**





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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

There was a case a few years ago (not too many though) where a 1.6 Å structure 
had been solved using an incorrect value for the wavelength (~5% too low, 
leading to a cell that was slightly too small for its contents to be 
comfortable). It was later corrected so we could compare their validation 
statistics. Some interesting observations:


- the geometry had been very tightly restrained so that didn't give a clue
  about the cell error (WhatCheck only suggested a very small change)

- somewhat surprisingly (I thought) the Ramachandran plot did not improve in
  the correct model (0.3% outliers in the wwPDB validation report), and the
  sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)

- the map looked surprisingly good for the incorrect cell

- however, RSR-Z told clearly that the map was not good enough for the claimed
  resolution - the model had 24% outliers! (3% in the corrected model which
  still only put it at the ~50th percentile)

- another good indicator was the clashscore (went from 44 to 7)

- the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
  resolution) ought to have provided a clue to the crystallographers and
  reviewers one would think

It would be interesting to see what would happen if the wavelength would be 
set 5% too high.


--Gerard



On Thu, 16 Jul 2020, Clemens Vonrhein wrote:


Hi Robbie,

On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:

At the same time if you have a a more relaxed approach to restraints
than you might find systematic deviations in bond lengths. A test
for that has been in WHAT_CHECK for decades and it actually works
surprisingly well to detect cell dimension problems.


Indeed.


That said, the problem is uncommon now.


Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

Hi Eleanor,

Yes, I remember those meetings, when the UK was still an EU member and Sweden 
not yet (so Uppsala couldn't be formally involved) :-)


Did Victor look into this too? I remember Gert doing it. And maybe Tom 
Oldfield?


Best wishes,

--Gerard



On Thu, 16 Jul 2020, Eleanor Dodson wrote:


Hmm - remember Gerard, the EU Validation initiative in the 1990s? We
analysed these effects, or at least Victor Lamsin did, and we applauded him.
Cheers Eleanor

On Thu, 16 Jul 2020 at 11:52, Clemens Vonrhein 
wrote:


Hi Robbie,

On Wed, Jul 15, 2020 at 07:23:15PM +, Robbie Joosten wrote:

At the same time if you have a a more relaxed approach to restraints
than you might find systematic deviations in bond lengths. A test
for that has been in WHAT_CHECK for decades and it actually works
surprisingly well to detect cell dimension problems.


Indeed.


That said, the problem is uncommon now.


Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.

This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).

Cheers

Clemens



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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Quote source inquiry

[Gerard DVD Kleywegt]

Thanks - very interesting paper, Jeffrey.

I think your analysis is correct, but you forgot: (4) the skill of the 
crystallographer...


Best wishes,

--Gerard


On Wed, 15 Jul 2020, Jeffrey B Bonanno wrote:


Hi Gerard and Bernhard,

As a postdoc in an unnamed small molecule lab, I was instructed by my lab head 
to get better unit cell estimates prior to data collection owing to error 
propagation from the uncertainty on cell dimensions through to the esd on 
atomic bond lengths and angles when refining in shelxl. To verify this (what, 
you believed everything your postdoc advisor told you?), I took a working 
dataset and increased (only) the error on unit cell dimensions in the 
instruction file for the final round of full matrix least squares refinement in 
shelxl. Sure enough, the errors on the bonds and angles shot up. I was more 
careful in determining the unit cell thereafter. That is, until, I became a 
macromolecular crystallographer...

After an inciteful (sp? lol) discussion with Wladek about cell dimensions, I 
was directed to read this paper:

Acta Crystallogr D Biol Crystallogr. 2015 Nov 1; 71(Pt 11): 2217–2226.

Have a look, it is interesting.

Having never followed up on these studies to see what happened to bonds and 
angles in proteins and their ligands when varying cell dimensions, I can't 
say with any confidence. However, I would guess that the quality of the 
refined ligand coordinates could only be as good as some combination of 
factors including but not limited to 1) the data (resolution, B factor, 
etc), 2) the actual occupancy of the ligand, and 3) the restraints employed.


jbb

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org


-Original Message-
From: CCP4 bulletin board  On Behalf Of Gerard DVD 
Kleywegt
Sent: Wednesday, July 15, 2020 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Quote source inquiry

Well, I've had this in my CSHL X-ray Course talk for many years.

In the attached 2007 Acta D paper it says (p 95): "Macromolecular X-ray 
crystallography is a notoriously poor method for determining the structure of small 
molecules that are bound to macromolecules [...]" and then goes on to explain why 
this is the case.

In the attached 2003 paper (pooling the wisdom of several of the usual 
suspects, including Eleanor) it says something similar (p 1057):

"Coordinates of molecules that have been determined in complex with 
macromolecules previously can of course also be retrieved from the PDB (Bernstein et 
al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones, 1998), or CHEMPDB 
(Boutselakis et al., 2003). However, one should keep in mind that these coordinates 
are the result of refinement against comparatively
low-resolu- tion data where the small molecule constituted only a minute 
fraction of the total scattering matter. This makes these coordinates 
inherently much less accurate than those obtained from the CSD. In addition, 
the coordi- nates may contain errors due to the use of incorrect restraints.
Hence, such coordinate sets should only be used as a last resort, and only 
after verification that they are reliable. The latter can be facilitated by 
inspection of the electron density for the compound in question, for instance 
at the Uppsala Electron-Density Server (http:// fsrv1.bmc.uu.se/eds) (G.J.K.
et al., submitted)."

Happy to be confused with George though!

--Gerard (no, the other one)



On Tue, 14 Jul 2020, Bernhard Rupp wrote:


Hi Fellows,



afaicrimps (as far as I can recall in my progressing senility)
someone once wrote/stated/cursed somewhere that "Macromolecular
refinement is not a small molecule structure determination method".



Any citable source - George Sheldrick might be a suspect.



Thanks & best regards, BR



--

Bernhard Rupp

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hofkristallamt.org%2Fdata=02%7C01%7Cjeffrey.bonanno%40einsteinmed
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2025%7C0%7C0%7C637304250594203532sdata=9FFCpYd9D%2BrHR48DtL%2BglM
W2dbZ%2FmSTw0fF88XRwR7o%3Dreserved=0>
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025%7C0%7C0%7C637304250594203532sdata=9FFCpYd9D%2BrHR48DtL%2BglMW
2dbZ%2FmSTw0fF88XRwR7o%3Dreserved=0

<mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

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Many plausible ideas vanish

at the presence of thought

--

Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

[Gerard DVD Kleywegt]

  Sorry to have taken this matter up in such a visible manner: I noticed
this very wrong formula in someone's paper, and that person then told me
where he had found it. Having landed on that page, I didn't know where to go


For the students:

"someone" = systematic absence of information = 0 bits
"person" = systematic absence of information = 0 bits
"he" = 1 bit of information!

--The other Gerard (1 bit of information!)

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
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Re: [ccp4bb] [3dem] Which resolution?

[Gerard DVD Kleywegt]

If this is the case, why can't we use model B factors to validate our 
structure? I know some people are skeptical about this approach because B 
factors are refinable parameters.


Rangana


It is not clear to me exactly what you are asking.

B factors _should_ be validated, precisely because they are refined parameters
that are part of your model.   Where have you seen skepticism?


Rangana said that B-values should not be used *to validate structures*, NOT 
that B-values themselves shouldn't be validated themselves.


I suppose I am at least in part to blame for the former notion and the reason 
for this (at least circa 1995 when the Angry Young Men from Uppsala first 
starting harping on about this) was that B-values tend(ed) to be error sinks 
which could "absorb" all sorts of errors and phenomena in addition to 
modelling atomic displacement (e.g., unresolved disorder, unresolved NCS 
differences, incorrect restraints, incorrect atom types modelled, partial 
ocupancies, etc.).


--Gerard

**
   Gerard J. Kleywegt

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**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
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**



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[ccp4bb] Examples of EM models at 4.0Å or better with serious modelling errors?

[Gerard DVD Kleywegt]

Dear colleagues,

We are developing a new validation method that takes EM maps and models into 
account. In order to understand the potential, the applicability and the 
limitations of the method we are looking for good test cases, which turn out 
to be surprisingly hard to find.


What we are looking for are EM structures with serious modelling errors, e.g. 
register errors (model sequence out-of-register with the map), connectivity 
errors (between (non-)adjacent secondary structure elements), directionality 
errors (e.g., a helix built backwards), substantial stretches of mistraced 
residues, etc.


The structures should be publicly available in PDB (model) and EMDB (map), 
they should be at 4.0Å resolution or better, and ideally there should be a 
higher resolution improved structure (EM or X-ray).


If the modelling errors have been confirmed and discussed in the literature 
that is ideal, but we are also interested if this is not the case.


Feel free to reply either in confidence to me (mailto:ger...@ebi.ac.uk), or to 
the entire list.


Many thanks in advance for any examples you can think of!

PS: apologies for cross-posting to two other mailing lists.

--Gerard

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Roisin Dunloppdbe_ad...@ebi.ac.uk



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Re: [ccp4bb] [OT] Structure-related pun needed urgently

[Gerard DVD Kleywegt]

“Can I speed up structure solution using different phases”…??

I’ll get my coat.

[Gerard - what is the audience? Crystallographers vs general public might make 
a difference..!]


Sorry - I should have mentioned that. It's all employees of the European 
Bioinformatics Institute, so a mix of biologists/chemists/gene jockeys, IT 
people and admin staff.


--Gerard





Ed

T.A.Edwards Ph.D.
Associate Professor of Biochemistry
Deputy Head of School
_
Astbury Centre for Structural Molecular Biology
School of Molecular and Cellular Biology
Faculty of Biological Sciences
===
Garstang 8.53d
University of Leeds, Leeds, LS2 9JT ?Telephone: 0113 343 3031
Faculty Staff 
Profile<https://biologicalsciences.leeds.ac.uk/molecular-and-cellular-biology/staff/61/thomas-a-edwards-ph-d->
Astbury Centre Web 
Page<http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=TE>
[signature_1707952708]<https://poppi.website/>
Perturbation of Protein-Protein Interactions

Invention, my dear friends, is 93% perspiration, 6% electricity, 4% 
evaporation, and 2% butterscotch ripple. ~Willy Wonka

[/Users/bmbtae/bmbtae/0_Docs/Astbury/0_AstburyConversation/2020/01784_Astbury 
Conversation 2020 email signature 
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From: CCP4 bulletin board  on behalf of "Daniel M. Himmel, Ph. 
D." 
Reply-To: "Daniel M. Himmel, Ph. D." 
Date: Thursday, 15 August 2019 at 15:57
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] [OT] Structure-related pun needed urgently

You're welcome to boo this one down, but how about something like, "With a some 
coaxing,
a protein can be X-cited to expose its structure."  I think that's poor, but 
maybe it's a starting point.

-Daniel


On Thu, Aug 15, 2019 at 7:42 AM Gerard DVD Kleywegt 
mailto:ger...@xray.bmc.uu.se>> wrote:
Dear CCP4BB-ers,

Once again I turn to you in my hour of need. I *urgently* need a
side-splittingly funny, and ideally punny, structure-related
sentence/statement/claim/expression to put in a speech bubble attached to a
life-size bobblehead version of yours truly (don't ask)!

I know there are some very funny people on CCP4BB. The best I've been able to
come up with myself so far is: "Protein structures are beautiful, but I try to
keep it platomic" - which is pretty lame, I know.

Many thanks in advance!

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   
mailto:ger...@xray.bmc.uu.se<mailto:ger...@xray.bmc.uu.se>
**
   The opinions in this message are fictional.  Any similarity
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   Little known gastromathematical curiosity: let "z" be the
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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] [OT] Structure-related pun needed urgently

[Gerard DVD Kleywegt]

Thanks Bill.

No need to restrict it to proteins - nucleic acids are fine (old chestnut: 
"DNA helicase unzips your genes!"), molecular machines are fine, even cellular 
structure is in scope.


(If I still did crystallography, I could have gone with: "You don't have to 
use MAD to work here, but it helps.")


--Gerard



On Thu, 15 Aug 2019, William G. Scott wrote:


After reflecting on this a bit, I rejected anything dealing with glide planes, 
and although I initially thought I had something good involving a screw axis of 
evil, I decided it, too, would probably be lost in translation, not to mention 
a bit dated.

Perhaps something more current, involving electrons, would help to resolve this?

I'll give it some thought this morning as I bicyle up the worst hill in the region. 
Unfortunately, it is still very early here, and I don't yet have the inspiration I 
possessed for my crowning achievement during my postdoc, which was to place a small, 
inconspicuous label on the outside door of the toilet facility that read "MRC 
Lavoratory of Molecular Biology.”  (I am flush with embarrassment every time I think 
of that.)

Can this also involve nucleic acids?  I’m afraid protein structure puns might 
be a bit outside my domain.


— Bill


On Aug 15, 2019, at 4:42 AM, Gerard DVD Kleywegt  wrote:

Dear CCP4BB-ers,

Once again I turn to you in my hour of need. I *urgently* need a 
side-splittingly funny, and ideally punny, structure-related 
sentence/statement/claim/expression to put in a speech bubble attached to a 
life-size bobblehead version of yours truly (don't ask)!

I know there are some very funny people on CCP4BB. The best I've been able to come up 
with myself so far is: "Protein structures are beautiful, but I try to keep it 
platomic" - which is pretty lame, I know.

Many thanks in advance!

--Gerard

**
  Gerard J. Kleywegt

 http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
  The opinions in this message are fictional.  Any similarity
  to actual opinions, living or dead, is purely coincidental.
**
  Little known gastromathematical curiosity: let "z" be the
  radius and "a" the thickness of a pizza. Then the volume
   of that pizza is equal to pi*z*z*a !
**



To unsubscribe from the CCP4BB list, click the following link:
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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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[ccp4bb] [OT] Structure-related pun needed urgently

[Gerard DVD Kleywegt]

Dear CCP4BB-ers,

Once again I turn to you in my hour of need. I *urgently* need a 
side-splittingly funny, and ideally punny, structure-related 
sentence/statement/claim/expression to put in a speech bubble attached to a 
life-size bobblehead version of yours truly (don't ask)!


I know there are some very funny people on CCP4BB. The best I've been able to 
come up with myself so far is: "Protein structures are beautiful, but I try to 
keep it platomic" - which is pretty lame, I know.


Many thanks in advance!

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] improper rotation matrix

[Gerard DVD Kleywegt]

If you have a copy of MOLEMAN2 lying around, you can use the XYz DIstort 
command to do exactly this: http://xray.bmc.uu.se/usf/moleman2_man.html#S77


--Gerard


On Mon, 12 Mar 2018, Franck Coste wrote:


Hi all,

I'd like to apply an improper rotation matrix to PDB files but it seems it's 
not allowed in pdbset. Does anyone know a program where I could do this ?


Thanks in advance.

Regards,

Franck.

--




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] EMBL-EBI user survey

[Gerard DVD Kleywegt]

Dear colleagues,

EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand 
usage of its resources (there are several dozen, including UniProt, Ensembl, 
ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you 
to forward this request within your department, company or institution. We are 
interested in responses from a wide range of scientists, in particular those 
who do not think of themselves as bioinformaticians. The results are extremely 
valuable to EBI in helping us to understand our users, and our users' needs.


Here is the link to the survey: 
https://www.surveymonkey.co.uk/r/2017_EBI_survey


Many thanks!

--Gerard

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Pauline Haslam   pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Refmac5 and Coot for refining cryo-EM structures

[Gerard DVD Kleywegt]

The main issue is that carboxyls seem to be invisible and Coot tries to fit 
them as though the map had them there


Well, if the atoms are part of the model, then Coot will try to fit them to 
the "data." I routinely chop off GLU and ASP side-chain when modelling into 
cryo-EM maps (that's what the K key is for).


That seems unnecessarily harsh. Remember that EM maps do not show electron 
density but electric potential, so undamaged negatively charged moieties 
should occur at negative density levels. There is an "Aha-Erlebnis" paper (at 
least, that's the effect it had on me :-) ) by Jimin Wang and Peter Moore 
(entitled "On the interpretation of electron microscopic maps of biological 
macromolecules") on this very topic in last month's EM-special of Protein 
Science, Vol 26, pp 122-129.


--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
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**
   Little known gastromathematical curiosity: let "z" be the
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of that pizza is equal to pi*z*z*a !
**

[ccp4bb] EMBL-EBI is recruiting a Team Leader, Cellular Structure and 3D Bioimaging

[Gerard DVD Kleywegt]

Hi all,

We are seeking to recruit a Team Leader for the Cellular Structure & 3D 
Bioimaging team at the European Bioinformatics Institute (EMBL-EBI) located at 
the Wellcome Trust Genome Campus near Cambridge in the UK. EMBL-EBI is a 
world-leader in archival and dissemination of 3D biomacromolecular and 
cellular structure data. We accept and curate depositions of structural data 
for three global archives, PDB, EMDB and EMPIAR. We also maintain a number of 
databases that support advanced search, analysis and visualisation services 
for structural biologists and the wider scientific community.


The Cellular Structure & 3D Bioimaging team at EMBL-EBI manages the EMDB and 
EMPIAR archives and thus plays a key role in the global archival and 
dissemination of 3DEM data. We are now looking to recruit a Team Leader to 
provide visionary leadership of this team. The team is relatively small at 
present (6 posts, funded by EMBL-EBI, NIH, MRC and BBSRC), but we expect it to 
grow under the new team leader, as EMBL-EBI is establishing itself as a global 
leader in image-data repositories. This is a faculty level position reporting 
to Gerard Kleywegt, Head of the Molecular and Cellular Structure cluster.


For more information, see: 
https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj=55513=15470


Feel free to bring this vacancy to the attention of any suitable candidates 
you might know.


Best wishes,

--Gerard

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Pauline Haslam   pdbe_ad...@ebi.ac.uk

[ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

[Gerard DVD Kleywegt]

Hi all,

After tirelessly serving the scientific community with (mostly) beautiful maps 
for two decades, the Uppsala Electron Density Server (EDS; 
http://eds.bmc.uu.se/) is now reaching the end of its life (in fact, it has 
been living on borrowed time for several years already). Some time in 2017 it 
will therefore be "phased" out and join the choir invisible (despite its 
beautiful plumage).


The good news is that much of the EDS functionality (and in particular the 
delivery of map and mtz files, as well as a much better 3D viewer) is now 
provided by the Protein Data Bank in Europe (PDBe; http://pdbe.org/).


There is a short write-up that explains what this means for users who just 
want to look at maps, for users who want to download files, for users of 
software that retrieves data from EDS, and for developers of such software 
(incl. URLs for map, mtz and other relevant files on the PDBe website) at:


  http://www.ebi.ac.uk/pdbe/eds

Toodle pip!

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Apply now for an EMBL-EBI course in Structural Bioinformatics

[Gerard DVD Kleywegt]

Hi all,

Applications are invited for a course on Structural Bioinformatics that is 
being organised by EMBL-EBI and that will be held from 12-16 October 2015. 
This course will explore bioinformatics data resources and tools that are 
available for the interpretation and exploitation of biomacromolecular 
structures, focusing on how best to use structural information to gain the 
most from it in specific research contexts. The five days will each have a 
different theme, viz.:


- Day 1 - Monday 12 October - Bringing structure to biology
- Day 2 - Tuesday 13 October - New structures from old
- Day 3 - Wednesday 14 October - Genetic variation and protein structure
- Day 4 - Thursday 15 October - From structure to function
- Day 5 - Friday 16 October - Small molecules with big effects

Besides EMBL-EBI staff, trainers will include a number of internationally 
recognised experts in the field.


For more information about the course and details of how to apply, please 
visit:


http://www.ebi.ac.uk/training/course/structural-bioinformatics

Feel free to pass on this information to anyone who might be interested!

Best wishes,

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

[Gerard DVD Kleywegt]

It works again now. Sorry for the inconvenience.

--Gerard


On Tue, 9 Jun 2015, Xiao Lei wrote:


Hi All,

I am trying to get electron density map of some pdb structures, I know
there is a database called Electron density server (EDS
http://eds.bmc.uu.se/eds). But somehow these days I can not connect to the
website and I keep getting the This webpage is not available message in
my browser (Internet connection is ok).  I also tried to go to PDB
databank, search a structure and click EDS link, but this did not connect
to the server neither.

Are there other ways to get electron density maps?

Thanks.


Xiao




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Vacancy at PDBe for an experienced scientific programmer (validation and structure analysis)

[Gerard DVD Kleywegt]

Dear CCP4BB-ers,

The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is urgently seeking 
to recruit an experienced scientific programmer to develop and maintain 
validation and analysis tools for biomacromolecular structure data. Applicants 
should ideally be established structural biologists with a proven track record 
in methods/software development in the area of protein-ligand crystallography, 
validation and structure analysis, and with an outstanding publication record.


The post holder will be responsible for:

- Developing and maintaining the wwPDB validation pipelines, used during and 
prior to structure deposition and after structure release, using input from 
the wwPDB Validation Task Forces and the PDBe Team Leader.


- Developing and maintaining structure analysis and comparison tools such as 
PDBePISA and PDBeFold.


- Developing innovative tools to present structural data and validation 
information on biomacromolecules and ligands.


- Working with other PDBe staff to integrate validation information into the 
PDBe query system and the PDB and EMDB entry pages.


- Acting as a source of expertise to the PDBe team on issues of validation and 
ligands (in the context of deposition, annotation, databases and services).


Note: in order to have overlap with the current post-holder we aim for a 
starting date no later than 1 July.


For more information about the post, see: 
https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jjid=53803aid=15470


Please feel free to pass on this information to any potentially suitable 
candidates you may be aware of.


Thanks!

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Job opening for a scientific programmer (PDB SAS) at PDBe

[Gerard DVD Kleywegt]

Hi all,

We have an opening for a scientific programmer to work (1) on the 
incorporation of small-angle scattering (SAS) data into the wwPDB Deposition 
and Annotation system and (2) on presentation and dissemination of SAS data 
through the PDBe website. The project (which will last for 18 months) will 
involve extensive collaboration with the wwPDB partners, members of the wwPDB 
SAS Task Force and the wider community and is based at the European 
Bioinformatics Institute (EMBL-EBI) located on the Wellcome Genome Campus near 
Cambridge in the UK.


For more information, see 
http://www.embl.de/jobs/searchjobs/index.php?ref=EBI_00525


For informal enquiries, please contact the Project Leader NMR in the PDBe 
team, Aleks Gutmanas gutma...@ebi.ac.uk.


Please feel free to pass this message on to any suitably qualified and 
potentially interested candidates. Thanks!


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Vacancy for a scientific database curator at PDBe

[Gerard DVD Kleywegt]

Hi all,

We are looking to recruit an expert structural biologist (with experience in 
structure determination) to join the Protein Data Bank in Europe curation team 
(PDBe: pdbe.org) at the European Bioinformatics Institute (EMBL-EBI, 
Cambridge, UK) as a Scientific Database Curator. The work involves annotating 
preliminary PDB and Electron Microscopy Data Bank (EMDB) submissions and 
extracting relevant biological information. In addition, curators contribute 
to training, outreach and user-support activities of PDBe and the EMBL-EBI.


For more information, please go to:

   http://www.embl.de/jobs/searchjobs/index.php?newlang=1ref=EBI_00522

Feel free to pass the information on to any potentially interested and 
qualified people you may know.


Thanks!

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Vacancy for a Scientific Programmer Bioimaging EMPIAR at PDBe

[Gerard DVD Kleywegt]

Hi all,

We are looking to recruit an experienced and motivated Scientific Programmer 
Bioimaging  EMPIAR to join the Protein Data Bank in Europe (PDBe) team at 
the European Bioinformatics Institute (EBI) located on the Wellcome Trust 
Genome Campus near Cambridge in the UK.


PDBe has recently launched EMPIAR (http://pdbe.org/empiar), an archive of raw 
2D image data from electron microscopy and electron tomography experiments. We 
now plan to extend and improve the archival, integration and dissemination of 
cellular imaging data from a range of other modalities including 3D scanning 
electron microscopy (3D-SEM), soft X-ray tomography (SXT) and correlative 
light and electron microscopy (CLEM). We are therefore seeking to recruit an 
enthusiastic scientific programmer with outstanding programming skills to join 
the EMPIAR development team.


For more information, see:

 https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jjid=53570aid=15470

For informal enquiries, please contact Ardan Patwardhan ar...@ebi.ac.uk, who 
is in charge of the EMPIAR project.


Best wishes,

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Reminder: 3 vacancies at PDBe - closing this week

[Gerard DVD Kleywegt]

Hi all,

This is just a quick reminder that the application period for our 3 vacancies 
is closing this Friday at midnight. We are seeking to recruit:


- two curators (PDB/EMDB) - 
http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=53264aid=15470


- one web front-end developer - 
http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=53259aid=15470


Thanks,

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Vacancy for a web-developer at PDBe

[Gerard DVD Kleywegt]

Hi all,

We are looking to recruit an experienced Web Front-End Developer with an 
interest in biological data to work within the Protein Data Bank in Europe 
team (PDBe; pdbe.org) at the European Bioinformatics Institute (EMBL-EBI) in 
Cambridge (UK).


For more information, please surf to:

   http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=53259aid=15470

Feel free to pass the information on to any potentially interested and 
qualified people you may know.


Thanks!

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Vacancies for *TWO* scientific database curators at PDBe

[Gerard DVD Kleywegt]

Hi all,

We are looking to recruit *TWO* expert structural biologists to join the 
Protein Data Bank in Europe curation team (PDBe: pdbe.org) at the European 
Bioinformatics Institute (EMBL-EBI, Cambridge, UK) as Scientific Database 
Curators. The work involves annotating preliminary PDB and Electron Microscopy 
Data Bank (EMDB) submissions and extracting relevant biological information. 
In addition, curators contribute to training, outreach and user-support 
activities of PDBe and the EMBL-EBI.


For more information, please go to:

   http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=53264aid=15470

Feel free to pass the information on to any potentially interested and 
qualified people you may know.


Thanks!

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Vacancies for scientific programmers in the EMDB team at the Protein Data Bank in Europe (PDBe)

[Gerard DVD Kleywegt]

Dear all,

The EMDB team at the Protein Data Bank in Europe (PDBe; http://pdbe.org) has 
two vacancies for scientific programmers to work on an exciting new MRC and 
BBSRC funded project to help bridge the worlds of cellular and molecular 
structural biology. The project aims to develop:


1) a web-based interactive 3D browser that will integrate structural data on 
scales from molecules to cells from the EMDB and PDB archives


2) support for annotating 3D volume segmentations so that they can be better 
integrated with other structural and bioinformatics resources


3) the recently announced Electron Microscopy Pilot Image ARchive (EMPIAR; 
http://pdbe.org/empiar).


Further details about the two posts can be found in the job adverts below and 
by contacting the EMDB project leader at PDBe, Ardan Patwardhan 
(ar...@ebi.ac.uk).


Please note that the application deadline is the 29th of June 2014. Interviews 
will be scheduled for 15 and 16 July.


More information on the two posts and on how to apply:

- Post I, Scientific Programmer EMPIAR 3D Browser: 
https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jjid=52642aid=15470


- Post II, Scientific Programmer EMPIAR Archive: 
https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jjid=52652aid=15470



--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] EDSTATS for an extracted fragment

[Gerard DVD Kleywegt]

What you want is a test for how well each model agrees with its own map. It 
is fair to argue that the model that is more self-consistent (agrees better 
with its own map) is the better model.  But you won't learn that by 
comparing model A to map B.


However, conversely, if your modified model fits the original map better than 
the model that was used to calculate the map itself, you've done a good bit of 
model building. If you want to do this calculation (with all the warnings and 
caveats), you can also use MAPMAN - 
http://xray.bmc.uu.se/usf/mapman_man.html#S41 . The method you propose is 
essentially the same as this one: http://www.ncbi.nlm.nih.gov/pubmed/18598022 
but for a fragment of your macromolecule instead of for a ligand (if you don't 
have access to the journal, you can request a reprint here: 
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=87 )


--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] AW: [ccp4bb] map manipulation questions

[Gerard DVD Kleywegt]

MAPMAN contains several related options, e.g. CEll, SPacegroup, TRanslate and 
GTranslate, PAste (see the manual for caveats - 
http://xray.bmc.uu.se/usf/mapman_man.html ). Saving as an ASCII file and 
editing may also work, if you know what you are doing.


--Gerard





On Tue, 20 May 2014, Edward A. Berry wrote:

But, if you convert to structure factors and recalculate the map in a 
different cell,
the features will be stretched to fill the cell, which I take it is the 
original problem.


I found Kleywegt's RAVE package very convenient for doing this,
but i believe the functionality is now available in
ccp4 mapmask and maprot programs.

The Phaser Wiki has a page with instructions
for cutting out electron density within a mask,
and putting it in a large P1 cell for use as a molecular
replacement model. Perhaps you could modify that to achieve
your aims.

http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model
eab

On 05/20/2014 03:07 AM, herman.schreu...@sanofi.com wrote:

Dear Niu,

Provided you have a complete asymmetric unit (unit cell in P1), you could 
also convert this map to
structure factors and manipulate those, e.g. with sftools. To calculate 
structure factors you could use

sfall and also clipper has utilities to convert a map to structure factors.

Best,

Herman

*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von 
*Niu Tou

*Gesendet:* Montag, 19. Mai 2014 23:25
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [ccp4bb] map manipulation questions

Dear All,

I have a ccp4 format map file in P1 spacegroup, I would like to manipulate 
it in several ways:


1. enlarge the cell dimension . When I tried CELL keyword in MAPMAN, the 
density scaled up together
with the cell dimension. Does anybody know how to do it without changing 
the density?


2. Change the space group to P2.

3. Move the density away from its original place, i.e. apply a 
translocation vector to it.


Does anybody know the answers? Thanks in advance!

Regards,

Niu






Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] 100.000?

[Gerard DVD Kleywegt]

Hi Tim,

Yes, the average is around 150-200 per week (as pointed out by others, weekly 
releases are highlighted on the website pdbe.org/latest, on Facebook 
facebook.com/proteindatabank and on Twitter twitter.com/PDBeurope). Last year, 
we had more than 10,000 depositions worldwide for the first time.


--Gerard


On Sat, 10 May 2014, Tim Gruene wrote:


Hi Gerard,

does that mean there are more than 70 structures released in a week? I
know the number of entries grows exponentially, yet having it cut down
to a graspable number makes it even more impressive.

Cheers,
Tim

On 05/10/2014 09:33 PM, Gerard DVD Kleywegt wrote:

See: http://www.wwpdb.org/news/news_2014.html#06-May-2014

Even if you don't deposit anything, we'll reach the 100,000-entry
milestone with next Wednesday's release :-)

--Gerard



On Fri, 9 May 2014, mesters wrote:


Great, just a few more structures to deposit and then 100.000
structures to celebrate and that in the IYCR2014 :-)

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

Institute of Biochemistry, University of L?beck
Ratzeburger Allee 160, 23538 L?beck, Germany

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

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


--
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
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The Institute will not accept any liability in respect of such
communication, and the employee responsible will be personally liable
for any damages or other liability arising. Employees who receive such
an email must notify their supervisor immediately.
--





Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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

GPG Key ID = A46BEE1A





Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] 100.000?

[Gerard DVD Kleywegt]

See: http://www.wwpdb.org/news/news_2014.html#06-May-2014

Even if you don't deposit anything, we'll reach the 100,000-entry milestone 
with next Wednesday's release :-)


--Gerard



On Fri, 9 May 2014, mesters wrote:

Great, just a few more structures to deposit and then 100.000 structures to 
celebrate and that in the IYCR2014 :-)


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

Institute of Biochemistry, University of L?beck
Ratzeburger Allee 160, 23538 L?beck, Germany

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

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


--
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 the 
individual named. If you are not the named addressee you should not 
disseminate, distribute or copy this e-mail. Please notify the sender 
immediately by e-mail if you have received this e-mail by mistake and delete 
this e-mail from your system.
* E-mail transmission cannot be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, arrive late or 
incomplete, or contain viruses. The sender therefore does not accept 
liability for any errors or omissions in the contents of this message, which 
arise as a result of e-mail transmission. If verification is required please 
request a hard-copy version. Please send us by fax any message containing 
deadlines as incoming e-mails are not screened for response deadlines.
* Employees of the Institute are expressly required not to make defamatory 
statements and not to infringe or authorize any infringement of copyright or 
any other legal right by email communications. Any such communication is 
contrary to Institute policy and outside the scope of the employment of the 
individual concerned. The Institute will not accept any liability in respect 
of such communication, and the employee responsible will be personally liable 
for any damages or other liability arising. Employees who receive such an 
email must notify their supervisor immediately.

--





Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] Validation reports for all X-ray structures in the PDB

[Gerard DVD Kleywegt]

Hi all,

I don't know why my posting about validation reports re-appeared several 
times. The mail headers show that all 4 came through the domain ouhsc.edu but 
why they would be resent to ccp4bb is not clear, nor why this only happened 
with my posting.


--Gerard

[ccp4bb] Validation reports for all X-ray structures in the PDB

[Gerard DVD Kleywegt]

Hi all,

You may not have noticed, but 19 March 2014 was VR Day - the day that new 
style wwPDB validation reports for all X-ray structures were made publicly 
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=ae7f982d2df966a2f95f73a794d46efffb16c227a75389fdd058f5cc62d1654d


The validation-related files for individual X-ray PDB entries can be accessed 
through the web sites and ftp sites of the various wwPDB partners. Speaking 
for PDBe, if you go to the summary page of an X-ray PDB entry, for instance:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=eaa2ef06948e08de06b7fbd47cbfe0ec2c5dac82a4c70b2ffd055bbdf10311ec

you will see the percentile sliders displayed in the PDBportfolio widget 
(https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=106d86fcfd3fb5e631ca04b4d6f0be2adb8a60edf33ca698248517e47de9e5c7) on the right of the page. (Clicking the big white 
arrow will start a slideshow of images related to this entry.) The legend of 
the percentile-slider plot contains a direct link to the validation report (as 
a PDF file; in this case 
https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=455ace0917c519ea7f631e3906413c60cf63deb9c4512491003cebf397e148d0).


If you are not yet familiar with these new style validation reports, have a 
look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=88f1dd8be8660e1657bae27e311478f5ed3dfbd2922c198277688efbe98e7ba1 - in particular the 
user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=26d1c36fa29104dc85265fe4997ceaafec2e797dded7fb1ea2e39ae02988262a


If you want to download the full report (which lists all outliers for many of 
the validation criteria, instead of just the worst 5 or the first 5), or a 
graphic image of the percentile-slider plot, or an XML file with all 
validation data in machine-readable form, go to the downloads page of any 
X-ray PDB entry, either through clicking the Downloads link in the menu on 
the left, or directly by going to a URL of the form:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=3f324c797061411513168635757d7fc61545406ac5203d849b72a712bbe5e644

The section labelled Validation of the table provides the relevant links.

Note that sites that include PDBportfolio in their pages now automatically 
display the percentile-slider plot and download link as well! To see this in 
action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.:


  
https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0Am=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0As=3f50278f4e3251a6c6efc1d0f293bed530f5fb4bcd94ef2a6426d1fbcffdfc7c

Please send any comments, questions or suggestions on the new style validation 
reports to validat...@mail.wwpdb.org


Questions about PDBe-specific pages and services can be sent to 
pdbeh...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Validation reports for all X-ray structures in the PDB

[Gerard DVD Kleywegt]

Hi all,

You may not have noticed, but 19 March 2014 was VR Day - the day that new 
style wwPDB validation reports for all X-ray structures were made publicly 
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=494f114fbff8c5913722a563f0fac87daa91b4a0943e65f0c0d0258697324e71


The validation-related files for individual X-ray PDB entries can be accessed 
through the web sites and ftp sites of the various wwPDB partners. Speaking 
for PDBe, if you go to the summary page of an X-ray PDB entry, for instance:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=ceb8a826f9fd1bcb945c2d5d2108bfcd5af42fb57dd42c876d8e434f7e44302f

you will see the percentile sliders displayed in the PDBportfolio widget 
(https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=c36bb823c5eab11a764ba159a174b979be73b6a5afb1bdcd821b991dd813850d) on the right of the page. (Clicking the big white 
arrow will start a slideshow of images related to this entry.) The legend of 
the percentile-slider plot contains a direct link to the validation report (as 
a PDF file; in this case 
https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=09ba089e02bd4ac32ff47acb46f1659bfc50fd8dbf4b0064917cc1622f5bc36f).


If you are not yet familiar with these new style validation reports, have a 
look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=30a7f6e1086c7cf681d793b223a5f56a794439dc12a51b952b7ee69db0dfd24f - in particular the 
user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=8384ec2de5f88f578d48e541831c47161606776d3787393f20fc9c6a59d4


If you want to download the full report (which lists all outliers for many of 
the validation criteria, instead of just the worst 5 or the first 5), or a 
graphic image of the percentile-slider plot, or an XML file with all 
validation data in machine-readable form, go to the downloads page of any 
X-ray PDB entry, either through clicking the Downloads link in the menu on 
the left, or directly by going to a URL of the form:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=0af71922028784db5dee672128cc8d1a9131aba3b56f4777dc2bcbaa15c96a2c

The section labelled Validation of the table provides the relevant links.

Note that sites that include PDBportfolio in their pages now automatically 
display the percentile-slider plot and download link as well! To see this in 
action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.:


  
https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0Am=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0As=4fe494878b502d19dedc40a0cfdeded207b166ca483a0d06643466303b4146b5

Please send any comments, questions or suggestions on the new style validation 
reports to validat...@mail.wwpdb.org


Questions about PDBe-specific pages and services can be sent to 
pdbeh...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Validation reports for all X-ray structures in the PDB

[Gerard DVD Kleywegt]

Hi all,

You may not have noticed, but 19 March 2014 was VR Day - the day that new 
style wwPDB validation reports for all X-ray structures were made publicly 
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=a4ec416976c036dba11dd2eba52f58ea7623cf9c77878158a2d68f57c854ea56


The validation-related files for individual X-ray PDB entries can be accessed 
through the web sites and ftp sites of the various wwPDB partners. Speaking 
for PDBe, if you go to the summary page of an X-ray PDB entry, for instance:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=e31ebbe11650822dcddc95c8d732073824315aaa1ef0a85f6947ca3e78d08cfe

you will see the percentile sliders displayed in the PDBportfolio widget 
(https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=bb14504b68d5ac31e4d37c4a21b543c89a6fe18fac33b6c8b54db86869a541dd) on the right of the page. (Clicking the big white 
arrow will start a slideshow of images related to this entry.) The legend of 
the percentile-slider plot contains a direct link to the validation report (as 
a PDF file; in this case 
https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=9cfce1c69787f7b3b8c7aed8266cbc1a2f80474cd3a0e092aa23b32b22482dcf).


If you are not yet familiar with these new style validation reports, have a 
look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=899dc883a72c9aefd1cfa143a8a33e2ecc7bc1a7b0e3b42563c71730ddb8d141 - in particular the 
user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=696eccc3065b76804f94f1b2ec49a7deede7cfe02e2251290f6a6d246cbaedff


If you want to download the full report (which lists all outliers for many of 
the validation criteria, instead of just the worst 5 or the first 5), or a 
graphic image of the percentile-slider plot, or an XML file with all 
validation data in machine-readable form, go to the downloads page of any 
X-ray PDB entry, either through clicking the Downloads link in the menu on 
the left, or directly by going to a URL of the form:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=3777dd064f5a5c7afd82c5e78bf77dc52fd85428c524d2083cd96316c6ff3527

The section labelled Validation of the table provides the relevant links.

Note that sites that include PDBportfolio in their pages now automatically 
display the percentile-slider plot and download link as well! To see this in 
action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.:


  
https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0Am=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0As=f8067c0121d03f420ec913cd927ad5a65c0bc1831b03ed4e43197317a3228336

Please send any comments, questions or suggestions on the new style validation 
reports to validat...@mail.wwpdb.org


Questions about PDBe-specific pages and services can be sent to 
pdbeh...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Validation reports for all X-ray structures in the PDB

[Gerard DVD Kleywegt]

Hi all,

You may not have noticed, but 19 March 2014 was VR Day - the day that new 
style wwPDB validation reports for all X-ray structures were made publicly 
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=4105ff6448d5bdbd51e474e89f5a06ee532f480bdcd7c0205ce5c6d91b48300e


The validation-related files for individual X-ray PDB entries can be accessed 
through the web sites and ftp sites of the various wwPDB partners. Speaking 
for PDBe, if you go to the summary page of an X-ray PDB entry, for instance:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=032b800b3e9b3f00999a10131c588183b134c5a44c0c6d5dafd999b619326c1e

you will see the percentile sliders displayed in the PDBportfolio widget 
(https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfoliok=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=66fbe101d6708d887924bdc5bf25021570f9885c97daf3d064f9f7258c3303ad) on the right of the page. (Clicking the big white 
arrow will start a slideshow of images related to this entry.) The legend of 
the percentile-slider plot contains a direct link to the validation report (as 
a PDF file; in this case 
https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdfk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=1e6916c73273cdcf0e20a5b7d4ff23d7961c1d97a12988b072d32fcec45e7570).


If you are not yet familiar with these new style validation reports, have a 
look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=fd35f5139833bb5700372d7bf5f2398f28706b2154d8bc1d907eef9e82ac517f - in particular the 
user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.htmlk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=11887d82818aef793f525049cf3b75a603cecba6cb0d7351fb3122b50d963f5a


If you want to download the full report (which lists all outliers for many of 
the validation criteria, instead of just the worst 5 or the first 5), or a 
graphic image of the percentile-slider plot, or an XML file with all 
validation data in machine-readable form, go to the downloads page of any 
X-ray PDB entry, either through clicking the Downloads link in the menu on 
the left, or directly by going to a URL of the form:


  
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloadsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=83fb53eb3391a94d7ad7de7d2fcd02804657e56c7c0b5fb8aa3d655715d9a966

The section labelled Validation of the table provides the relevant links.

Note that sites that include PDBportfolio in their pages now automatically 
display the percentile-slider plot and download link as well! To see this in 
action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.:


  
https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbsk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0Am=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0As=57e3ff9f13e2ce786081e6f02d66213a2911f3d14ba6003a495ea2d5dd9c1650

Please send any comments, questions or suggestions on the new style validation 
reports to validat...@mail.wwpdb.org


Questions about PDBe-specific pages and services can be sent to 
pdbeh...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Validation reports for all X-ray structures in the PDB

[Gerard DVD Kleywegt]

Bonjour Philippe,

The reports are based on the recommendations of the wwPDB X-ray validation 
task force - see http://www.wwpdb.org/workshop/2011/index.html and the report 
published by this task force at 
http://www.cell.com/structure/abstract/S0969-2126%2811%2900285-1


Of course, if you have specific suggestions for improvements, we'd be 
interested to hear from you - feel free to mail them to 
validat...@mail.wwpdb.org


A stand-alone server already exists - see 
http://www.wwpdb.org/validation-servers.html - hope this turns your Good 
Friday into a Great Friday :-)


Best wishes,

--Gerard





On Wed, 16 Apr 2014, Philippe BENAS wrote:


Dear Gerard CD/DVD/Blue Ray (;-) ),

Yes, these new reports are great although they should/will improve over time.

Another point that would be also really helpful would be to have the 
opportunity to run the associated scripts either locally or on a remote server 
from the PDB, prior to the submission itself. Hence they should provide strong 
guidelines the crystallographers during their rebuilding/refinement stages. I 
know Phenix for instance has already some of these tools, but not all.

Could the PDB provide something in that way for the everyday use of a poor 
X-ray crystallographer ?

Best regards,
Philippe

 


Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS

E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18








De : Gerard DVD Kleywegt ger...@xray.bmc.uu.se
? : CCP4BB@JISCMAIL.AC.UK 
Envoy? le : Mercredi 16 avril 2014 19h01

Objet : [ccp4bb] Validation reports for all X-ray structures in the PDB


Hi all,

You may not have noticed, but 19 March 2014 was VR Day - the day that new 
style wwPDB validation reports for all X-ray structures were made publicly 
available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014


The validation-related files for individual X-ray PDB entries can be accessed 
through the web sites and ftp sites of the various wwPDB partners. Speaking 
for PDBe, if you go to the summary page of an X-ray PDB entry, for instance:


          http://pdbe.org/1cbs

you will see the percentile sliders displayed in the PDBportfolio widget 
(http://pdbe.org/portfolio) on the right of the page. (Clicking the big white 
arrow will start a slideshow of images related to this entry.) The legend of 
the percentile-slider plot contains a direct link to the validation report (as 
a PDF file; in this case 
http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf).


If you are not yet familiar with these new style validation reports, have a 
look here: http://www.wwpdb.org/validation-reports.html - in particular the 
user guide may be of interest: http://www.wwpdb.org/ValidationPDFNotes.html


If you want to download the full report (which lists all outliers for many of 
the validation criteria, instead of just the worst 5 or the first 5), or a 
graphic image of the percentile-slider plot, or an XML file with all 
validation data in machine-readable form, go to the downloads page of any 
X-ray PDB entry, either through clicking the Downloads link in the menu on 
the left, or directly by going to a URL of the form:


          http://pdbe.org/1cbs/downloads

The section labelled Validation of the table provides the relevant links.

Note that sites that include PDBportfolio in their pages now automatically 
display the percentile-slider plot and download link as well! To see this in 
action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.:


          http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs

Please send any comments, questions or suggestions on the new style validation 
reports to validat...@mail.wwpdb.org


Questions about PDBe-specific pages and services can be sent to 
pdbeh...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk



Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Validation reports for all X-ray structures in the PDB

[Gerard DVD Kleywegt]

Hi all,

You may not have noticed, but 19 March 2014 was VR Day - the day that new 
style wwPDB validation reports for all X-ray structures were made publicly 
available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014


The validation-related files for individual X-ray PDB entries can be accessed 
through the web sites and ftp sites of the various wwPDB partners. Speaking 
for PDBe, if you go to the summary page of an X-ray PDB entry, for instance:


  http://pdbe.org/1cbs

you will see the percentile sliders displayed in the PDBportfolio widget 
(http://pdbe.org/portfolio) on the right of the page. (Clicking the big white 
arrow will start a slideshow of images related to this entry.) The legend of 
the percentile-slider plot contains a direct link to the validation report (as 
a PDF file; in this case 
http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf).


If you are not yet familiar with these new style validation reports, have a 
look here: http://www.wwpdb.org/validation-reports.html - in particular the 
user guide may be of interest: http://www.wwpdb.org/ValidationPDFNotes.html


If you want to download the full report (which lists all outliers for many of 
the validation criteria, instead of just the worst 5 or the first 5), or a 
graphic image of the percentile-slider plot, or an XML file with all 
validation data in machine-readable form, go to the downloads page of any 
X-ray PDB entry, either through clicking the Downloads link in the menu on 
the left, or directly by going to a URL of the form:


  http://pdbe.org/1cbs/downloads

The section labelled Validation of the table provides the relevant links.

Note that sites that include PDBportfolio in their pages now automatically 
display the percentile-slider plot and download link as well! To see this in 
action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.:


  http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs

Please send any comments, questions or suggestions on the new style validation 
reports to validat...@mail.wwpdb.org


Questions about PDBe-specific pages and services can be sent to 
pdbeh...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Stand-alone wwPDB X-ray validation server

[Gerard DVD Kleywegt]

Dear colleagues,

The wwPDB partners are pleased to announce that X-ray structure validation 
reports can now be generated on demand by macromolecular crystallographers by 
using the new stand-alone wwPDB validation server.


For the full scoop, see: http://wwpdb.org/news/news_2013.html#27-November-2013

If you want to skip the propaganda, go to 
http://wwpdb.org/validation-servers.html to read the technical notes and from 
there follow the link to the server.


This version of the validation server is still in beta testing. We appreciate 
your feedback and suggestions for improvement - please mail these to: 
validat...@mail.wwpdb.org (not to me or the list). Thanks!


Best wishes,

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Electron density server

[Gerard DVD Kleywegt]

The server has been rebooted and appears to be working again.

--Gerard




On Fri, 25 Oct 2013, Rojan Shrestha wrote:


Hello,



Is EDS (electron density server) dead? In the absence of EDS, how can be mtz
file directly downloaded?



Regards,



Rojan





Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] What kind of reflection data to deposit to PDB

[Gerard DVD Kleywegt]

Hi all,

Sorry for contributing to the noise as well as the signal in the discussion. 
To clarify:


It is not an issue of not having a place to put the data as we certainly have 
definitions for this and for intermediate phasing data sets. You cannot simply 
put the data into the current REFLN category which is where we presently 
collect reflection data.


At present, there is no official wwPDB policy in place describing how this 
data is to be processed, validated and distributed. Stuffing it into the 
structure factor files, as has been done informally by some depositors, is not 
a good long term solution as there is no way for people to easily find the 
information. What we'll likely end up doing is store these data in separate 
files (just like for NMR the raw NOE peak lists and distance restraints are 
likely to be archived and distributed as separate files).


As I tried to explain yesterday, the case for both unmerged Is and unassigned 
NOE peak lists has been made, and this will get implemented. It will just take 
a bit of time.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk




On Tue, 17 Sep 2013, Miller, Mitchell D. wrote:


Hi Martyn,

 I too was puzzled by the statement that unmerged data
cannot be handled properly as part of a PDB deposition.

 We have deposited the unmerged original index intensities
for the refinement wavelength (and for additional wavelengths
used for phasing in the case of MAD) since 2005.

 This was based on recommendation #2 from the Report of Task Force
on Numerical Criteria in Structural Genomics from the 2001
Airlie meeting (2nd Intl. Struct. Genomics Mtg.).
http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc
http://www.isgo.org/organization/members07/010410.html
Which states that For X-ray data, unmerged integrated intensities (omitting
outliers but including systematically-absent axial reflections) should be 
deposited
along with the final, merged intensities and amplitudes for all wavelengths 
and/or
derivatives.

We worked the RCSB staff to refine the format of the mmCIF formatted
reflection containing multiple data loops for our depositions and this
has been used for more than 1300 JCSG depositions and the data is retrievable
from all wwPDB partner sites.


Regards,
Mitch


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn 
Symmons
Sent: Tuesday, September 17, 2013 3:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB

Sorry to contradict,

But the mmCIF data model certainly does not seem to require hkl unique
within the reflection data.

Like CIF the mmCIF formalism has been developed to allow a complete
description of a diffraction experiment and the data arising from it.
There is a full description at
http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html
(I am grateful to Rachel Kramer Green at the RCSB for pointing out these
links to the dictionary and the papers describing its development).

Having chosen mmCIF for the archive and then not using its flexibility
seems a bit like having your cake and NOT eating it.

It is strange to hear on a discussion board that recently considered the
advantages of depositing complete image data, that a case will have to
be made for allowing the deposition of full unmerged datasets.

++Martyn


On 16/09/2013 14:03, Gerard DVD Kleywegt wrote:

Dear all,

At present, unmerged data cannot be handled properly as part of a PDB
deposition. One reason for this is that changes to the mmCIF/PDBx data
model will be required (at the moment, hkl must be unique within the
reflection data, which is logical for merged data but precludes
handling of unmerged data). There are other (easier to resolve) issues
to work out, e.g. having to do with file naming and distribution via
the wwPDB ftp archive.

The wwPDB partners are presently focusing all efforts on rolling out
the new joint deposition and annotation system. Once this system is
reasonably stable we will look into accepting/validating/distributing
new kinds of data. This concerns not only unmerged Is for X-ray but
also unassigned NOE peak lists for NMR. We will seek the advice of the
corresponding wwPDB VTFs (Validation Task Forces) to help define the
data items that need to be captured, how the data should be processed
by wwPDB, and what kind(s) of validation is/are required.

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk




On Thu, 5 Sep 2013, Raji Edayathumangalam wrote:


Hi Folks,

Sorry for the non-ccp4 post.

I am trying to determine what is the best form of unmerged reflection
data
to deposit to the PDB. I have single wavelength anomalous data for my
structure and I have two flavors

Re: [ccp4bb] What kind of reflection data to deposit to PDB

[Gerard DVD Kleywegt]

Dear all,

At present, unmerged data cannot be handled properly as part of a PDB 
deposition. One reason for this is that changes to the mmCIF/PDBx data model 
will be required (at the moment, hkl must be unique within the reflection 
data, which is logical for merged data but precludes handling of unmerged 
data). There are other (easier to resolve) issues to work out, e.g. having to 
do with file naming and distribution via the wwPDB ftp archive.


The wwPDB partners are presently focusing all efforts on rolling out the new 
joint deposition and annotation system. Once this system is reasonably stable 
we will look into accepting/validating/distributing new kinds of data. This 
concerns not only unmerged Is for X-ray but also unassigned NOE peak lists for 
NMR. We will seek the advice of the corresponding wwPDB VTFs (Validation Task 
Forces) to help define the data items that need to be captured, how the data 
should be processed by wwPDB, and what kind(s) of validation is/are required.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk




On Thu, 5 Sep 2013, Raji Edayathumangalam wrote:


Hi Folks,

Sorry for the non-ccp4 post.

I am trying to determine what is the best form of unmerged reflection data
to deposit to the PDB. I have single wavelength anomalous data for my
structure and I have two flavors of scaled files from the same exact set of
diffraction images: (1) data indexed and scaled in p1, and (2) data indexed
in p222, scaled in Scalepack using the no merge original index option and
converted to .mtz since the unit cell in the header of the output .sca file
was missing.

The space group for the dataset is p212121.

Please could you let me know what might be the best approach.

Many thanks and cheers,
Raji

--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] structural search for homologs in pdb?

[Gerard DVD Kleywegt]

On Thu, 22 Aug 2013, Gloria Borgstahl wrote:


We have a protein sequence that probably contains OB folds.  What is the
best way to search for the top structural homologs to this sequence in the
pdb?  G


Hi Gloria,

If you expect decent sequence simnilarity to one or more proteins in the PDB, 
and if you don't have the structure of your protein, a simple FASTA search 
should give you the list of hits and alignments quickly. I would do that using 
the PDBeXplore FASTA archive browser - http://pdbe.org/fasta


Simply provide your sequence (or UniProt accession) and submit. If there are 
hits, they will be presented in a way that allows for rapid further 
exploration, e.g. in terms of their CATH classifications, bound ligands or 
Pfam families. You can also sort the hits by E-value or %-age identity 
(amongst many other things) and get the alignments with your sequence in the 
results page.


If you want to explore the interface, try 
http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/?seq=SVRKFTEKHEWVTTENGVGTVGISNFAQEALGDVVYCSLPEVGTKLNKQEEFGALESVKAASELYSPLSGEVTEINKALAENPGLVNKSCYEDGWLIKMTFSNPSELDELMSEEAYEKYIKSIEEtab=PDB%20entries 
(this uses the sequence of PDB entry 3KLR which also has an OB fold, CATH 
class 2.40.50).


There are a number of PDBeXplore modules available (http://pdbe.org/explore), 
including a CATH-based browser (if you should like to analyse all the 
structures that contain an OB fold according to CATH).


If you should have a structure, you can use PDBeFold (SSM; 
http://pdbe.org/fold) to quickly find and compare similar structures without 
taking sequence into consideration.


--Gerard

[ccp4bb] Announcement: wwPDB Workshop on mmCIF/PDBx for Programmers, 20/21 Nov-13, Cambridge (UK)

[Gerard DVD Kleywegt]

wwPDB Workshop on mmCIF/PDBx for Programmers


What, why and how?
--
The world of the PDB will be changing rapidly and profoundly over the next few 
years. A major change will involve the transition from PDB to mmCIF/PDBx as 
the principal deposition and dissemination format (see 
http://www.wwpdb.org/news/news_2013.html#22-May-2013 and 
http://wwpdb.org/workshop/wgroup.html). To help software developers in the 
area of structural biology to make the transition and begin supporting the 
mmCIF/PDBx format in their own programs, wwPDB (http://wwpdb.org/) is 
organising a programmers workshop. This two-day event will include lectures by 
experts in mmCIF/PDBx (http://mmcif.rcsb.org/) and developers of 
language-specific libraries or packages (C/C++, Java, Python). Ample time will 
be devoted to tutorials and individual code hacking, with the experts 
available to assist the workshop participants. Confirmed tutors include Paul 
Adams (Phenix), Eugene Krissinel (CCP4), Garib Murshudov (Refmac), Andreas 
Prlic (RCSB), Sameer Velankar (PDBe) and John Westbrook (RCSB).


When and where?
---
The workshop will be held at the EMBL-EBI (http://ebi.ac.uk/) in Hinxton, 
Cambridge, UK, on 20 and 21 November 2013.


How much?
-
If you are selected as a participant, we expect you to pay for your own travel 
to and from Cambridge. However, there is no fee for this workshop, and we will 
provide accommodation (at the HolidayInn Express in nearby Duxford; 
http://www.hiexpresscambridgeduxford.co.uk/), lunches and a workshop dinner on 
the 20th (all thanks to generous funding from the Wellcome Trust to PDBe).


Who can apply and how?
--
This workshop is intended for high-powered software developers in any area 
of structural biology and structural bioinformatics whose products process 
(read/write) PDB data - e.g., X-ray, NMR, 3DEM, SAXS/SANS, hybrid methods, 
visualisation, validation, modelling, docking, structure prediction, etc. To 
ensure a high ratio of tutors to workshop participants, the number of 
participants is limited to 15.


You can apply for the workshop by sending an e-mail to Sameer Velankar at PDBe 
(sam...@ebi.ac.uk) no later than 31 August 2013. Please include:


- a brief description of the software program(s) or package(s) you have 
developed or are developing, what it does, in which field, how many users, 
relevant publications, etc.;

- what programming language(s) you are specifically interested in;
- how you would benefit from this workshop;
- any specific topics or questions you would like to see addressed in the 
workshop.


If the workshop is oversubscribed, we will use the information and motivation 
provided by the applicants to select the participants.


Participants are expected to bring their own laptop with compilers etc. 
installed. No previous knowledge of mmCIF/PDBx is strictly needed, but 
participants who are aware of the basic principles of the format will probably 
gain more from the workshop.


Applicants will be informed by mid-September if they have been selected or 
not, or if they are on the stand-by list.


For informal inquiries about the workshop, please contact Sameer Velankar at 
PDBe (sam...@ebi.ac.uk).


Please feel free to distribute this announcement to other interested people or 
fora!



--Gerard Kleywegt  Sameer Velankar
  Protein Data Bank in Europe
  A member of the Worldwide Protein Data Bank

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Definition of diffractometer

[Gerard DVD Kleywegt]

As for Gerard's follow up, I remind him of the immortal wisdom of Jack 
Handey:


Maybe in order to understand mankind, we have to look at the word itself. 
Basically, it's made up of two separate words ? mank and ind. What do 
these words mean? It's a mystery, and that's why so is mankind.


Being the misanthrope that I am, I would like to point out that it's also an 
anagram of damn kin.


--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] Definition of diffractometer

[Gerard DVD Kleywegt]

So, in SI units it would be a kilometerometer?

--dvd

On Wed, 19 Jun 2013, Edward A. Berry wrote:


an Odometer measures hod?s:
wikipedia: The word derives from the Greek words hod?s (path or gateway) 
and m?tron (measure).
In countries where Imperial units or US customary units are used, it is 
sometimes called a mileometer or milometer, or, colloquially, a tripometer.


Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Yes, but you need to know the 'geo' has to do with earth, so geometers
measure the earth to make maps, odo, I believe has to do with  smell,
and kilometer is hyphenated kilo-meter, no kil-ometer, so the origin
of that word is nothing to do with 'ometer'. Remembering stuff from
your school days help a great deal understanding the world around you ;-)

Best,
Tim

On 06/20/2013 01:14 AM, Gerard DVD Kleywegt wrote:

Wait, so a geometer measures ges, an odometer measures ods, and a
kilometer measures kils?

--dvd


On Thu, 20 Jun 2013, Tim Gruene wrote:

Dear Ed,

to me, an '-ometer' is a device that measures whatever you put in
front of the 'o', so in case of a diffractometer that's a device
that measures diffraction.

Best, Tim

On 06/19/2013 08:11 PM, Edward A. Berry wrote:

Somewhere I got the idea that a diffractometer is an
instrument that measures one reflection at a time. Is that
the case, and if so what is the term for instruments like
rotation camera, weisenberg, area detector? (What is an area
detector?).

Logically I guess a diffractometer could be anything that
measures diffraction, and that seems to be view of the
wikipedia article of that name. eab








Best wishes,

--Gerard

**
Gerard J. Kleywegt

http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
The opinions in this message are fictional.  Any similarity to
actual opinions, living or dead, is purely coincidental.
**
Little known gastromathematical curiosity: let z be the radius
and a the thickness of a pizza. Then the volume of that pizza is
equal to pi*z*z*a !
**



- --
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 Mozilla - http://enigmail.mozdev.org/

iD8DBQFRwmb2UxlJ7aRr7hoRAm3QAKCtXvSgkJsdEsyTHlZcNIRA4HPn/ACfTdil
j50Wu3GYaoAEl8RNIDAd92M=
=nZ6U
-END PGP SIGNATURE-






Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] Definition of diffractometer

[Gerard DVD Kleywegt]

Wait, so a geometer measures ges, an odometer measures ods, and a kilometer 
measures kils?


--dvd


On Thu, 20 Jun 2013, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Ed,

to me, an '-ometer' is a device that measures whatever you put in
front of the 'o', so in case of a diffractometer that's a device that
measures diffraction.

Best,
Tim

On 06/19/2013 08:11 PM, Edward A. Berry wrote:

Somewhere I got the idea that a diffractometer is an instrument
that measures one reflection at a time. Is that the case, and if so
what is the term for instruments like rotation camera, weisenberg,
area detector? (What is an area detector?).

Logically I guess a diffractometer could be anything that measures
diffraction, and that seems to be view of the wikipedia article of
that name. eab



- --
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 Mozilla - http://enigmail.mozdev.org/

iD8DBQFRwiyEUxlJ7aRr7hoRAuJkAKDGtawLHRpOnErm9o1HQPpaNTQAfwCeOj4E
LufTOxcBtrkHVM2XGcK9/pM=
=4rop
-END PGP SIGNATURE-




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Formageddon is upon us... Important news from wwPDB!

[Gerard DVD Kleywegt]

Dear colleagues,

I would like to draw your attention to a notification from the wwPDB partners 
about Deposition and Release of PDB Entries Containing Large Structures - 
see:


  http://www.wwpdb.org/news/news_2013.html#22-May-2013

There are major changes afoot in the way large structures are handled in the 
PDB, as well as in the deposition and annotation procedures and software used 
by the wwPDB sites. This is of immediate relevance for depositors and users of 
large structures, but also for software developers and anyone who routinely 
processes the entire PDB archive or its weekly releases (bioinformatics 
resources, etc.). From 2014, it will affect essentially everyone who deposits, 
uses or processes PDB entries.


If you have any questions about the new deposition system or the procedures 
for handling large structures or any of the other changes, please contact: 
i...@wwpdb.org


Please pass on this information to anyone likely to be affected by the 
upcoming changes. Thanks!



On behalf of the Worldwide Protein Data Bank,

--Gerard Kleywegt

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Vacancy at PDBe for an enthusiastic junior annotator

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit a 
junior structural biologist to join the PDBe curation team at the EBI near 
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD 
in some area of structural biology or structural chemistry as well as a broad 
knowledge in molecular biology or biochemistry. An in-depth knowledge of 
protein structure (including structure determination, analysis and validation) 
is essential. A few years of post-doctoral research experience in structural 
biology, as well as hands-on experience in the determination of protein 
structure is desirable. Given the extensive interactions with colleagues in 
the PDBe team as well as with international collaborators, depositors and 
users, excellent written and oral communication skills, fluency in English, 
ability to work in a team and attention to detail are required.


More details and a link to the electronic application procedure can be found 
here:


http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=bkMjPUrEcTFkHhTczjobid=49714,9371342323

Feel free to pass this on to suitable candidates!

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] dihedral backbone generator

[Gerard DVD Kleywegt]

If you have an old copy of MOLEMAN (not MOLEMAN2!) lying around, this can be 
done very easily (ever since it was programmed on Valentine's Day 1993, in 
fact - I even remember who my Valentine was :-) - see:


  http://xray.bmc.uu.se/usf/moleman_man.html#S13

- READ your original model (PDB file)
- EXPOrt as an internal coordinates file
- then edit the file to modify the torsion angles
- IMPOrt the edited file back into MOLEMAN
- WRITe as a PDB file again

Your molecule will now have the first atom at (0,0,0) and the x-axis along the 
first bond etc., so use LSQMAN to superimpose it back onto the starting model 
if you like.


You can download source and executables for MOLEMAN, LSQMAN etc. here: 
http://xray.bmc.uu.se/markh/usf/


Example: read and export 3CBS - the first few lines of the internal 
coordinates file will look like this:


BAD   1  N   PRO A   1   0.000   0.000   0.000  1.00 31.62 0 0 
0
BAD   2  CA  PRO A   1   1.481   0.000   0.000  1.00 31.16 1 0 
0
BAD   3  C   PRO A   1   1.520 106.499   0.000  1.00 29.86 2 1 
0
BAD   4  O   PRO A   1   1.233 121.844-171.561  1.00 30.08 3 2 
1
BAD   5  CB  PRO A   1   2.511  34.402-114.723  1.00 31.63 3 2 
1
BAD   6  CG  PRO A   1   1.540  94.603 100.767  1.00 32.44 5 3 
2
BAD   7  CD  PRO A   1   1.535 100.667 -80.739  1.00 31.82 6 5 
3
BAD   8  N   ASN A   2   1.325 114.622   8.082  1.00 27.88 3 2 
1


the torsion of atom 8 is the psi torsion of residue 1 (8 degrees)

BAD   9  CA  ASN A   2   1.452 122.416-179.619  1.00 25.61 8 3 
2


this torsion is omega of residue 1 (-180)

BAD  10  C   ASN A   2   1.528 107.300-118.190  1.00 23.37 9 8 
3


this torsion is phi of residue 2 (-118)

BAD  11  O   ASN A   2   1.227 119.971 -58.453  1.00 21.7110 9 
8
BAD  12  CB  ASN A   2   1.529 109.276 122.858  1.00 27.00 9 8 
3
BAD  13  CG  ASN A   2   1.510 112.642-171.476  1.00 28.5212 9 
8
BAD  14  OD1 ASN A   2   1.228 120.881 -44.498  1.00 27.401312 
9
BAD  15  ND2 ASN A   2   1.329 116.425 136.488  1.00 30.351312 
9
BAD  16  N   PHE A   3   1.330 117.436 121.273  1.00 22.0910 9 
8


this torsion is psi of residue nr 2 (121)

BAD  17  CA  PHE A   3   1.466 120.994 179.948  1.00 21.611610 
9


this is omega of residue nr 2 (180)

etc.

--Gerard




On Mon, 12 Nov 2012, Ed Pozharski wrote:



Does anyone know of a tool that would generate a protein molecule
backbone from a set of phi/psi angles?

I actually had written my own code to do this eons ago, but those were
days of Matlab.  My actual question is if in a particular protein the
conformational change observed upon substrate binding can be accounted
for by half a dozen residues changing their backbone conformation.  I
only expect to do it once, and thus trying to save time and not
translate my old code (looks more like a cipher now).

Cheers,

Ed.

--
After much deep and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
   Julian, King of Lemurs




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] fragment searching

[Gerard DVD Kleywegt]

This sounds like a job for SPASM. We used it to find instances of left-handed 
helices in the PDB. See:


- SPASM: http://www.ncbi.nlm.nih.gov/pubmed/9917419

- Left-handed helices: http://www.ncbi.nlm.nih.gov/pubmed/15740737

The database for SPASM hasn't been updated for a few years, but it may give 
you some leads.


It's probably easiest to use Mark Harris' SPASM server in Uppsala:

http://eds.bmc.uu.se/eds/spana.php?spasm=true

Brief help: http://eds.bmc.uu.se/eds/spasm_help.html

SPASM manual: http://xray.bmc.uu.se/usf/spasm_man.html

Good luck!

--Gerard




On Thu, 1 Nov 2012, eugene.krissi...@stfc.ac.uk wrote:


CCP4's gesamt should help you here. It can search a collection of PDB/mmCIF 
files for a structural match, any mainchain fragment with C-alphas would do.

For searching through an archive, you need to use it off-line, from a terminal 
window. Run $CCP4/bin/gesamt without parameters, it will print usage 
instructions, you need 2nd or 3rd command line template depending on how you'd 
like to specify your query fragment.

Beware that SSM/Superpose is not the best choice here and may not work at all. 
Gesamt should be reasonably fast on short fragments, I'd expect that execution 
time will be that required for opening/reading all files in the PDB :)

Hope this helps,

Eugene


On 31 Oct 2012, at 15:31, rui wrote:

Does anyone know a good way to search for a fragment matches(~16 residue long 
helix or loop) from pdb?I have a fragment of pdb and want to pull out all the 
similar structures from the pdb, any easy way to do that? Thanks a lot.



On Tue, Oct 30, 2012 at 9:34 AM, David Briggs 
drdavidcbri...@gmail.commailto:drdavidcbri...@gmail.com wrote:
Hello Adrian,

I use Research Gate and there are a few occasions where I have found
it useful, particularly the questions feature.

HTH,

Dave

David C. Briggs PhD
http://about.me/david_briggs


On 30 October 2012 16:13, Adrian Goldman 
adrian.gold...@helsinki.fimailto:adrian.gold...@helsinki.fi wrote:

Hi,

At the risk of starting another series of rants, and somewhat off-topic, is
anyone actively using ResearchGate?  It is bombarding me with email
messages, but I am uncertain as to whether people are really using it or
whether it is just scientific spam.

Adrian Goldman


Adrian Goldman

Institute of Biotechnology, University of Helsinki, Finland









--
Scanned by iCritical.




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Vacancy at PDBe for an enthusiastic junior annotator

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an 
expert structural biologist to join the PDBe curation team at the EBI near 
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD 
in some area of structural biology or structural chemistry as well as a broad 
knowledge in molecular biology or biochemistry. An in-depth knowledge of 
protein structure (including structure determination, analysis and validation) 
is essential. A few years of post-doctoral research experience in structural 
biology, as well as hands-on experience in the determination of protein 
structure is highly desirable.


The ideal candidate will be familiar with Linux/Unix operating systems and 
molecular graphics software. Basic programming skills, e.g. with Perl, Python 
or Java, would be an advantage. Given the extensive interactions with 
colleagues in the PDBe team as well as with international collaborators, 
depositors and users, excellent written and oral communication skills, fluency 
in English, ability to work in a team and attention to detail are required.


More details and a link to the electronic application procedure can be found 
here:


http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=bkMjPUrEcTFkHhTczjobid=49714,9371342323

Feel free to pass this on to suitable candidates!

--Gerard

PS: Some hints for prospective applicants: it doesn't hurt to add a nice cover 
letter in which you explain why you would love to be a PDB annotator and why 
PDBe strikes you as a brilliant place to work. Also, if you should get invited 
for an interview and we ask you what the main colour of our website is, please 
don't answer blue...


---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] EDS server woes resolved

[Gerard DVD Kleywegt]

Dear all,

The EDS server was unfortunately down for a number of days. However, as of 
yesterday it is up and running again. Apologies for the inconvenience.


  http://eds.bmc.uu.se/

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] A little bit of sunshine from the Protein Data Bank in Europe (pdbe.org)

[Gerard DVD Kleywegt]

Hi all,

Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases 
new, improved and updated versions of its tools and resources. Below is a 
brief description of new features and services that have been released this 
summer (or what passes as summer in the UK). As always, the URL 
http://pdbe.org will take you to the PDBe website. Many of the features can be 
accessed through the PDBe Tools menu on the left side of the front page, or 
you can use the shortcut URLs mentioned below.


  --

The executive summary for the busy PI:

#1. Slice viewer for tomograms in EMDB

#2. Improved analysis and validation of NMR entries

#3. Enhanced FASTA browser for the PDB archive (http://pdbe.org/fasta)

#4. New features on some PDB entry pages

#5. Weekly release history for PDB entries, EMDB entries and PDB compounds 
(http://pdbe.org/latest)


#6. Advanced SQL queries for power-users (http://pdbe.org/sqldemo)

And many other smaller (or under-the-hood) improvements.

  --

The nitty-gritty details for the eager structure user:

#1. Slice viewer for tomograms in EMDB
--
The major piece of new functionality is a slice viewer for tomograms in EMDB. 
The viewer, developed in collaboration with the Open Microscopy Environment 
(OME), works within the context of most common web browsers and does not 
require any installation of software locally. To access the slice viewer for a 
particular EMDB entry, e.g. emd-1053, navigate to the entry page, in this case 
http://pdbe.org/emd-1053, select the Visualization page (from the menu on 
the left) and click on Slice viewer (PDBe). Hover over the question mark 
icon for a brief explanation of options and controls.


#2. Improved analysis and validation of NMR entries
---
Vivaldi (http://pdbe.org/vivaldi), our interactive server for display, 
analysis and validation of NMR entries (including experimental data and 
violations, where available), has been improved and enhanced, thanks in part 
to user feedback. New types of data and analysis include angular restraints 
and their violations and circular variance plots for main-chain torsions. You
can view your favourite NMR entry by using a shortcut URL such as 
http://pdbe.org/vivaldi/2k4v or from the main Vivaldi page. If you're not an 
expert in NMR and feel intimidated by ensembles and distance restraints, take 
Vivaldi for a spin!
  PDBe also generates OLDERADO pages for NMR ensembles 
(http://pdbe.org/olderado) - these show useful information about rigid domains 
and clusters of models in the ensemble. Where non-experts often take MODEL 1 
from an ensemble for display, molecular replacement, docking, homology 
modelling etc., OLDERADO will tell you which model is most representative. 
These pages are accessible from the OLDERADO start page, or directly, e.g. 
http://www.ebi.ac.uk/pdbe-apps/nmr/olderado/searchEntry?pdbCode=2k4v. Note how 
the colouring of the rigid domains and cluster representatives is repeated in 
the tables to make identification easy. There are also buttons to launch 
Vivaldi showing the same information in 3D.
  The Experiment pages for NMR entries (e.g., 
http://pdbe.org/2k4v/experimental) link to both OLDERADO and Vivaldi (among 
many other things).


#3. Enhanced FASTA browser for the PDB archive
--
PDBe offers a number of (PDBeXplore) browsers that allow analysis of the 
archive based on a variety of biological and chemical classification systems 
(EC code, Pfam family, GO classifications, taxonomy, etc. - see 
http://pdbe.org/pdbexplore). One of these browsers allows you to study all PDB 
entries that contain proteins that show sequence similarity to a protein of 
your interest (as identified by a FASTA search; http://pdbe.org/fasta). This 
browser has now been improved and can take UniProt and PDB identifiers as 
input to retrieve sequences itself - after providing one of these identifiers, 
the Fetch sequence button will retrieve the sequence (if it can find it) and 
put it in the sequence box. After that, change the E-value and/or %-identity 
cut-off and hit Submit to retrieve any and all hits in the PDB. In addition, 
there is a new tab in the browser panel (Unreleased entries) that shows any 
hits to proteins found in PDB entries that have not yet been released but 
whose sequences are public.


#4. New features on some PDB entry pages

PDB entry pages can be accessed quickly with URLs like http://pdbe.org/1cbs. 
For some time now, we have provided links to corresponding PDB_REDO pages 
(http://www.cmbi.ru.nl/pdb_redo/), but these have been somewhat hard to find. 
Now, when PDB_REDO has data about an X-ray entry, we provide an explicit link 
on the downloads page of that entry, e.g. http://pdbe.org/1cbs/downloads shows 
a link to 

[ccp4bb] Sunhats for plants

[Gerard DVD Kleywegt]

Hi all,

Plants suffer from DNA damage caused by ultraviolet light in the same way that 
humans do. Unlike us though, they cant put on a sunhat (or move to England) to 
avoid the suns rays. Read more about how plants sense UV-B light and turn on a 
suite of genes to protect their DNA against its deleterious effects in the 
latest installment of Quips (QUite Interesting Pdb Structures; pdbe.org/quips) 
at:


   http://pdbe.org/quips?story=Sunhats

The accompanying mini-tutorial shows you how PDBeFold can be used to compare 
and superimpose structures of proteins even if their sequences show circular 
permutation.


If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips article, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] pdb sequence search

[Gerard DVD Kleywegt]

Because I want all the structures of a particular protein itself, not it's 
homologues.  I just went through several cycles of reducing E-value down to


If you know the UniProt accession code of your protein, then UniPDB is your 
friend - pdbe.org/unipdb


If not, try pdbe.org/fasta where you can supply the sequence and the %-age SI 
cut-off


--Gerard

[ccp4bb] Software and servers in Uppsala

[Gerard DVD Kleywegt]

Hi all,

In the past couple of years, Mark Harris in Uppsala has developed a bunch of 
programs and servers that are useful for crystallographers, structural 
biologists and structural bioinformaticians. Some of his programs are listed 
here:


 http://xray.bmc.uu.se/markh/programs.html

My favourite is O on a stick for Macs. If you download a tarball from an EDS 
entry, you can unzip it and drop it on the O on a stick icon on your desktop 
and O will start up and execute a bunch of macros. Within seconds you have the 
PDB entry and the EDS maps on your screen, ready for scrutiny!


Mark's servers are listed here:

http://xray.bmc.uu.se/markh/servers.html

Several of these provide a user-friendly interface to some of my old programs:

- Australis allows you to do a quick and dirty superposition of two protein 
structures, and it will show the result in Jmol as well as allow you to 
download the superimposed coordinates, structure-based sequence alignment, 
etc. Australis is driven by LSQMAN.


- Borealis does essentially the same as Australis, but for nucleic acid 
structures instead of proteins (try out the default example, 1HR2 versus 
1U9S). Borealis is also driven by LSQMAN.


- Spasm is a server to run SPASM (unsurprisingly, perhaps) which allows you to 
detect small motifs (that you provide) in existing PDB entries. Use the 
default example to find out how it works.


- Spana runs a program that I've never even published, SPANA - it does the 
same as SPASM, but for nucleic acid motifs and structures. Use the default 
example to find out what it can do.


- CavitySearch can be used to find cavities and tunnels in proteins. It can 
use either VOIDOO or MAMA (implementing Delaney's method). You can download 
the results and view the cavity(ies) with the AstexViewer. Try 1CEL chain A, 
looking for the biggest cavity using Delaney's method - this shows how a 
tunnel in a structure can be visualised. See also: 
http://xray.bmc.uu.se/usf/vis_tunnel.html


- Morphtician allows you to do simple morphs between protein chains in the 
same or different structures. It uses LSQMAN under the hood. Interpolated 
coordinates can be downloaded and the morphing visualised in Jmol. See also: 
http://xray.bmc.uu.se/usf/mol_morph.html


- ValLiGURL has been around for a few years.


Note: since Mark is no longer employed at Uppsala University, these programs 
and servers come with no warranty or support.



--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Quite interesting Lord of the RING

[Gerard DVD Kleywegt]

Hi all,

E3 ubiquitin ligase is responsible for flagging proteins for degradation by 
transferring ubiquitin from a donor protein onto the molecule to be degraded. 
It is activated by phosphorylation of a tyrosine which promotes a huge 
conformational change, swinging its RING domain 180 degrees to put the 
enzyme's two substrates in proximity.


Read more about this enzyme and see the conformational changes happen before 
your very own eyes in this latest installment of Quips (QUite Interesting Pdb 
Structures; pdbe.org/quips) at:


   http://pdbe.org/quips?story=LordCBL

If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips article, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] sequence format conversion

[Gerard DVD Kleywegt]

A good tool should leave b as is: it is ASX (the standard ambiguity
code for ASP or ASN). j, o and u are a different matter :-)


http://www.uniprot.org/manual/non_std

Selenocyteine [sic!] and pyrrolysine are represented in the sequence using 
the one-letter codes U for selenocysteine and O for pyrrolysine


--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] wwPDB and CCDC

[Gerard DVD Kleywegt]

Hi Paul,

You saw the wwPDB/CCDC JPG in my PPT at GSK :-)

Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means, 
amongst a number of other things, that wwPDB will be allowed to use Mogul in 
its validation pipeline and that wwPDB will be allowed to incorporate and 
redistribute CSD coordinates of small molecules that occur in both PDB and 
CSD.


--Gerard (K)



On Fri, 13 Apr 2012, Paul Emsley wrote:


On 13/04/12 14:30, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Paul,

you are not referring to Gerard Bricogne's announcement for the
grade-server, are you?
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg25770.html


:) No.


If not - what type of agreement do you have in mind?



IIRC, I remember a picture of Gerard (K), Helen, Haruki and a smiling Colin 
Groom sitting along a table signing something. I was wondering if more 
details are available on the web.


Paul.




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] A creative and challenging job in science communication - join PDBe as its Outreach Coordinator!

[Gerard DVD Kleywegt]

Are you an aspiring science communicator who has a wonderful way with words? 
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is looking for an 
enthusiastic 'jack of all trades', to coordinate its outreach activities. We 
are looking for someone who will raise the profile of PDBe through media 
outreach and user training. This job provides an exciting opportunity for you 
to have a real impact on the scientific community by helping biologists make 
the most of structural information. The main responsibilities include:


* Developing and implementing an effective outreach strategy, which may 
involve new activities (e.g. short video tutorials);

* Organising and running training 'roadshows', workshops and courses;
* Producing tutorials and course materials;
* Coordinating our presence at professional conferences;
* Drafting scientific reports, blog entries, news items, posters, slide 
presentations and promotional materials;

* Maintaining and maximising the impact of our presence in social media;
* Operating the PDBe help desk;
* Soliciting, handling and analysing user feedback;
* Coordinating our activities with the EMBL-EBI Outreach and Training Team;
* In the interests of remaining grounded in the resource, annotate structure 
entries (~25% of the time, this only applies if you have a background in 
chemistry or biology).


For full details about this position, surf to:

http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=48567aid=15470

When you apply through the EMBL website, you have to submit examples of three 
different kinds of communications materials that you have personally produced 
(they need not have been published). This could include a scientific paper, 
popular article, blog entry, poster, short video, brochure, press release, 
conference booth or anything along those lines. Please provide the materials 
either as attachments or as URLs. We expect your cover letter to demonstrate 
your enthusiasm for this position as well as your excellent writing skills. If 
you are shortlisted for an interview, you will be asked to provide additional 
materials.


Please note that knowledge of (structural) biology is desirable but not 
necessary. However, superb communication skills and a keen eye for layout and 
design are required.



--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] CCP-EM positions now available

[Gerard DVD Kleywegt]

[Cross-posted from the 3DEM mailing list.]

--Gerard

-- Forwarded message --
Date: Wed, 4 Apr 2012 16:34:39 +0100
From: Helen Saibil h.sai...@mail.cryst.bbk.ac.uk
To: 3DEM Mailing List 3...@ncmir.ucsd.edu
Subject: [3dem] CCP-EM positions now available

Dear Colleagues,

We have been awarded a Partnership grant by the MRC to provide computational 
support for UK scientists using electron cryo-microscopy for structural 
biology. One of the major aims is to create a Collaborative Computational 
Project, CCP-EM, by analogy with similar successful projects in macromolecular 
crystallography (CCP4) and biological nuclear magnetic resonance spectroscopy 
(CCPN). We seek two excellent and motivated computational scientists to 
support the Partnership grant and the CCP-EM project. These posts will have a 
wide variety of responsibilities, including writing community code, improving 
the useability of existing code, providing training, and supporting individual 
scientists. The first post will focus on technical aspects, building community 
tools and improving the programs available. The second post will focus more on 
the scientific requirements of the community. The posts are located at the 
Research Complex at Harwell, alongside the core group of CCP4, but the 
postholders will be expected to travel throughout the UK and interact with 
international groups to support the collaboration.


Applications must be made through the RCUK Shared Services recruitment portal 
https://ext.ssc.rcuk.ac.uk/ using the references IRC50385 and IRC50666. 
Informal enquiries may be made to Martyn Winn (martyn.w...@stfc.ac.uk).


Best wishes,

Martyn Winn, Richard Henderson, Alan Roseman, Peter Rosenthal, Helen Saibil 
and Ardan Patwardhan

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Gerard DVD Kleywegt]

Dear Manfred,

Outside Germany, such excursions are called humour. If you are interested, 
here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour


--Gerard

PS: It was on a Sunday so all levity was perpetrated in people's own time. 
Today we'll all be serious again and frown and tut-tut appropriately.




On Mon, 2 Apr 2012, Manfred S. Weiss wrote:


Dear all,

I find this discussion most amazing. Here, we are dealing with the most
serious issue
that happened to Macromolecular Crystallography since the Alabama case,
and the
whole discussion is centered around singular and plural and Greek and
Latin words
and what not.

In psychology such phenomenon is referred to as displacement activity.

If you are interested, here is the MacMillon definition of it:

http://www.macmillandictionary.com/dictionary/british/displacement-activity

Cheers,

Manfred


On 01.04.2012 19:35, Gerard Bricogne wrote:

On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote:

On 04/01/12 10:18, Gerard Bricogne wrote:

Dear Paul,

   May I join the mostly silent chorus of Greek/Latin-aware grumps 
who

wince when seeing data treated as singular when it is plural.

When it are plural?

  Good nit-picking :-) . In my mind the quotes around data would have
had the same effect as writing 'the word data', and referring to that 
word

by the 'it'. So there is only one word, while its grammatical number is
plural.


At any rate, I heard a Nobel laureate use it incorrectly just two days 
ago.

  We shouldn't learn to write by imitating Nobel laureates, then.


  With best wishes,

   Gerard.


--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin f?r Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren 
e.V.


Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph

Gesch?ftsf?hrerin: Prof. Dr. Anke Rita Kaysser-Pyzalla

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Gerard DVD Kleywegt]

Dear Andreas,

That page confirms the old adage: German humour is no laughing matter.

--Gerard


On Mon, 2 Apr 2012, Andreas F?rster wrote:


Dear Gerard,

inside Germany it's apparently called German Humour.  There's a Wikipedia 
entry for that as well.  Go figure:


http://en.wikipedia.org/wiki/German_humor


Andreas

(still living on Sunday time)


On 02/04/2012 4:03, Gerard DVD Kleywegt wrote:

Dear Manfred,

Outside Germany, such excursions are called humour. If you are
interested, here is the Wikipedia page for it:
http://en.wikipedia.org/wiki/Humour

--Gerard

PS: It was on a Sunday so all levity was perpetrated in people's own
time. Today we'll all be serious again and frown and tut-tut appropriately.






Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Gerard DVD Kleywegt]

Is it to late to refer to data as if there were more than one of them?


Is it too late to explain the difference between to and too?

--A much mellowed CD

Re: [ccp4bb] very informative - Trends in Data Fabrication

[Gerard DVD Kleywegt]

http://trololololololololololo.com/


Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis.



David C. Briggs PhD
Father, Structural Biologist and Sceptic

University of Manchester E-mail:
david.c.bri...@manchester.ac.uk

Webs : http://flavors.me/xtaldave
Twitter: @xtaldave
Skype: DocDCB




On 1 April 2012 21:27, Kendall Nettles knett...@scripps.edu wrote:

What is the single Latin word for troll?

Kendall

On Apr 1, 2012, at 3:06 PM, Kevin Jin kevin...@gmail.com wrote:

?I hope and believe that this is not the case.  Even basically-trained
crystallographers should be able to calculate and    interpret difference
maps of the kind described by Bernhard.  And with the EDS and PDB_REDO
server, one does not even need to know how to make generate a difference
map...?

You are right!

Actually, I am not an experienced protein crystallographer. I have learnt a
lot from CCP4BB. I may have paid too much attention to bonding angle and
bond length, like in small molecule. This may be an example to share with
you.

When I worked on those nitroreductase complexed with FMN in 2009 (?), I
always observed that the flavin ring presented a strange geometry after
refinement. Indeed, I had used the definition of FMN from CCP4 library all
the time.

In some cases, the methyl group at position of either 7a or 8a was bent off
the aromatic ring, if the whole the rest of flavin was restrained in a flat
plane.  According to my limited knowledge from organic chemistry, carbon of
7 and 8 on the flavin ring is sp2 hybridized in a coplanar manner. How could
those methyl groups be bent as sp3 hybridization? Any chemistry behind?

With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron
density map was a bent along the N5-N10 axis. The bend angle was around ~16
degree.   Again, I questioned myself why it was bent? Should this be
correct?

According to my limited knowledge in chemistry, N10 should be sp3
configuration even if FMN is in its oxidization form, in which the flavin
ring should be bent. A quick ?google? immediately gave me a link to a very
nice paper published by David W. Rodgers in 2002.

http://www.jbc.org/content/277/13/11513.full.pdf+html

According to this paper, Yes!  ?In the oxidized enzyme, the flavin ring
system adopts a strongly bent (16?) conformation, and the bend increases
(25?) in the reduced form of the enzyme,??

When I reported this in the group meeting, I was laughed and told that this
is just a model bias. It was over interpreted.  Nobody has such sharp vision
on electron density map.  If this was correct, why nobody could find this
and report to CCP4 within last 7 years?

Eventually, a senior team member emailed to CCP4 about this issue. Since
then, the definition of FMN was updated, according to my suggestion.

I was asked ?how did you find it. ?why you believed you are so right??
 I really don?t how to answer.

Je pense donc je suis

Kevin


On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk
wrote:

On 31/03/12 23:08, Kevin Jin wrote:


I really wish PDB could have some people to review those important
structures, like paper reviewer.


So do the wwPDB, I would imagine.

But they can't just magic funding and positions into existence...

If the coordinate is downloaded for modeling and docking, people may not
check the density and model by themself. However this is not the worst
case,
since the original data was fabricated.


1. All of data was correct and real,


Hmmm...

 It will be very difficult for people to check the density and coordinated
if he/she is not a well-trained crystallographer.


I hope and believe that this is not the case.  Even basically-trained
crystallographers should be able to calculate and interpret difference
maps
of the kind described by Bernhard.  And with the EDS and PDB_REDO server,
one does not even need to know how to make generate a difference map...

Paul.






--
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/








Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Let's GO, with Dora the PDBeXplorer!

[Gerard DVD Kleywegt]

Hi all,

As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) has 
launched a number of PDB archive browsers in the past two years. These allow 
users to explore and analyse what is in the PDB based on concepts and 
classifications they are familiar with, such as the EC system, chemical 
compounds, taxonomy or amino-acid sequences (see http://pdbe.org/browse for 
more information).


The most recent addition is a browser that is based on the GO system 
(http://pdbe.org/go). GO stands for Gene Ontology, a major bioinformatics 
initiative with the aim of standardizing the representation of gene and gene 
product attributes across species and databases (http://geneontology.org/). 
The SIFTS project (http://pdbe.org/sifts) maps GO annotations from UniProt to 
all proteins and protein fragments that occur in the PDB. These GO terms 
describe:


* molecular function, the elemental activities of a gene product at the 
molecular level (e.g., catalysis of free radical formation)


* cellular component, the localisation of a gene product in a cell or its 
extracellular environment (e.g., outer membrane-bounded periplasmic space)


* biological process, operations or sets of molecular events with a defined 
beginning and end, pertinent to the functioning of integrated living units: 
cells, tissues, organs, and organisms (e.g., neuron apoptosis)


To start exploring, surf to http://pdbe.org/go

In the left panel you can either:

- click on one of the three examples and then hit the Submit button

- start exploring the GO classification by expanding the molecular_function, 
cellular_component or biological_process term. Clicking on any of these will 
expand the classification to show the underlying terms, and these can be 
clicked on for further drilling. If a term is shown on a grey background, it 
means that there are no proteins in the PDB that have been annotated with that 
term.


- start typing a term in the input box (above the Submit button). Once you 
have typed a few characters, an auto-complete function will show you a list of 
all the matching GO terms. Select any one of these and hit the Submit button.


Once you have selected a GO term that is of interest to you, the browser will 
load all PDB entries that contain a protein (fragment) that has been annotated 
with that term in the central panel of the browser. (The right panel contains 
more information about the GO term and how it fits in the GO classification - 
click on the image to get a bigger version.) In the central panel, the PDB 
entries tab shows a simple list of the PDB entries. However, there are other 
tabs that provide different views on this set of entries, such as:


- which ligands are found in these entries?

- what folds are represented (CATH)?

- what quaternary structures occur (PISA)?

- what sequence families are present (Pfam)?

- from which taxa have structures been determined?

- who has determined these structures?

For instance, if your are interested in purine nucleotide biosynthetic 
process, you may find that:


- there are 310 relevant structures in the PDB

- the most common ligands are Mg, SO4, PO4, GDP, K, CL, AMP and ADP

- the structures are mostly of the alpha/beta type (82%), with 45% of all 
domains adopting a 3-layer ABA sandwich fold


- 70% of the entries contain homo-oligomeric structures (and 50% of those are 
homodimers, but there are also 5 homohexameric structures)


- the set of entries covers 43 different Pfam families

- there are 11 proteins in 5 distinct entries from Yersinia pestis

- R.B. Honzatko is the most prolific depositor of PDB entries in this category 
(useful to know if you are looking for collaborators or referees)


As you can see, the GO browser can be used to explore many aspects of what is 
known in terms of 3D structures for proteins with a given function, role or 
localisation.


If you have any questions, comments or suggestions, please use the button 
marked FEEDBACK in the top right corner of any PDBe webpage.


---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Server or software for B factor analysis

[Gerard DVD Kleywegt]

MOLEMAN2 is your friend.

Stats: http://xray.bmc.uu.se/usf/moleman2_man.html#S50

Plots: http://xray.bmc.uu.se/usf/moleman2_man.html#S57

--dvd


Will you please tell me a server of software which can draw a curve for the 
B factor of the atoms in a protein PDB file from the first residue to the 
residue?Or a server or software by which we can easily order the B factors 
of the atoms in the PDB file according to the B factor in decrease or in 
increase? Or to get the residues with the highest B factor and the lowest B 
factor?


**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] EMBO Practical Course: Computational structural biology - from data to structure to function

[Gerard DVD Kleywegt]

Hi all,

In April we will once again organise the EMBO practical course on 
Computational structural biology - from data to structure to function. The 
application deadline is only a week away - 24 February.


For more information about the course and how to apply, surf to:

http://www.ebi.ac.uk/training/onsite/120416_structures.html

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Winter wotsits from the Protein Data Bank in Europe (pdbe.org)

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new, improved 
and updated versions of its tools and resources twice a year. Now it's time 
for the winter update. Below is a brief description of new features and 
services. As always, the URL http://pdbe.org will take you to the PDBe 
website. Many of the features can be accessed through the PDBe Tools menu on 
the left side of the front page, or you can use the shortcut URLs mentioned 
below.


  --

The executive summary for the busy PI:

#1 - A browser of the PDB archive based on GO, the Gene Ontology 
(http://pdbe.org/go)


#2 - A service to investigate the status of any PDB entry code ever released 
(http://pdbe.org/status)


#3 - New and improved modules to carry out advanced analyses of the PDB 
archive with a very simple interface (http://pdbe.org/express)


#4 - A new advanced search tool for EMDB (http://pdbe.org/emsearch)

#5 - New visual analysis pages and volume/model viewers for EMDB entries 
(http://pdbe.org/emdb)


#6 - Improved atlas pages for PDB entries

#7 - BioBar made compatible with the latest version of Firefox 
(http://pdbe.org/biobar)


#8 - Many other smaller (or under-the-hood) improvements

  --

The nitty-gritty details for the eager structure user:

#1 - A new PDB archive browser has been added (see http://pdbe.org/browse for 
an overview of all available browser modules). The new module allows analysis 
of the archive by the GO terms (http://geneontology.org/) assigned to the 
protein(s) in each entry. GO, or Gene Ontology, terms are assigned to UniProt 
(http://uniprot.org/) entries and this annotation is mapped onto relevant 
proteins or protein fragments in PDB entries as part of the SIFTS project 
(http://pdbe.org/sifts). This means that for almost every protein in the PDB, 
there is annotation about its molecular function, cellular component and 
biological process. For example, if you want to find out what structures are 
in the PDB related to programmed cell death, from which species, representing 
which protein families, etc., the GO browser will give you the answer in 
seconds. You can also traverse the GO graph interactively and select terms 
above or below programmed cell death, e.g. autophagic cell death. You can 
access the new PDB browser module at http://pdbe.org/go


#2 - PDBe have developed a new service to provide information about the status 
of any or all entries (PDB codes) that are, have been, or will be part of the 
archive. You can search in various ways, e.g. by PDB code (if you want to know 
the status of an entry you deposited), by author or keyword (to find out what 
the competition is doing), by method, by period and by status. So, if you want 
to find out how many NMR entries were made obsolete in 2011, or how many 
ribosome structures are on hold until publication, this is the tool for you. 
Try it out at http://pdbe.org/status


#3 - PDBeMotif (http://pdbe.org/motif) is a very powerful tool for analysing 
PDB entries in terms of structure, sequence and chemistry. However, it is also 
quite complex to use. For this reason, we are developing small modules of 
PDBeMotif (and other) functionality that are presented in such a way that they 
are very easy to use by non-experts and provide answers to common but complex 
questions. We have developed a new module to answer the question Which 
enzymes interact with this ligand?, and we have improved one of the earlier 
modules. Try it out at http://pdbe.org/express


#4 - PDBe have developed a new and flexible search service for the EMDB 
archive. Give it a go at http://pdbe.org/emsearch


#5 - EMDataBank serves summary pages about EMDB entries from RCSB and PDBe. 
Both sites now serve pages with an OpenAstexViewer-based volume and model 
viewer - for example: 
http://www.ebi.ac.uk/emdb-srv/atlas/5119_openastexviewer.html - so you can 
easily see how the fitted model from the PDB fits inside the volume from EMDB. 
PDBe also serves visual map analysis pages - e.g. 
http://www.ebi.ac.uk/emdb-srv/atlas/1564_mapoverview.html - with graphs and 
static images that enable you to assess if the density was masked, if the 
contour level is appropriate, how each of the PDB models fits inside the 
density, etc.


#6 - The atlas pages for many PDB entries have been improved:
  * for entries with ligands for which there is bioactivity data available in 
ChEMBL (https://www.ebi.ac.uk/chembl/), we include a widget on the ligand page 
- try http://pdbe.org/1cbs/ligands - you can click on the graphs and further 
explore the available data in ChEMBL
  * annotation (e.g., InterPro and GO classifications) for chimeric proteins 
has been properly separated for the constituent proteins, e.g. for 
http://pdbe.org/3rze
  * for entries containing fragments of proteins, the GO and other annotations 
now pertain only to the fragment that was included in the sample, not the 
entire UniProt 

[ccp4bb] Quipping about clamping...

[Gerard DVD Kleywegt]

Hi all,

As many of you know by now, the Protein Data Bank in Europe (PDBe; 
http://pdbe.org) regularly produces Quips, short interactive stories about 
QUite Interesting Pdb Structures (http://pdbe.org/quips). Quips articles 
address biologically interesting aspects of one or more PDB entries from a 
structural perspective, using animated and interactive graphics views and 
usually a mini-tutorial or suggestions for further exploration using PDBe 
tools, services and resources.


Today a new interactive Quips story was released, exploring the structure of 
bacterial polymerase III and in particular the beta-clamp and its interaction 
with DNA. The accompanying mini-tutorial shows how you can explore a structure 
further and produce your own customised views using the OpenAstexViewer (which 
is used in Quips for 3D animations and graphics).


To access this Quips episode, point your browser at: 
http://pdbe.org/quips?story=BetaClamp


To go straight to the OpenAstexViewer tutorial, surf to: 
http://pdbe.org/quips?story=BetaClampauxpage=AVtut


There is also an RSS feed that informs you whenever there is a new Quips 
article available. For links to this and several other feeds, see 
http://pdbe.org/rss


If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips article, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] reliable/unreliable maps?

[Gerard DVD Kleywegt]

There can be many different reasons why EDS calculates an R-value that is 
different from the one reported by the authors - some of these are listed 
here: http://eds.bmc.uu.se/eds/eds_help.html#PROBLEMS


Back in the dark ages (actually, the late 90s) we arbitrarily decided to use 
a tolerance of 5 percentage points. If the difference is greater, we assume 
that -as some people have subtly put it- we are a bunch of incompetent morons 
who can't even calculate a map, and we choose not to make the maps and 
statistics derived in the process of calculating them available. So, if 
anything, the phrase unreliable map means just that - we cannot be sure that 
we have done a good job at calculating the map, and would rather be safe than 
sorry.


Once upon a time, we asked crystallographers to help us trace the causes of 
any discrepancies for their entries so that we could improve EDS and the 
public archive. However, no good deed goes unpunished (ask Colin), and this 
request resulted in so much abuse from several prominent crystallographers 
(incl. a Nobelist) that we abandoned that effort. (I don't think any of them 
had actually tried to download the coordinates and structure factors from the 
PDB and calculate maps from those themselves... one of them subsequently tried 
and found himself unable to reproduce his own R-value...)


Nowadays, EDS in Uppsala is unfunded and unstaffed. It is an automatic script 
that runs every weekend. Obviously, that means that we cannot offer support, 
let alone do new development work. In the future, EDS will rise from its ashes 
at PDBe - at that stage, we can reconsider many choices we made for the 
Uppsala version and will also have resources to maintain and support it 
properly.


--Gerard




Dear all,

A minor point but worth mentioning, I think...

The EDS server does not produce a density map for PDB entries for which it 
cannot calculate R-factors within 5 percentage points of the published 
values. I understand that the server was set up in the dark ages of 
crystallographic refinement, when people perhaps took some liberties with 
their refinement protocols. Hopefully, the educational point now has been 
made so wouldn't it be better to calculate the map together with a warning 
of the discrepancy in R-factor values?


Coot does display a map for such a PDB entry, but with a pop-up window 
warning the user that This is not a reliable map. Without explanation, 
this statement is at least as unreliable as the map that it refers to and 
bound to confuse and alarm the user who - in the large majority of cases - 
finds himself/herself staring at a perfectly decent (reliable?) map.


Luca

Luca Pellegrini
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge CB2 1GA - UK

Email: lp...@cam.ac.uk
Tel: 0044-1223-760469
Fax: 0044-1223-766002
Sanger building, room 3.59




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] EBI and PDBe services temporarily unavailable

[Gerard DVD Kleywegt]

Due to an as yet unspecified explosion in a network duct in London, the EBI 
in Hinxton (where all PDBe services, including deposition, are hosted) is 
currently cut-off from its London data centres (through which all EBI web and 
ftp traffic is routed). At present, it looks like normal PDBe service will not 
be resumed for at least 12 hours. We apologise for the inconvenience.


NOTES FOR DEPOSITORS:

If you were in the middle of a deposition with AutoDep or EmDep, all data you 
entered and uploaded up until the last time you pressed Save (and the page 
was refreshed in your browser) will have been saved on our disks. So there is 
no need to panic - simply continue the deposition session once we are back 
on-line.


If you have any concerns or questions, please contact our help desk and we 
will try and help you as best we can:


For questions about PDB structure deposition, processing, and updates, please 
contact pdb...@ebi.ac.uk or call +44 (0)1223 494 550.


For questions about EMDB map deposition, processing, and updates, please 
contact em...@ebi.ac.uk or call +44 (0)1223 494 550.


(Note: phone number only until 5 pm GMT today, Friday.)

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Seasonal Quips about Christmas Disease

[Gerard DVD Kleywegt]

Hi all,

If you should suffer from Christmas Disease, and you were to cut yourself 
while carving the turkey, you could be in trouble! Find out why in the last 
episode for 2011 of Quips, PDBe's collection of interactive stories about 
QUite Interesting Pdb Structures.


To access this Quips episode, point your browser at: 
http://pdbe.org/quips?story=XmasFactor


The accompanying mini-tutorial shows you how to carry out a fragment search 
with PDBeChem so as to identify all small molecules in the PDB archive that 
contain a benzothiophene moiety.


---

On behalf of all PDBe staff: best wishes for the coming holiday season and a 
well-structured 2012! (Unless you're working on natively unfolded proteins, in 
which case we wish you an unstructured or partially structured 2012, of 
course.)


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Heads-up: Reduced PDBe services between 24 December and 2 January

[Gerard DVD Kleywegt]

Hi all,

This is to inform PDB/EMDB depositors (note: at PDBe only) and users of PDBe 
services (http://pdbe.org/) that we will be operating with a reduced level of 
service in the holiday season:


- this week, we will do our best to process entries that are deposited before 
Friday, but cannot guarantee that we will succeed in all cases. The sooner you 
deposit, the more likely that we will be able to process your entry or entries 
by Friday.


- from 24 December to 2 January (inclusive), the EBI will be closed. You may 
still deposit structures and data into the PDB and EMDB with us, but there 
will be no annotation and processing taking place. We will monitor our web 
services in this period and will endeavour to fix any serious problems. Please 
note that e-mail sent to PDBe in this period is unlikely to receive a reply 
until the beginning of January.


- from 3-6 January, we will resume normal service and catch up with the 
annotation and e-mail backlogs.


We apologise for any inconvenience.

On behalf of all PDBe staff: best wishes for the coming holiday season and a 
well-structured 2012!


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] (Off-topic) X-mas gift idea for cool scientists?

[Gerard DVD Kleywegt]

Hi all,

Someone pointed me to this: 
http://cdn3.spiegel.de/images/image-287176-galleryV9-qokb.jpg


Apparently, it is a page from this book: 
http://www.amazon.co.uk/Science-Ink-Tattoos-Obsessed/dp/1402783604


Personally, if I had to get a tramp stamp, it would obviously be of 1cbs 
(http://pdbe.org/1cbs)


--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] Superpositions: Deviation by Residue

[Gerard DVD Kleywegt]

Dear Crystallographers,

is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues between two superposed structures?


You mean to produce something like this? 
http://xray.bmc.uu.se/usf/pics/distplot_1chr.gif


That can be done with LSQMAN - http://xray.bmc.uu.se/usf/lsqman_man.html#S65

Of course, there are lots of other interesting metrics and plots to assess 
structural differences between two models - 
http://xray.bmc.uu.se/usf/lsqman_man.html#H17


One of my favourite ones is the CD plot, for comparing multiple models, which 
looks a bit like a gel: http://xray.bmc.uu.se/usf/pics/cdplot_1ldn.gif


For other options, see http://xray.bmc.uu.se/usf/lsqman_man.html#H19

--DVD

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Quips about the receptor-binding needle of bacteriophage T4

[Gerard DVD Kleywegt]

Hi all,

As you may know, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly 
produces Quips, short stories about QUite Interesting Pdb Structures 
(pdbe.org/quips). Quips address biologically interesting aspects of one or 
more PDB entries, coupled with animated and interactive graphics views and 
usually a mini-tutorial or suggestions for further exploration using PDBe 
services and resources.


Today a new episode of Quips was released, about the structure of the 
receptor-binding region of gp37 from bacteriophage T4 and its probable 
interaction with one of the receptors on the bacterial host's outer membrane. 
This episode of Quips was produced together with Mark van Raaij. The 
accompanying mini-tutorial shows how the iron coordination in gp37 can be 
analysed using the PDBeMotif (pdbe.org/motif) service.


To access this Quips episode, point your browser at: 
http://pdbe.org/quips?story=T4tail


There is also an RSS feed that informs you whenever there is a new Quips 
article available. For links to this and several other feeds, see 
http://pdbe.org/rss


If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips article, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Oops-a-daisy! [Re: In the mood for some LEGO DNA to celebrate PDB40?]

[Gerard DVD Kleywegt]

Hi again,

It turns out that, due to copyright restrictions, our German friends cannot 
view the Lego-DNA clip on YouTube (no, it was not in retalliation for your 
football team beating the Dutch last night!). Especially for them, the author 
of the clip has put an MP4 version on his website:


   http://proteinkemi.dk/upload/PDB40_LEGO_DNA_EN_wwPDB.mp4

Speaking of the author, in yesterday's announcement I got his surname wrong... 
His real name is Tommy Carstensen tommy.carsten...@gmail.com - and any kudos 
should go his way! I, on the other hand, should apply better validation 
methods to my own writing before I hit ^X send, obviously.


--Gerard



On Tue, 15 Nov 2011, Gerard DVD Kleywegt wrote:


Hi all,

I came across this YouTube clip the other day that is well worth 3 1/2 
minutes of your time:


   http://www.youtube.com/watch?v=Dhs1YO5nqXA

It was made by Tommy Christensen and shows how he built a model of DNA out of 
LEGO bricks (of PDB entry 2DAU, to be precise) to celebrate the 40th 
anniversary of the PDB. The clip also has educational value, explaining some 
of the basics of DNA structure and more. And all this to the tunes of my 
favourite big band (http://www.imdb.com/title/tt0047030/).


Check it out!

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] In the mood for some LEGO DNA to celebrate PDB40?

[Gerard DVD Kleywegt]

Hi all,

I came across this YouTube clip the other day that is well worth 3 1/2 minutes 
of your time:


http://www.youtube.com/watch?v=Dhs1YO5nqXA

It was made by Tommy Christensen and shows how he built a model of DNA out of 
LEGO bricks (of PDB entry 2DAU, to be precise) to celebrate the 40th 
anniversary of the PDB. The clip also has educational value, explaining some 
of the basics of DNA structure and more. And all this to the tunes of my 
favourite big band (http://www.imdb.com/title/tt0047030/).


Check it out!

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] To archive or not to archive, that's the question!

[Gerard DVD Kleywegt]

Hi all,

It appears that during my time here at Cold Spring Harbor, I have missed a 
small debate on CCP4BB (in which my name has been used in vain to boot).


I have not yet had time to read all the contributions, but would like to make 
a few points that hopefully contribute to the discussion and keep it with two 
feet on Earth (as opposed to La La Land where the people live who think that 
image archiving can be done on a shoestring budget... more about this in a 
bit).


Note: all of this is on personal title, i.e. not official wwPDB gospel. Oh, 
and sorry for the new subject line, but this way I can track the replies more 
easily.


It seems to me that there are a number of issues that need to be separated:

(1) the case for/against storing raw data
(2) implementation and resources
(3) funding
(4) location

I will say a few things about each of these issues in turn:

---

(1) Arguments in favour and against the concept of storing raw image data, as 
well as possible alternative solutions that could address some of the issues 
at lower cost or complexity.


I realise that my views carry a weight=1.0 just like everybody else's, and 
many of the arguments and counter-arguments have already been made, so I will 
not add to these at this stage.


---

(2) Implementation details and required resources.

If the community should decide that archiving raw data would be scientifically 
useful, then it has to decide how best to do it. This will determine the level 
of resources required to do it. Questions include:


- what should be archived? (See Jim H's list from (a) to (z) or so.) An 
initial plan would perhaps aim for the images associated with the data used in 
the final refinement of deposited structures.


- how much data are we talking about per dataset/structure/year?

- should it be stored close to the source (i.e., responsibility and costs for 
depositors or synchrotrons) or centrally (i.e., costs for some central 
resource)? If it is going to be stored centrally, the cost will be 
substantial. For example, at the EBI -the European Bioinformatics Institute- 
we have 15 PB of storage. We pay about 1500 GBP (~2300 USD) per TB of storage 
(not the kind you buy at Dixons or Radio Shack, obviously). For stored data, 
we have a data-duplication factor of ~8, i.e. every file is stored 8 times (at 
three data centres, plus back-ups, plus a data-duplication centre, plus 
unreleased versus public versions of the archive). (Note - this is only for 
the EBI/PDBe! RCSB and PDBj will have to acquire storage as well.) Moreover, 
disks have to be housed in a building (not free!), with cooling, security 
measures, security staff, maintenance staff, electricity (substantial cost!), 
rental of a 1-10 Gb/s connection, etc. All hardware has a life-cycle of three 
years (barring failures) and then needs to be replaced (at lower cost, but 
still not free).


- if the data is going to be stored centrally, how will it get there? Using 
ftp will probably not be feasible.


- if it is not stored centrally, how will long-term data availability be 
enforced? (Otherwise I could have my data on a public server until my paper 
comes out in print, and then remove it.)


- what level of annotation will be required? There is no point in having 
zillions of files lying around if you don't know which 
structure/crystal/sample they belong to, at what wavelength they were 
recorded, if they were used in refinement or not, etc.


- an issue that has not been raised yet, I think: who is going to validate 
that the images actually correspond to the structure factor amplitudes or 
intensities that were used in the refinement? This means that the data will 
have to be indexed, integrated, scaled, merged, etc. and finally compared to 
the deposited Fobs or Iobs. This will have to be done for *10,000 data sets a 
year*... And I can already imagine the arguments that will follow between 
depositors and re-processors about what software to use, what resolution 
cut-off, what outlier-rejection criteria, etc. How will conflicts and 
discrepancies be resolved? This could well end up taking a day of working time 
per data set, i.e. with 200 working days per year, one would need 50 *new* 
staff for this task alone. For comparison: worldwide, there is currently a 
*total* of ~25 annotators working for the wwPDB partners...


Not many of you know that (about 10 years ago) I spent probably an entire year 
of my life sorting out the mess that was the PDB structure factor files 
pre-EDS... We were apparently the first people to ever look at the tens of 
thousands of structure factor files and try to use all of them to calculate 
maps for the EDS server. (If there were others who attempted this before us, 
they had probably run away screaming.) This went well for many files, but 
there were many, many files that had problems. There were dozens of different 
kinds of issues: non-CIF files, CIF files with wrong headers, Is instead of 
Fs, 

Re: [ccp4bb] To archive or not to archive, that's the question!

[Gerard DVD Kleywegt]

Gerard
I said in INCREASING order of influence/power i.e. you are in first place.


Ooo! *Now* it makes sense! :-)

--Gerard



The joke comes from
 I used to think if there was reincarnation, I wanted to come back as the 
President or the Pope or a .400 baseball hitter. But now I want to come back 
as the bond market. You can intimidate everyone.

--James Carville, Clinton campaign strategist

Thanks for the comprehensive reply
Regards
  Colin

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard 
DVD Kleywegt
Sent: 28 October 2011 22:03
To: ccp4bb
Subject: [ccp4bb] To archive or not to archive, that's the question!

Hi all,

It appears that during my time here at Cold Spring Harbor, I have missed a
small debate on CCP4BB (in which my name has been used in vain to boot).

I have not yet had time to read all the contributions, but would like to make
a few points that hopefully contribute to the discussion and keep it with two
feet on Earth (as opposed to La La Land where the people live who think that
image archiving can be done on a shoestring budget... more about this in a
bit).

Note: all of this is on personal title, i.e. not official wwPDB gospel. Oh,
and sorry for the new subject line, but this way I can track the replies more
easily.

It seems to me that there are a number of issues that need to be separated:

(1) the case for/against storing raw data
(2) implementation and resources
(3) funding
(4) location

I will say a few things about each of these issues in turn:

---

(1) Arguments in favour and against the concept of storing raw image data, as
well as possible alternative solutions that could address some of the issues
at lower cost or complexity.

I realise that my views carry a weight=1.0 just like everybody else's, and
many of the arguments and counter-arguments have already been made, so I will
not add to these at this stage.

---

(2) Implementation details and required resources.

If the community should decide that archiving raw data would be scientifically
useful, then it has to decide how best to do it. This will determine the level
of resources required to do it. Questions include:

- what should be archived? (See Jim H's list from (a) to (z) or so.) An
initial plan would perhaps aim for the images associated with the data used in
the final refinement of deposited structures.

- how much data are we talking about per dataset/structure/year?

- should it be stored close to the source (i.e., responsibility and costs for
depositors or synchrotrons) or centrally (i.e., costs for some central
resource)? If it is going to be stored centrally, the cost will be
substantial. For example, at the EBI -the European Bioinformatics Institute-
we have 15 PB of storage. We pay about 1500 GBP (~2300 USD) per TB of storage
(not the kind you buy at Dixons or Radio Shack, obviously). For stored data,
we have a data-duplication factor of ~8, i.e. every file is stored 8 times (at
three data centres, plus back-ups, plus a data-duplication centre, plus
unreleased versus public versions of the archive). (Note - this is only for
the EBI/PDBe! RCSB and PDBj will have to acquire storage as well.) Moreover,
disks have to be housed in a building (not free!), with cooling, security
measures, security staff, maintenance staff, electricity (substantial cost!),
rental of a 1-10 Gb/s connection, etc. All hardware has a life-cycle of three
years (barring failures) and then needs to be replaced (at lower cost, but
still not free).

- if the data is going to be stored centrally, how will it get there? Using
ftp will probably not be feasible.

- if it is not stored centrally, how will long-term data availability be
enforced? (Otherwise I could have my data on a public server until my paper
comes out in print, and then remove it.)

- what level of annotation will be required? There is no point in having
zillions of files lying around if you don't know which
structure/crystal/sample they belong to, at what wavelength they were
recorded, if they were used in refinement or not, etc.

- an issue that has not been raised yet, I think: who is going to validate
that the images actually correspond to the structure factor amplitudes or
intensities that were used in the refinement? This means that the data will
have to be indexed, integrated, scaled, merged, etc. and finally compared to
the deposited Fobs or Iobs. This will have to be done for *10,000 data sets a
year*... And I can already imagine the arguments that will follow between
depositors and re-processors about what software to use, what resolution
cut-off, what outlier-rejection criteria, etc. How will conflicts and
discrepancies be resolved? This could well end up taking a day of working time
per data set, i.e. with 200 working days per year, one would need 50 *new*
staff for this task alone. For comparison: worldwide, there is currently a
*total* of ~25 annotators working for the wwPDB partners

Re: [ccp4bb] To archive or not to archive, that's the question!

[Gerard DVD Kleywegt]

On Friday, October 28, 2011 02:02:46 pm Gerard DVD Kleywegt wrote:

 I'm a tad disappointed to be only in fourth place, Colin!
 What has the Pope ever done for crystallography?


  http://covers.openlibrary.org/b/id/5923051-L.jpg


Fock'n'Pope! Great find, Ethan! So maybe he deserves fourth place after all.

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let z be the
   radius and a the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

[ccp4bb] Heads-up: PDBe service interruption 21-24 October

[Gerard DVD Kleywegt]

Dear PDBe users and depositors,

Due to essential maintenance of the computers in the campus data centre this 
coming weekend, all web, ftp and e-mail services of the Protein Data Bank in 
Europe (PDBe; pdbe.org), as well as most other EBI services, will be 
unavailable from Friday 21 October 11 am BST until Monday 24 October 11 am BST 
(*). This includes our deposition services for PDB (Autodep) and EMDB (Emdep). 
However, the other wwPDB and EMDB deposition sites will not be affected, so if 
you are in a hurry to deposit, please use the deposition services of one of 
our partners.


We apologise for any inconvenience this may cause.

(*) BST = British Summer Time. To convert to your local time zone, try 
http://www.timeanddate.com/worldclock/converter.html


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] First contours of a vision for the future of validation at the PDB

[Gerard DVD Kleywegt]

(Posted on behalf of wwPDB)

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is pleased to direct PDB 
depositors and users to the recommendations of the wwPDB X-ray Validation Task 
Force (VTF) that were published in the journal Structure this week (2011, vol. 
19: 1395-1412; http://www.cell.com/structure/abstract/S0969-2126(11)00285-1).


The wwPDB X-ray VTF was convened in 2008 to collect expert recommendations and 
develop consensus on validation methods that should be applied to crystal 
structures (models and data) in the PDB and to identify software applications 
to perform these validation tasks. These recommendations are the basis of a 
new validation suite that will be part of the new Common Tool for Deposition 
and Annotation (DA) that is currently being developed by the wwPDB partners. 
The DA tool and the X-ray validation pipeline will go into production by the 
end of 2012 at all wwPDB deposition sites (RCSB PDB, PDBe, PDBj and BMRB). 
From that moment in time on, depositors of X-ray crystal structures at the PDB 
will be provided with a detailed validation report. Such reports can be 
submitted to journals to accompany manuscripts describing new structures, and 
several publishers are working towards making such reports mandatory. Once the 
DA tool is in production, the wwPDB partners also plan to provide the 
validation pipeline as a server, allowing crystallographers to assess their 
models before deposition and publication. Additional VTFs have been convened 
for NMR (by wwPDB) and 3DEM (by EMDataBank).


The wwPDB greatly appreciates the efforts of the authors of the X-ray VTF 
report: Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, 
Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, 
Thomas Ltteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, 
William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend and Peter H. 
Zwart.


--

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Quips about stunning software and the first structure it helped solve

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; pdbe.org) regularly produces Quips, 
short stories about QUite Interesting Pdb Structures (pdbe.org/quips). Quips 
address biologically interesting aspects of one or more PDB entries, coupled 
with interactive graphics views and often a mini-tutorial or suggestions for 
further exploration using PDBe services and resources.


Today another Quips episode was released. It looks back at the first crystal 
structure that was solved with the program Phaser and also tries to explain in 
(almost) layman's terms how Molecular Replacement works. The accompanying 
mini-tutorial shows you how to do multiple structure superimposition using 
PDBeFold (SSM).


The Quips story can be found here: http://pdbe.org/quips?story=Phaser

There is also an RSS feed that informs you whenever there is a new Quips 
article available. For links to this and several other feeds, see 
http://pdbe.org/rss


---

If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips episode, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Vacancy at PDBe for an enthusiastic junior annotator

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an 
expert structural biologist to join the PDBe curation team at the EBI near 
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD 
in some area of structural biology or structural chemistry as well as a broad 
knowledge in molecular biology or biochemistry. An in-depth knowledge of 
protein structure (including structure determination, analysis and validation) 
is essential. A few years of post-doctoral research experience in structural 
biology, as well as hands-on experience in the determination of protein 
structure is highly desirable.


The ideal candidate will be familiar with Linux/Unix operating systems and 
molecular graphics software. Basic programming skills, e.g. with Perl, Python 
or Java, would be an advantage. Given the extensive interactions with 
colleagues in the PDBe team as well as with international collaborators, 
depositors and users, excellent written and oral communication skills, fluency 
in English, ability to work in a team and attention to detail are required.


More details and a link to the electronic application procedure can be found 
here:


http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=MbkMjPUrEcTFkHhTczjobid=46332,8998483234

Feel free to pass this on to suitable candidates!

--Gerard

PS: Some hints for prospective applicants: it doesn't hurt to add a nice cover 
letter in which you explain why you would love to be a PDB annotator and why 
PDBe strikes you as a brilliant place to work. Also, if you should get invited 
for an interview and we ask you what the main colour of our website is, please 
don't answer blue...


---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Quips about greasy pockets

[Gerard DVD Kleywegt]

Hi all,

As you may recall, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly 
produces Quips, short stories about QUite Interesting Pdb Structures 
(pdbe.org/quips). Quips address biologically interesting aspects of one or 
more PDB entries, coupled with interactive graphics views and often a 
mini-tutorial or suggestions for further exploration using PDBe services and 
resources.


Today another Quips episode was released. It is about autotaxins, 
physiologically important proteins that are pursued as anti-cancer drug 
targets. This Quips was developed together with scientists from the 
Netherlands Cancer Institute (Tassos Perrakis and Wouter Moolenaar) to 
accompany their review paper in Nature Reviews Molecular Cell Biology on 
autotaxin structure and function that was also published today.


- For the Quips story (Autotaxins: inhibiting a greasy pocket), go to: 
http://pdbe.org/quips?story=Autotaxin


- For the review paper (Insights into autotaxin: how to produce and present a 
lipid mediator), go to: 
http://www.nature.com/nrm/journal/vaop/ncurrent/full/nrm3188.html


---

If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips episode, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Reminder - EMBO Practical Course on Computational structural biology - from data to structure to function

[Gerard DVD Kleywegt]

Hi all,

Just a quick reminder that the deadline for applications for this EMBO 
practical course is 30 September. See: 
http://www.ebi.ac.uk/training/handson/course_110912_structures.html#registration


--Gerard

-- Forwarded message --

Hi all,

From 14-18 November, an EMBO Practical Course on Computational structural 
biology - from data to structure to function will be held at the EBI in 
Cambridge (UK). The course is organised by James Watson, Rosemary Wilson, 
Gerard Kleywegt, Victor Lamzin, Christine Orengo and Gert Vriend.


The course will address computational aspects of protein structure 
determination, validation and analysis. Students will learn to critically 
examine and validate data from the Protein Data Bank and use a variety of 
analysis tools to identify similarities that can help identify function. The 
course will also provide an introductory session to homology modelling for use 
with proteins less amenable to structure determination. Finally, the 
importance of protein structure to drug development will be illustrated with a 
day focussing on protein interactions, small molecules, chemoinformatics and 
docking. The course is aimed at PhD students and post-docs working on the 
collection and analysis of protein structure data. The goal is to provide them 
with insight into the protein structure determination process, how to 
critically assess the quality of data from models and also provide expertise 
in the analysis of protein structure data with a view to predicting protein 
function.


Registration for the course is now open. For more information, surf to: 
http://www.ebi.ac.uk/training/handson/course_110912_structures.html


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] EDS server

[Gerard DVD Kleywegt]

Hi all,

Simple question, is there a way I can upload my own data into the EDS 
server? I see only place for it to take from data already published in the 
PDB.


First of all, if you deposit at PDBe, EDS will be run on your deposition and 
you can access the results after annotation. Second, RCSB operates a 
validation server that carries out similar calculations and which you can use 
prior to deposition.


Having said that, yes, there is actually an *unsupported* version of EDS to 
which you can upload your model and structure factors (MTZ or CIF file). Note 
that it is unsupported, unofficial, unmaintained, buyer beware and your 
mileage may vary.


In the future, there will of course be a shiny new wwPDB X-ray validation 
server which will include EDS-style calculations. (I won't make any promises 
as to when, but it will be before we all travel to work with jetpacks or 
flying cars.)


--Gerard

PS: If you want to try out the *unsupported* etc. PRedeposition EDS server 
(PREDS), throw your browser at http://eds.bmc.uu.se/eds/preds.php (but read 
http://eds.bmc.uu.se/eds/preds_help.html first).


**
   Gerard J.  Kleywegt

http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

[ccp4bb] Asset stripping the Uppsala Software Factory...

[Gerard DVD Kleywegt]

Hi all,

Unfortunately, I am no longer able to support or maintain (let alone develop 
or port to new OS versions) any of my old USF programs. For this reason, Mark 
Harris (http://xray.bmc.uu.se/markh/email.html) has made a distribution kit 
with source code (yes, Fortran77...) and compilation scripts and instructions 
for about three dozen of the USF programs (mostly from the RAVE and X-UTIL 
packages, but also including LSQMAN).


If you want to keep (some of) the USF programs running on future hardware or 
OS versions, or if you want to modify or re-use some of the code, feel free to 
download the whole caboodle. (If you should want to publish or redistribute 
modified versions that use substantial chunks of my code, I would appreciate 
it if you talked to me first though.)


The download site is:

  http://xray.bmc.uu.se/markh/usf/

You can also download sets of ready-made binaries for a few OSes (but these 
will not be kept up-to-date in the future).


Send any comments, bug reports, questions, suggestions, requests, feedback, 
experiences with new OS versions, etc. to Mark - not to me! Mark will do his 
best to provide basic support for a few months - after that, you're on your 
own.


--Gerard

PS: Little known gastromathematical curiosity: let z be the radius and a 
the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! 
(Hmmm - I'm getting hungry.)


**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

Re: [ccp4bb] Finding obsolete pdb entries

[Gerard DVD Kleywegt]

!Hola!

About 6 years ago I noted a couple of structures I was interested in were 
removed from the pdb. I saw in a recent email discussion that it is possible 
to access obsolete entries, however unfortunately I do not have the pdb code 
of the structure I am interested in - and neither does the original 
publication list the pdb code. Is there a way of searching 
withdrawn/obsolete entries for author name, macromolecule etc. or are 
structures that were withdrawn over 5 years ago lost for good?


Actually, you can. Tom Oldfield has written a web interface to query the PDBe 
search database directly using SQL - it lives here:


 http://www.ebi.ac.uk/pdbe-as/pdbedatabase/

If you want to look for obsoleted entries by molecule name, paste the 
following into the SQL box:


Select * from pdb_status WHERE status_code in ('OBS')  and
upper(TITLE) like '%ISOMERASE%';

Hit the Submit SQL button and you will get a list of hits with the word 
ISOMERASE in their title. Hit the Get (Text) button to save the complete 
list of hits.


If you know one of the authors, try the following query instead:

Select * from pdb_status WHERE status_code in ('OBS')  and
upper(AUTHOR_LIST) like '%JONES%';

!No hay de que!

--Gerard

[ccp4bb] PDBe introduces PDBeXpress - easy-to-use yet powerful PDB analysis tools

[Gerard DVD Kleywegt]

Hi all,

As part of its recent summer update, the Protein Data Bank in Europe (PDBe; 
http://pdbe.org) introduced PDBeXpress (http://pdbe.org/express), an umbrella 
name for a set of easy-to-use yet powerful PDB analysis tools. The first two 
modules can be used to answer questions such as what residues are found in 
the binding sites of vitamin B1? and given that I have a cavity lined with 
Asp, Trp, Ile, Val and His, what compounds are known to bind to such a set of 
residues?


-

There are many advanced tools and resources available worldwide to search, 
browse and analyse the contents of the PDB at the level of entire entries or 
molecules. However, when it comes to the nitty-gritty of analysing the core 
structural data contained in the PDB, i.e. atoms and their interactions, the 
situation is different. PDBeMotif (http://pdbe.org/motif) is one of the most 
powerful services available (freely) for analysing PDB entries in terms of 
detailed structure, sequence and chemistry. A practical example is described 
here: 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Structural_motifs_in_the_PDB


However, PDBeMotif is also quite complex to use. For this reason, PDBe has 
begun to develop small modules of PDBeMotif (and other) analysis functionality 
that are presented in such a way that they are very easy to use by non-experts 
and provide answers to common but complex questions. The first two PDBeXpress 
modules were released in the recent PDBe summer update; both provide 
information and statistics about ligands in the PDB. They can be accessed from 
http://pdbe.org/express (help and documentation are available from there as 
well).



What residues interact?
---
For any ligand in the PDB that you specify, this tool (using PDBeMotif behind 
the scenes) will retrieve the residues with which this ligand interacts, as 
observed in current PDB entries. The results are plotted on an interactive 
graph, which can be used to further view the PDB entries in which the 
interactions occur, or to perform further analyses using PDBeMotif.


When you start the service, all you need to provide is the name or 3-letter 
code of the compound of interest (or do a search at PDBeChem - 
http://pdbe.org/chem - if you are unsure). You can select your favourite 
compound, or compare closely related compounds such as GBC, GLC and GLO.


The results page contains a graph that shows the relative occurrence of the 
amino acids in the binding sites of the compound (extracted from the PDBeMotif 
database). If you hover your mouse over the bars, you see the total number of 
interactions between a residue type and your compound. If you click on a bar, 
you will get more details (e.g., 15.6% of the total interactions are with ASP 
(16 interactions with 9 occurrences of GLO in 7 PDB entries)). Below this are 
links that take you to the corresponding PDB entries or further analyses using 
PDBeMotif.



What binds here?

This tool enables you to search for ligands in the PDB that interact with a 
given set of residues and the results are also shown in an interactive graph. 
When you use this tool, you simply click on the amino-acid types that are 
present in the binding site. If you require that a residue occurs twice, click 
it twice, etc. For instance, what do you think is the most frequently found 
compound to interact with ARG ARG ARG LYS LYS LYS?


-

We hope that you will find PDBeXpress useful. As always, we welcome 
constructive criticism, comments, suggestions, bug reports, etc. through the 
feedback button at the top of any PDBe web page. We also welcome your 
suggestions for future PDBeXpress modules!


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Improved EM-related resources at PDBe

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; http://pdbe.org) continues to improve 
its services to the scientific community. As part of our recent website 
update, the EM resources at PDBe (http://pdbe.org/emdb) have been improved.


EMDB (http://emdatabank.org) contains over 1000 maps and is expected to grow 
5-10 fold over the next 10 years. The data held in EMDB form a treasure trove 
of information on the state of, and trends in, the 3DEM field. Examples of 
interesting information that can be mined from the archive are trends in the 
resolution obtained using different techniques and comparisons of the relative 
popularity of microscopes and software packages. A new service 
(http://pdbe.org/emstats) has been developed at PDBe to mine the database for 
such information and present the results as interactive charts. The charts are 
generated dynamically and represent the current state of the information in 
the database. The charts are active, i.e. when clicked, a query is sent to the 
database and the results are shown below the charts. Clearly, the current set 
of charts represents only a fraction of the interesting information that can 
be extracted from the database and we invite the 3DEM community as well as the 
wider structural biology community to engage with us in expanding this 
service.


Atlas pages for EMDB entries can now be accessed directly using URLs of the 
type: pdbe.org/emd-, where  is the 4-digit numerical EMDB accession 
code. For example, http://pdbe.org/emd-1831 takes you to the entry Pig 
Gastric H,K-ATPase with bound BeF and SCH28080 by Abe, Tani and Fujiyoshi.


The look and feel of the EMDB atlas pages (served at both EMDataBank sites, 
PDBe and RCSB) have also been improved - for instance, empty boxes are not 
shown so as to create a cleaner and more concise look and an enhanced version 
of the OpenAstexViewer can be accessed from an entry's visualisation page. The 
viewer can overlay fitted PDB models on maps (for an example, see 
http://pdbe.org/emd-1180) and use symmetry information to generate 
symmetry-related copies of models. (See also: 
http://www.emdatabank.org/improved_3d_viewing.html)


We hope that you will find the EM resources at PDBe useful. As always, we 
welcome constructive criticism, comments, suggestions, bug reports, etc. 
through the feedback button at the top of any PDBe web page.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] Lion kills moleman (and all other USF programs on the Mac)

[Gerard DVD Kleywegt]

Hi all,

Just a heads-up - if you upgrade to OSX Lion, your trusty old USF executables 
will no longer work.


Help is on its way - in the near future the indefatigable and intrepid 
Lion-taming heroes of the USF will release a distribution kit that includes 
source code. However, for now you may want to postpone upgrading to Lion if 
your will to live would be compromised by not being able to run Moleman, 
Mapman, Lsqman, etc.


--Mr Anchovy (Proud owner of a lion taming hat. A hat with 'lion tamer' 
written on it. And it lights up saying 'lion tamer' in big red neon letters, 
so you can tame them after dark when they're less stroppy.)


PS: http://www.youtube.com/watch?v=XMOmB1q8W4Y

**
   Gerard J.  Kleywegt

http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**

[ccp4bb] PDBe introduces UniPDB - a UniProt-PDB sequence-coverage widget

[Gerard DVD Kleywegt]

Hi all,

As part of its recent summer update, the Protein Data Bank in Europe (PDBe; 
http://pdbe.org) introduced UniPDB (http://pdbe.org/unipdb), a widget for 
graphical display of the coverage in the PDB of any UniProt entry (e.g., 
http://pdbe.org/unipdb?uniprot=P19909). The widget can be used on the PDBe 
website or included in your own web pages.


For a quick overview of the functionality of the widget, see this 
illustration:


   http://www.ebi.ac.uk/pdbe-apps/widgets/html/unipdbsnap.png

Note how the PDBlogos instantly reveal which are X-ray or NMR entries, which 
entries contain DNA or ligands, etc. Pressing the button Related PDB 
sequences (to the left in the top bar of the widget) will launch a FASTA 
search of the PDB using the UniProt sequence. The results will be presented 
(and can be analysed) in the PDBeXplore browser (http://pdbe.org/fasta).


A simple way to make a link or bookmark to the UniPDB widget for your 
favourite protein is to use a URL in the following format: 
http://pdbe.org/unipdb?uniprot=P29373 (replacing P29373 by the UniProt code 
of your chosen protein, either its UniProt name, e.g. NGF_MOUSE, or its 
accession number, e.g. P01139). Incorporating the UniPDB widget in your own 
web pages is so easy even I can do it:


   http://xray.bmc.uu.se/gerard/unipdb_pdbportfolio.html

-

Why UniPDB?
---

UniProt (http://www.uniprot.org/) is the primary resource for information 
about protein sequence and function and the PDB is the single global archive 
of 3D structures of biomacromolecules and their complexes. Many PDB entries 
contain proteins that are also archived in UniProt. As a biologist interested 
in a particular protein, you may want to find out which entries in the PDB (if 
any) contain structures for (parts of) your favourite protein, and how these 
structures map to the UniProt sequence.


Structural biologists often work on partial sequences (e.g., stably folded 
domains) and sometimes have to modify the natural sequence to facilitate 
expression or crystallisation or to allow investigation of the effect of a 
mutation on the behaviour of the protein (such as catalytic activity or 
ligand-binding specificity). In addition, the same structure can be determined 
many times, e.g. in different laboratories, with different techniques, under 
different conditions, with different ligands, etc. For these reasons, it is 
not always easy to do sequence-based searches of the PDB and synthesise the 
results into an overview of what structural information is available for which 
parts of your favourite protein. This problem is addressed by the UniPDB 
widget. It uses the up-to-date mappings between UniProt sequences and PDB 
entries that are provided by the SIFTS resource (a collaboration between the 
UniProt and PDBe teams at the EBI; http://pdbe.org/sifts). SIFTS provides 
mappings from PDB entries to other bioinformatics resources as well, including 
Pfam (sequence-based protein domains), CATH and SCOP (both of these are 
structural fold classifications).


For more information about UniPDB (including instructions on how to include it 
in your own web pages), see: http://pdbe.org/unipdb


-

We hope that you will find the UniPDB tool useful. As always, we welcome 
constructive criticism, comments, suggestions, bug reports, etc. through the 
feedback button at the top of any PDBe web page.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] NMR resources at PDBe (pdbe.org/nmr)

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; http://pdbe.org/) continues to improve 
its services to the scientific community. As part of our recent website 
update, we have reorganised and simplified the way information about NMR 
entries is shown. We have also released Vivaldi (Visualisation and Validation 
Display; http://pdbe.org/vivaldi), an interactive tool that allows you to 
inspect available validation reports and check for restraint violations or RDC 
fits. For an example, try http://pdbe.org/vivaldi/2keo


The pages describing the NMR resources at PDBe (http://pdbe.org/nmr) have been 
revised and streamlined. They allow you to search the VASCO, OLDERADO, RECOORD 
and logRECOORD databases (see below) and also provide information about 
deposition of NMR structures and accompanying data, as well as some work 
related to the CCPN framework. The NMR statistics page shows the current 
status of NMR-related information in the PDB and at PDBe 
(http://www.ebi.ac.uk/pdbe-apps/nmr/statistics).


On the PDBe atlas pages of a particular NMR entry (e.g., http://pdbe.org/2keo 
- cytochrome-b5-like domain of the HERC2 E3 ligase - or try 
http://pdbe.org/hasnmr for a randomly picked NMR entry), you can access 
available experimental information by clicking on the Experiment link in the 
navigation menu on the left of the page. Alternatively, whenever you see a 
PDBprint (http://pdbe.org/pdbprints) for an NMR entry, you can click on the 
NMR icon to get to the NMR experimental information page. Finally, if you 
know the PDB code, you can go there directly (e.g., 
http://pdbe.org/2keo/experimental). When you click a View link in the table 
on the experimental information page, it will redirect you to a predefined 
Vivaldi view (e.g., restraints or validation reports).


The experimental information page allows you to navigate to the corresponding 
Biological Magnetic Resonance Bank (BMRB) entry containing assigned chemical 
shifts. (Note: experimentally determined chemical shifts are now mandatory 
when depositing NMR structures). Sometimes, more than one BMRB entry relates 
to the same PDB entry, for instance in the case of close homologues or 
alternate protein constructs (97% sequence identity). You can download 
deposited restraints from the PDB archive or navigate to the remediated 
restraints from the NMR Restraints Grid (NRG) at BMRB. For most NMR entries 
there is an in-depth validation report from the NRG-CING database, hosted at 
the Radboud University of Nijmegen.


VASCO - Validation of assigned chemical shifts through coordinates - is a 
database of 2000+ validation reports, which can be downloaded as text files or 
viewed interactively in Vivaldi. OLDERADO reports on domain composition, 
clustering and representative models of a deposited ensemble are available for 
most NMR entries that contain proteins. They can be viewed in Vivaldi or in a 
tabular format. Two databases of recalculated ensembles are hosted by PDBe: 
RECOORD, with 500+ entries, which compares four common structure-determination 
protocols, and logRECOORD, with 300+ entries, which uses a log-normal 
potential for interpreting NOE data.


Finally, you may be interested in some recent NMR-related papers co-authored 
by current and former PDBe staff:


1. Lemak et al., A novel strategy for NMR resonance assignment and protein 
structure determination, Journal of Biomolecular NMR 49, 27-38, 2011 
(http://dx.doi.org/10.1007/s10858-010-9458-0)


2. Bernard et al., Bayesian estimation of NMR restraint potential and weight: 
a validation on a representative set of protein structures, Proteins 79, 
1525-1537, 2011 (http://dx.doi.org/10.1002/prot.22980)


3. Penkett et al., Straightforward and complete deposition of NMR data to the 
PDBe, Journal of Biomolecular NMR 48, 85-92, 2010 
(http://dx.doi.org/10.1007/s10858-010-9439-3)


4. Fogh et al., MEMOPS: data modelling and automatic code generation, 
Journal of Integrative Bioinformatics 7, 123, 2010 
(http://dx.doi.org/10.2390/biecoll-jib-2010-123)


5. Rieping  Vranken, Validation of archived chemical shifts through atomic 
coordinates, Proteins 78, 2482-2489, 2010 
(http://dx.doi.org/10.1002/prot.22756)


We hope that expert and non-expert users alike will find the NMR resources at 
PDBe useful. As always, we welcome constructive criticism, comments, 
suggestions, bug reports, etc. through the feedback button at the top of any 
PDBe web page.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Multi crystal averaging : data on same scale before averaging?

[Gerard DVD Kleywegt]

This is correct - see http://xray.bmc.uu.se/usf/dataman_man.html#S27

At the time I wrote this (1993...), I was a recovering NMRtist and The Other 
Gerard was doing a sabbatical in Uppsala and in fact in the office next to 
mine. He pointed out that I had to do this and also provided code.


--The other other Gerard



On Thu, 14 Jul 2011, Edward A. Berry wrote:


If I recall correctly DATAMAN does Wilson scaling in which the scale
and B-factor are adjusted so the average reflection intensity in
resolution bins are the same. I suspect it may not be required if
all the data have been put on an approximately absolute scale by
e.g. truncate (although that doesn't adjust the B-factor).

If you do end up scaling your data in dataman, be sure to go back
to the original data for refinement once you solve the structure,
or your B-factors will not be right.

eab


Francis E Reyes wrote:

Hi all

Walking through multi xtal averaging with RAVE. I finally got a good
mask and optimized NCS for my xtal forms. However, in the CRAVE manual
I see this

- the reflections in the input MTZ files *MUST* have been put on the
same temperature factor scale prior to cross-crystal averaging (see
the DATAMAN manual on how to do this) !!!

Scale the separate datasets together? Wouldn't this just be a mess
since the crystal should be non isomorphous to each other?

Or does this say that within each dataset, all the data should be on
the same scale (which would be if I used scala to scale) ?

Am I interpreting this correctly?

Thanks!

F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder






Best wishes,

--Gerard

**
   Gerard J.  Kleywegt

http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**