Re: [ccp4bb] Please share your experience about "ugly" crystals showing good diffraction

2018-06-29 Thread Artem Evdokimov 
Good evening,

Over the years I've seen great diffraction from any number of hideous
brittle plates with perforated edges, 'Krypton skyscrapers', curved
whiskers, 'hypodermic needles', even from crystals that looked like cat
vomit (hairballs), and so forth.

The structure *ab ovo* story is my favorite, though:

Similar to Debanu's case - we've had crystals (of a novel insecticidal
toxin) that were perfectly egg-shaped, and every one of them was the same
shape - regardless of differences in their size. I mounted them on a bet
with my colleagues and we were cracking all kinds of jokes about making
omelets with X-rays, and so forth - right until the very first egg
diffracted better than 1.6A and produced a lovely structure.

On top of this bit of weirdness, the only way these crystals could be grown
was by reductive methylation followed by proteolysis. Opposite order of
steps did not work, and each step in itself did not work.

This story brings to mind the hellish experience of polishing small
molecule crystals down to little balls in order to minimize absorption
effects (great, now I made myself feel old).

Artem




- Cosmic Cats approve of this message

On Thu, Jun 28, 2018 at 8:07 PM, Anirban Banerjee  wrote:

>
> Dear all,
>
> Apologies for the non-CCP4 related question.
>
> If you have concrete experience about visually unappealing, i.e. ugly
> crystals ( your own take on ugly is fine)  diffracting better than
> comparably similar sized nicer looking crystals of the same protein, will
> you please share here ? Even better if that led to a published structure.
> Might you also have pictures ?
>
> We have all heard anecdotes about not using visual appearance to judge the
> quality of crystals as far as their ability to give good diffraction data
> is concerned but I am trying to gather some concrete pointers here to
> motivate trainees.
>
> Thanks very much for any help.
>
> Best,
>
> Anirban
>
> P.S. I know that there is probably a lot of thought and wisdom  on this
> this specific topic but I am really looking for actual experience.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Please share your experience about "ugly" crystals showing good diffraction

2018-06-29 Thread Mahmudul Hasan 
Hi Anirban,
Never thought someone will ask for image of 'ugly' crystals, but
fortunately I have found some saved pictures which is more than 8 years old!

I think I have a perfect example. The pictures can be found in the folder
by following the link:
https://drive.google.com/drive/folders/0B1M5Wq4437-CN0pLWXdOUG44MlE?usp=sharing

These ugly crystals diffracted to 1.95 Å as opposed to some nice looking
crystals (grown in different condition) that diffracted to quite lower
resolution.

The structure from these crystals have PDB ID is 2XQ0 (
https://www.rcsb.org/structure/2XQ0). The structure is described in JMB
journal (
https://www.sciencedirect.com/science/article/pii/S0022283610012969?via%3Dihub
).

Best wishes,
Mahmudul
Lund
Sweden

On Fri, Jun 29, 2018 at 8:57 AM Janet Newman  wrote:

> Hi Anirban,
>
> Single easy example to find (see attached images) - gorgeous crystals -
> sub 3A (grown in sodium malonate)
> Lozenge crystals - better than 2A (grown in ammonium sulfate)
>
> (Barbiturase protein )
>
> Cheers, Janet
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Debanu Das
> Sent: Friday, 29 June 2018 4:36 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Please share your experience about "ugly" crystals
> showing good diffraction
>
> Hi Anirban,
>
> At JCSG, we subjected ~180,000 crystals from ~3500 unique/novel
> proteins/complexes to X-ray diffraction screening, resulting in >1500
> novel structures in the PDB at an average resolution ~2.0A. In theory,
> if we had the bandwidth now to sort through all that data to pull out
> images of the mounted crystals and their diffraction quality, we could
> probably get some good analysis done on this.
>
> However, as an alternative, I can certainly provide some examples that
> we have dealt with recently that I hope will add substance to the
> anecdotes to motivate your trainees!
>
> a) For one protein, our first crystals were oval shaped, without sharp
> geometry/edges, much like a pebble. We got a high quality 1.9A
> structure out of it. Subsequent optimization led to much nicer looking
> crystals with nice shapes and we collected ~50 data sets from them all
> resulting in ~2A structures so not much improved compared to the
> initial visually poorer crystals.
>
> b) For another protein, crystals grow nicely but some of the crystals
> remain suspended in solution whereas other settle to the bottom and
> stick. For the ones which stick, some can be dislodged by gentle
> prodding with a nylon loop while harvesting and they result in (along
> with the ones that are not stuck) in ~1.8-2A structures. For the ones
> which are stuck and cannot be gently dislodged, a nudge with a plastic
> tip (out of desperation!) is sufficient to dislodge them, and they
> retain their nice visual appearance and shape, but have total loss in
> diffraction.
>
> c) We see this too for crystals soaked with ligands. In some cases
> after soaking the crystals appear fine but suffer in diffraction
> quality, and in some cases they appear to have suffered visually but
> result in usable data sets/structures.
>
> So at the end of the day there are crystals that appear nice but do
> not diffract well and there are crystals that do not appear nice but
> lead to good/usable structures. So it's all about inner beauty. Never
> give up on crystals/crystal optimization without testing them by
> X-rays.
>
> Best,
> Debanu
>
> On Thu, Jun 28, 2018 at 5:07 PM, Anirban Banerjee 
> wrote:
> >
> > Dear all,
> >
> > Apologies for the non-CCP4 related question.
> >
> > If you have concrete experience about visually unappealing, i.e. ugly
> > crystals ( your own take on ugly is fine)  diffracting better than
> > comparably similar sized nicer looking crystals of the same protein, will
> > you please share here ? Even better if that led to a published structure.
> > Might you also have pictures ?
> >
> > We have all heard anecdotes about not using visual appearance to judge
> the
> > quality of crystals as far as their ability to give good diffraction
> data is
> > concerned but I am trying to gather some concrete pointers here to
> motivate
> > trainees.
> >
> > Thanks very much for any help.
> >
> > Best,
> >
> > Anirban
> >
> > P.S. I know that there is probably a lot of thought and wisdom  on this
> this
> > specific topic but I am really looking for actual experience.
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
>

Re: [ccp4bb] [ccp4bb] Oxford University Press

2018-06-29 Thread Keller, Jacob 
The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime. 

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
> 
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
> 
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
> 
> Anyway, if people want to read your papers and cannot get them from 
> ResearchGate, I'm sure they can find them on another online 
> collection, a hub of some sort ;)
> 
> Cheers,
> Robbie
> 
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>> 
>> Agreed, but for 10 years old papers this seems a bit of overkill
>> 
>> 
>> 
>> From: CCP4 bulletin board  On Behalf Of Robbie 
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Were they open access papers? If they were, than OUP is being too 
>> aggressive (IMO), but otherwise it makes sense. I also find the 
>> ResearchGate is rather aggressive in bugging you to upload papers 
>> that are readily available from the publisher. The whole business bit 
>> in scientific publishing is a necessary (?) evil, but I guess if 
>> given the choice one should publish somewhere where you as an author retain 
>> copyright.
>> 
>> 
>> 
>> Cheers,
>> 
>> Robbie
>> 
>> 
>> 
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Bernhard Rupp
>> Sent: Friday, June 29, 2018 11:42
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Hi Fellows,
>> 
>> 
>> 
>> just an advisory that Oxford University Press is pretty aggressive in
>> 
>> enforcing copyright - I had to remove 2 Bioinformatics papers
>> 
>> from ResearchGate.
>> 
>> 
>> 
>> Fortunately, authors have choices, too
>> 
>> 
>> 
>> Cheers, BR
>> 
>> --
>> 
>> Bernhard Rupp
>> 
>> http://www.hofkristallamt.org/
>> 
>> b...@hofkristallamt.org
>> 
>> +1 925 209 7429
>> 
>> +43 676 571 0536
>> 
>> --
>> 
>> Many plausible ideas vanish
>> 
>> at the presence of thought
>> 
>> --
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>>

Re: [ccp4bb] [ccp4bb] Oxford University Press

2018-06-29 Thread Petr Leiman 
Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime. 

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
> 
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie 
> Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
> 
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
> 
> Anyway, if people want to read your papers and cannot get them from 
> ResearchGate, I'm sure they can find them on another online collection, a hub 
> of some sort ;)
> 
> Cheers,
> Robbie 
> 
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>> 
>> Agreed, but for 10 years old papers this seems a bit of overkill
>> 
>> 
>> 
>> From: CCP4 bulletin board  On Behalf Of Robbie 
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Were they open access papers? If they were, than OUP is being too 
>> aggressive (IMO), but otherwise it makes sense. I also find the 
>> ResearchGate is rather aggressive in bugging you to upload papers that 
>> are readily available from the publisher. The whole business bit in 
>> scientific publishing is a necessary (?) evil, but I guess if given 
>> the choice one should publish somewhere where you as an author retain 
>> copyright.
>> 
>> 
>> 
>> Cheers,
>> 
>> Robbie
>> 
>> 
>> 
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Bernhard Rupp
>> Sent: Friday, June 29, 2018 11:42
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Hi Fellows,
>> 
>> 
>> 
>> just an advisory that Oxford University Press is pretty aggressive in
>> 
>> enforcing copyright - I had to remove 2 Bioinformatics papers
>> 
>> from ResearchGate.
>> 
>> 
>> 
>> Fortunately, authors have choices, too
>> 
>> 
>> 
>> Cheers, BR
>> 
>> --
>> 
>> Bernhard Rupp
>> 
>> http://www.hofkristallamt.org/
>> 
>> b...@hofkristallamt.org
>> 
>> +1 925 209 7429
>> 
>> +43 676 571 0536
>> 
>> --
>> 
>> Many plausible ideas vanish
>> 
>> at the presence of thought
>> 
>> --
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] AW: [ccp4bb] Oxford University Press

2018-06-29 Thread Hughes, Jon 
whose paper? our universities pay subscriptions for these journals and we even 
pay on top of that for the pages of our publications (even when they're not 
actually printed!), whilst we review papers for free! sounds like a 
well-validated way to use taxpayers' money to keep the expensive company cars 
etc. nice and shiny. why don't universities just require reimbursement for the 
time we invest to insure that the merchandise is up to standard? €100 per hour 
would be cheap. seems to me as though some capitalists need to add a few lines 
to their balance sheets
best, jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie 
Joosten
Gesendet: Freitag, 29. Juni 2018 13:42
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Oxford University Press

Yes, but think of all the money they miss due to your pirating of their paper 
;) It's the typical discussion about whether piracy of copyrighted material 
leads to loss or gain of revenue. There are a lot of models here, but not 
necessarily well-validated.

Anyway, if people want to read your papers and cannot get them from 
ResearchGate, I'm sure they can find them on another online collection, a hub 
of some sort ;)

Cheers,
Robbie 

> -Original Message-
> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
> Sent: Friday, June 29, 2018 13:23
> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] Oxford University Press
> 
> Agreed, but for 10 years old papers this seems a bit of overkill
> 
> 
> 
> From: CCP4 bulletin board  On Behalf Of Robbie 
> Joosten
> Sent: Friday, June 29, 2018 12:11
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Oxford University Press
> 
> 
> 
> Were they open access papers? If they were, than OUP is being too 
> aggressive (IMO), but otherwise it makes sense. I also find the 
> ResearchGate is rather aggressive in bugging you to upload papers that 
> are readily available from the publisher. The whole business bit in 
> scientific publishing is a necessary (?) evil, but I guess if given 
> the choice one should publish somewhere where you as an author retain 
> copyright.
> 
> 
> 
> Cheers,
> 
> Robbie
> 
> 
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
> Bernhard Rupp
> Sent: Friday, June 29, 2018 11:42
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Oxford University Press
> 
> 
> 
> Hi Fellows,
> 
> 
> 
> just an advisory that Oxford University Press is pretty aggressive in
> 
> enforcing copyright - I had to remove 2 Bioinformatics papers
> 
> from ResearchGate.
> 
> 
> 
> Fortunately, authors have choices, too
> 
> 
> 
> Cheers, BR
> 
> --
> 
> Bernhard Rupp
> 
> http://www.hofkristallamt.org/
> 
> b...@hofkristallamt.org
> 
> +1 925 209 7429
> 
> +43 676 571 0536
> 
> --
> 
> Many plausible ideas vanish
> 
> at the presence of thought
> 
> --
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Two PhD positions in protein-based material science at RWTH Aachen University

2018-06-29 Thread Tobias Beck 
Dear all,

We have two open PhD positions in my lab at RWTH Aachen University.

Please find the two job advertisements at:

https://web-p.zhv.rwth-aachen.de/mainzhv.php?scriptid=job=vorschau=23666=engl
https://web-p.zhv.rwth-aachen.de/mainzhv.php?scriptid=job=vorschau=23667=engl

More information about our current research and recent publications may be
found at http://www.ac.rwth-aachen.de/extern/beck/

Please pass this on to interested candidates.

Best wishes, Tobias.


-- 
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web:  http://www.ac.rwth-aachen.de/extern/beck/
___



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Oxford University Press

2018-06-29 Thread Robbie Joosten 
Yes, but think of all the money they miss due to your pirating of their paper 
;) It's the typical discussion about whether piracy of copyrighted material 
leads to loss or gain of revenue. There are a lot of models here, but not 
necessarily well-validated.

Anyway, if people want to read your papers and cannot get them from 
ResearchGate, I'm sure they can find them on another online collection, a hub 
of some sort ;)

Cheers,
Robbie 

> -Original Message-
> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
> Sent: Friday, June 29, 2018 13:23
> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] Oxford University Press
> 
> Agreed, but for 10 years old papers this seems a bit of overkill
> 
> 
> 
> From: CCP4 bulletin board  On Behalf Of Robbie
> Joosten
> Sent: Friday, June 29, 2018 12:11
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Oxford University Press
> 
> 
> 
> Were they open access papers? If they were, than OUP is being too
> aggressive (IMO), but otherwise it makes sense. I also find the ResearchGate
> is rather aggressive in bugging you to upload papers that are readily 
> available
> from the publisher. The whole business bit in scientific publishing is a
> necessary (?) evil, but I guess if given the choice one should publish
> somewhere where you as an author retain copyright.
> 
> 
> 
> Cheers,
> 
> Robbie
> 
> 
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Bernhard Rupp
> Sent: Friday, June 29, 2018 11:42
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Oxford University Press
> 
> 
> 
> Hi Fellows,
> 
> 
> 
> just an advisory that Oxford University Press is pretty aggressive in
> 
> enforcing copyright - I had to remove 2 Bioinformatics papers
> 
> from ResearchGate.
> 
> 
> 
> Fortunately, authors have choices, too
> 
> 
> 
> Cheers, BR
> 
> --
> 
> Bernhard Rupp
> 
> http://www.hofkristallamt.org/
> 
> b...@hofkristallamt.org
> 
> +1 925 209 7429
> 
> +43 676 571 0536
> 
> --
> 
> Many plausible ideas vanish
> 
> at the presence of thought
> 
> --
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] ORCIDs To Become Mandatory for OneDep Contact Authors

2018-06-29 Thread John Berrisford 
The wwPDB OneDep system for deposition, validation and biocuration will
require contact authors to provide their unique ORCID identifiers
(https://orcid.org/) when preparing depositions later this summer. This
change will enable wwPDB efforts to correctly attribute PDB structures to
contact authors. At a later point, ORCID will be used to authenticate and
reorganize access to deposition data within OneDep.

 

Regards

 

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  https://www.pdbe.org

 
https://www.facebook.com/proteindatabank

  https://twitter.com/PDBeurope

 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Oxford University Press

2018-06-29 Thread Bernhard Rupp 
Agreed, but for 10 years old papers this seems a bit of overkill..

 

From: CCP4 bulletin board  On Behalf Of Robbie
Joosten
Sent: Friday, June 29, 2018 12:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Oxford University Press

 

Were they open access papers? If they were, than OUP is being too aggressive
(IMO), but otherwise it makes sense. I also find the ResearchGate is rather
aggressive in bugging you to upload papers that are readily available from
the publisher. The whole business bit in scientific publishing is a
necessary (?) evil, but I guess if given the choice one should publish
somewhere where you as an author retain copyright.

 

Cheers,

Robbie 

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Bernhard Rupp
Sent: Friday, June 29, 2018 11:42
To: CCP4BB@JISCMAIL.AC.UK  
Subject: [ccp4bb] Oxford University Press

 

Hi Fellows,

 

just an advisory that Oxford University Press is pretty aggressive in

enforcing copyright - I had to remove 2 Bioinformatics papers

from ResearchGate.

 

Fortunately, authors have choices, too..

 

Cheers, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB
 =1 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB
 =1 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Oxford University Press

2018-06-29 Thread Robbie Joosten 
Were they open access papers? If they were, than OUP is being too aggressive 
(IMO), but otherwise it makes sense. I also find the ResearchGate is rather 
aggressive in bugging you to upload papers that are readily available from the 
publisher. The whole business bit in scientific publishing is a necessary (?) 
evil, but I guess if given the choice one should publish somewhere where you as 
an author retain copyright.

Cheers,
Robbie

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard 
Rupp
Sent: Friday, June 29, 2018 11:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Oxford University Press

Hi Fellows,

just an advisory that Oxford University Press is pretty aggressive in
enforcing copyright - I had to remove 2 Bioinformatics papers
from ResearchGate.

Fortunately, authors have choices, too

Cheers, BR
--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
+1 925 209 7429
+43 676 571 0536
--
Many plausible ideas vanish
at the presence of thought
--




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Oxford University Press

2018-06-29 Thread Bernhard Rupp 
Hi Fellows,

 

just an advisory that Oxford University Press is pretty aggressive in

enforcing copyright - I had to remove 2 Bioinformatics papers

from ResearchGate.

 

Fortunately, authors have choices, too..

 

Cheers, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Crystals Special Issue "Crystal Growth in Gels"

2018-06-29 Thread Leonardo Lo Presti 

Dear all,

Hoping to please you, I inform you that submissions of contributions for 
a special issue of "Crystals" (IF 2.144) dedicated to crystallization in 
gels are welcome. Manuscripts can be related to theoretical and/or 
experimental aspects of crystallization in gel media. High-quality works 
dealing with biological polymers will be particularly appreciated.


If interested, you can find more information at 
http://www.mdpi.com/journal/crystals/special_issues/Crystal_Growth_Gels.


Best,

Leonardo

Leonardo Lo Presti, PhD
Università degli Studi di Milano
Chemistry Department
Via Golgi 19
20133 Milano, Italy
Phone: +39-02-50314252
Fax: +39-02-50314300






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Please share your experience about "ugly" crystals showing good diffraction

2018-06-29 Thread Debanu Das 
Hi Anirban,

At JCSG, we subjected ~180,000 crystals from ~3500 unique/novel
proteins/complexes to X-ray diffraction screening, resulting in >1500
novel structures in the PDB at an average resolution ~2.0A. In theory,
if we had the bandwidth now to sort through all that data to pull out
images of the mounted crystals and their diffraction quality, we could
probably get some good analysis done on this.

However, as an alternative, I can certainly provide some examples that
we have dealt with recently that I hope will add substance to the
anecdotes to motivate your trainees!

a) For one protein, our first crystals were oval shaped, without sharp
geometry/edges, much like a pebble. We got a high quality 1.9A
structure out of it. Subsequent optimization led to much nicer looking
crystals with nice shapes and we collected ~50 data sets from them all
resulting in ~2A structures so not much improved compared to the
initial visually poorer crystals.

b) For another protein, crystals grow nicely but some of the crystals
remain suspended in solution whereas other settle to the bottom and
stick. For the ones which stick, some can be dislodged by gentle
prodding with a nylon loop while harvesting and they result in (along
with the ones that are not stuck) in ~1.8-2A structures. For the ones
which are stuck and cannot be gently dislodged, a nudge with a plastic
tip (out of desperation!) is sufficient to dislodge them, and they
retain their nice visual appearance and shape, but have total loss in
diffraction.

c) We see this too for crystals soaked with ligands. In some cases
after soaking the crystals appear fine but suffer in diffraction
quality, and in some cases they appear to have suffered visually but
result in usable data sets/structures.

So at the end of the day there are crystals that appear nice but do
not diffract well and there are crystals that do not appear nice but
lead to good/usable structures. So it's all about inner beauty. Never
give up on crystals/crystal optimization without testing them by
X-rays.

Best,
Debanu

On Thu, Jun 28, 2018 at 5:07 PM, Anirban Banerjee  wrote:
>
> Dear all,
>
> Apologies for the non-CCP4 related question.
>
> If you have concrete experience about visually unappealing, i.e. ugly
> crystals ( your own take on ugly is fine)  diffracting better than
> comparably similar sized nicer looking crystals of the same protein, will
> you please share here ? Even better if that led to a published structure.
> Might you also have pictures ?
>
> We have all heard anecdotes about not using visual appearance to judge the
> quality of crystals as far as their ability to give good diffraction data is
> concerned but I am trying to gather some concrete pointers here to motivate
> trainees.
>
> Thanks very much for any help.
>
> Best,
>
> Anirban
>
> P.S. I know that there is probably a lot of thought and wisdom  on this this
> specific topic but I am really looking for actual experience.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1