Re: [ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread John R Helliwell
Dear Aaron,
I think that the Zenodo limit is as their email to you states, per dataset 
cited from an article ie equals one doi. I recall that at International Data 
Week in Denver 2016 I mentioned in open discussion at the session on data 
repositories the zenodo limit per dataset of 5 Gbytes and that 50 Gbytes would 
be much better and eg thereby allow for a time resolved diffraction sequence of 
datasets. One week later it had increased from 5 to 50 Gbytes per data set. 
Greetings,
John 
Emeritus Professor John R Helliwell DSc



> On 18 Jan 2019, at 16:41, Aaron Finke  wrote:
> 
> This is what Zenodo emailed me: "By default, we provide a one-time quota 
> increase up to 100GB for a dataset that will be cited from a peer-reviewed 
> article. Zenodo is a free-to-use service, an in order to keep it this way, we 
> have to restrict the incoming data volume rate as very large datasets 
> contribute significantly to the overall data volume in Zenodo. Unfortunately, 
> at this point, we also cannot receive payment for quota increases, though we 
> do hope that this will be possible in the future, at which point we will 
> announce this possibility.”
> 
> I suppose I could split the dataset over multiple DOIs but it feels like 
> “cheating the system” a bit. The CXIDB sounds promising, though!
> 
> Thanks,
> Aaron
> 
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
> 
>> On Jan 18, 2019, at 11:16 AM, Herbert J. Bernstein  wrote:
>> 
>> The zenodo policies seem to the most workable as a start.  I would suggest 
>> contacting them for the cases that go over 50GB, but at worst splitting into 
>> 50GB chunks.  -- Herbert
>> 
>>> On Fri, Jan 18, 2019 at 10:49 AM Andreas Förster 
>>>  wrote:
>>> Hi Aaron,
>>> 
>>> can you slice your data and then link to the bits?
>>> 
>>> We're currently trying to find out what "unlimited Google Drive storage" 
>>> means by uploading pi in chunks of 70 GB or so.
>>> 
>>> All best.
>>> 
>>> 
>>> Andreas
>>> 
>>> 
>>> 
 On Fri, Jan 18, 2019 at 4:31 PM Aaron Finke  wrote:
 Dear CCP4ites,
 
 Is anyone aware of online repositories that will store huge sets of raw 
 data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is 
 typically 50 GB and their absolute limit is 100 GB. SBGrid has yet to 
 respond to my emails.
 
 I could host them myself, but the involuntary dry heaving response I got 
 when I brought up the idea to our IT department implied they were less 
 enthused with the idea than I was. So a cloud service would be far more 
 preferable as a long term solution.
 
 Thanks,
 Aaron
 
 --
 Aaron Finke
 Staff Scientist, MacCHESS
 Cornell University
 e-mail: af...@cornell.edu
 
 
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>>> 
>>> 
>>> -- 
>>> Andreas Förster, Ph.D.
>>> Application Scientist Crystallography, Scientific Sales
>>> Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: 
>>> andreas.foers...@dectris.com
>>> DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | 
>>> www.dectris.com
>>> 
>>> 
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Re: [ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread Aaron Finke
This is what Zenodo emailed me: "By default, we provide a one-time quota 
increase up to 100GB for a dataset that will be cited from a peer-reviewed 
article. Zenodo is a free-to-use service, an in order to keep it this way, we 
have to restrict the incoming data volume rate as very large datasets 
contribute significantly to the overall data volume in Zenodo. Unfortunately, 
at this point, we also cannot receive payment for quota increases, though we do 
hope that this will be possible in the future, at which point we will announce 
this possibility.”

I suppose I could split the dataset over multiple DOIs but it feels like 
“cheating the system” a bit. The CXIDB sounds promising, though!

Thanks,
Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Jan 18, 2019, at 11:16 AM, Herbert J. Bernstein 
mailto:yaya...@gmail.com>> wrote:

The zenodo policies seem to the most workable as a start.  I would suggest 
contacting them for the cases that go over 50GB, but at worst splitting into 
50GB chunks.  -- Herbert

On Fri, Jan 18, 2019 at 10:49 AM Andreas Förster 
mailto:andreas.foers...@dectris.com>> wrote:
Hi Aaron,

can you slice your data and then link to the bits?

We're currently trying to find out what "unlimited Google Drive storage" means 
by uploading pi in chunks of 70 GB or so.

All best.


Andreas



On Fri, Jan 18, 2019 at 4:31 PM Aaron Finke 
mailto:af...@cornell.edu>> wrote:
Dear CCP4ites,

Is anyone aware of online repositories that will store huge sets of raw data 
(>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is typically 50 
GB and their absolute limit is 100 GB. SBGrid has yet to respond to my emails.

I could host them myself, but the involuntary dry heaving response I got when I 
brought up the idea to our IT department implied they were less enthused with 
the idea than I was. So a cloud service would be far more preferable as a long 
term solution.

Thanks,
Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu




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Re: [ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread Herbert J. Bernstein
The zenodo policies seem to the most workable as a start.  I would suggest
contacting them for the cases that go over 50GB, but at worst splitting
into 50GB chunks.  -- Herbert

On Fri, Jan 18, 2019 at 10:49 AM Andreas Förster <
andreas.foers...@dectris.com> wrote:

> Hi Aaron,
>
> can you slice your data and then link to the bits?
>
> We're currently trying to find out what "unlimited Google Drive storage"
> means by uploading pi in chunks of 70 GB or so.
>
> All best.
>
>
> Andreas
>
>
>
> On Fri, Jan 18, 2019 at 4:31 PM Aaron Finke  wrote:
>
>> Dear CCP4ites,
>>
>> Is anyone aware of online repositories that will store huge sets of raw
>> data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is
>> typically 50 GB and their absolute limit is 100 GB. SBGrid has yet to
>> respond to my emails.
>>
>> I could host them myself, but the involuntary dry heaving response I got
>> when I brought up the idea to our IT department implied they were less
>> enthused with the idea than I was. So a cloud service would be far more
>> preferable as a long term solution.
>>
>> Thanks,
>> Aaron
>>
>> --
>> Aaron Finke
>> Staff Scientist, MacCHESS
>> Cornell University
>> e-mail: af...@cornell.edu
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
> 
> Andreas Förster, Ph.D.
> Application Scientist Crystallography, Scientific Sales
> Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
> andreas.foers...@dectris.com
> DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
> www.dectris.com
>
>
>
> 
> 
> 
> 
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Re: [ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread Thomas White
Hi,

> Is anyone aware of online repositories that will store huge sets of
> raw data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s
> limit is typically 50 GB and their absolute limit is 100 GB. SBGrid
> has yet to respond to my emails.

The Coherent X-ray Imaging Data Bank may be appropriate:
http://cxidb.org

The definition of "imaging" is taken quite widely, e.g. the data
there includes many serial crystallography diffraction data sets.  A
lot of them are MUCH bigger than 100 GB.

Tom

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Re: [ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread Andreas Förster
Hi Aaron,

can you slice your data and then link to the bits?

We're currently trying to find out what "unlimited Google Drive storage"
means by uploading pi in chunks of 70 GB or so.

All best.


Andreas



On Fri, Jan 18, 2019 at 4:31 PM Aaron Finke  wrote:

> Dear CCP4ites,
>
> Is anyone aware of online repositories that will store huge sets of raw
> data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is
> typically 50 GB and their absolute limit is 100 GB. SBGrid has yet to
> respond to my emails.
>
> I could host them myself, but the involuntary dry heaving response I got
> when I brought up the idea to our IT department implied they were less
> enthused with the idea than I was. So a cloud service would be far more
> preferable as a long term solution.
>
> Thanks,
> Aaron
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


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Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
andreas.foers...@dectris.com
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Re: [ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread graeme.win...@diamond.ac.uk
Hi Aaron

I would guess most places would start to want $$ for storing multiples of 100 GB

Google, Amazon, Microsoft all offer this kind of thing. Getting the data in and 
out can be slow, and I would expect as the data size tends towards big and the 
time tends to a long time it would be comparable to doing it yourself in terms 
of cost

Unless you can tag yourself onto a CERN Tier1 
http://wlcg-public.web.cern.ch/tier-centres

Cheers Graeme

On 18 Jan 2019, at 15:31, Aaron Finke 
mailto:af...@cornell.edu>> wrote:

Dear CCP4ites,

Is anyone aware of online repositories that will store huge sets of raw data 
(>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is typically 50 
GB and their absolute limit is 100 GB. SBGrid has yet to respond to my emails.

I could host them myself, but the involuntary dry heaving response I got when I 
brought up the idea to our IT department implied they were less enthused with 
the idea than I was. So a cloud service would be far more preferable as a long 
term solution.

Thanks,
Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu




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[ccp4bb] Open Access Repositories for Big Data?

2019-01-18 Thread Aaron Finke
Dear CCP4ites,

Is anyone aware of online repositories that will store huge sets of raw data 
(>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is typically 50 
GB and their absolute limit is 100 GB. SBGrid has yet to respond to my emails.

I could host them myself, but the involuntary dry heaving response I got when I 
brought up the idea to our IT department implied they were less enthused with 
the idea than I was. So a cloud service would be far more preferable as a long 
term solution.

Thanks,
Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu




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Re: [ccp4bb] covalent link to aa

2019-01-18 Thread Paul Emsley

On 15/01/2019 20:49, Markus Heckmann wrote:


I have a structure where CYS is bound to OCA (octanoic acid). I
started with Jligand and created a CYS-OCA covalent link. It then
output a CIF file (verified looks OK). Add the LINK record to PDB
file:

LINK SG  CYS A 161 C1  OCA A 902CYS-OCA

Place OCA to the model using Coot. When I now use RealSpaceRefinement,
the OCA is placed on top of CYS itself. Coot does not recognise that
OCA-CYS link but why? therefore, I just place OCA at Place it in
*reasonable* position without any overlaps.


All files are located at
https://gist.github.com/ort163/e6b8411f45e5224f7d46fc36c3324e6f


Not all of them.

I tried to reproduce the problem and your dictionary worked OK for me. You will
need to make sure that the ligand is in the same chain as the protein to which 
you
wish to link it (I see from above that that is the case here).



Now in REFMAC, input MTZ,PDB and the CIF file (from jligand). After
refinement, I find that the oxygen in the OCA is pointing wrongly. The
thioester bond is also NOT ideal distance (though density is good).


For me, refining to the wrong map (of course) the resulting bond length is 1.63 
A.

Maybe if I had your files then I would see what you see.



Is there anything wrong with my procedure? *Shouldnt* the refinement
optimise everything in OCA-CYS link?


Yes, it should.

This, by the way, is not how I make links these days. More recently an Acedrg 
interface
has been added to Coot: Extensions -> Modules -> CCP4 -> Acedrg -> Make a Link
You'll need to delete the O2 of course.

Paul.



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[ccp4bb] Open position Structural Biology

2019-01-18 Thread Joris MESSENS
Dear structural biology friends,

I would like to let you know that I have an open position in my lab for a 
postdoctoral researcher.

Please find the vacancy attached.

Kind regards,

Joris





Prof. dr. Joris Messens | Group Leader - Redox Signaling lab - VIB
Exchange Coordinator Department of Bioengineering Sciences - VUB

Center for Redox Biology |  http://redox.vub.ac.be/
Center for Structural Biology, 
VIB
Structural Biology Brussels, Vrije Universiteit 
Brussel

Building E, room 4.16, Pleinlaan 2, 1050 Brussel, Belgium
phone: +32 2 6291992 | fax: +32 2 6291963

e-mail: joris.mess...@vub.be


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vacature structural biology_final.pdf
Description: vacature structural biology_final.pdf


[ccp4bb] Structural Biologist for Malaria

2019-01-18 Thread Wai-Hong Tham
https://www.wehi.edu.au/postdoctoral-fellow-tham-laboratory

An opportunity exists for a Postdoctoral Fellow to join the Infection and 
Immunity Division at the Walter and Eliza Hall Institute to study the molecular 
events that occur during malaria parasite entry into human red blood cells and 
to decipher the structure of invasion complexes.

This is a postdoctoral position for a researcher with structural biology 
experience. The position is available for 3 years in the first instance. Salary 
range ranging from AUD $86,472 - $92,817 and is dependent on qualifications and 
experience.

Application deadline is February 22nd 2019. To apply, please follow the link 
above. For additional questions, please contact A/Prof. Wai-Hong Tham at 
t...@wehi.edu.au. To learn more about our lab: 
https://www.wehi.edu.au/people/wai-hong-tham



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Re: [ccp4bb] unmodeled blobs

2019-01-18 Thread Pearce, N.M. (Nick)
Hi,

I think it's unlikely to be “just one” molecule — It’s much more likely an 
average over multiple states in the crystal (i.e. that site is disordered).
Therefore, IMHO, modelling anything more than a couple of waters is highly 
misleading to anyone interpreting your model afterwards.

If you do try to model it with something, make sure check what the refined 
B-factor is — if they're much larger than the surroundings, then delete what 
you added and leave the site unmodelled because you "cannot determine the 
likely local model based on the quality of the crystallographic data and the 
local chemical environment”.

You don’t need to model every single blob in the crystal — only model the 
clearly resolved ones, or the ones for which you can construct a “sensible" 
model.

Nick

On 18 Jan 2019, at 12:03, Satvik Kumar 
mailto:kumarsatvi...@gmail.com>> wrote:

Dear Community,

I am solving a structure by MR at 2.1 A. I am unable to figure out what to fit 
in the two electron density blobs that I see.

The protein in Tris buffer and DTT was suplemented with sodium pyrophosphate 
before setting up the trays. The crystals were grown using MIB buffer (Malonic 
acid, Imidazole and Boric acid) and PEG 1500.

The images show the 2Fo-Fc electron density contoured at 1.3 sigma.

Can the experts kindly suggest what I can fit in these blobs?

Thanks,
Satvik






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Re: [ccp4bb] Partially occupied C-terminus

2019-01-18 Thread Norbert Straeter
Dear Lea and Andreas,

given the excellent resolution, it might be possible to check the densities to 
decide if hydrolysis is the more likely cause. If the negative density starts 
more or less sharply after the C-terminal carboxylate group of the cleaved 
terminus (i.e. after the peptide nitrogen in the uncleaved part), this would 
favour cleavage as opposed to flexibility. I have never tried this, but maybe 
the refinement programs would allow for a refinement of the occupancies of the 
individual atoms of the last four residues to check if there is a clear drop 
right after the nitrogen atom.

Best wishes,

Norbert



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