[ccp4bb] Postdoctoral positions at Karolinska Institutet, Stockholm

[Luca Jovine]

Fertilization is a fundamental event in the life cycle of all 
sexually-reproducing organisms, and our laboratory at Karolinska Institutet 
(http://jovinelab.org) investigates the molecular basis of egg-sperm 
interaction by integrating biochemistry, X-ray crystallography, cryo-EM and 
deep learning-based protein structure prediction.

We are looking for highly motivated postdoctoral fellows who'd like to focus on 
a topic that is both highly important from a basic science point of view and 
directly relevant for human reproductive medicine.

For more information and to submit an application, please visit:

https://ki.varbi.com/en/what:job/jobID:687262

You are of course always welcome to also contact me directly for informal 
queries.

With best wishes for a successful and inspiring start to the new year, we look 
forward to receiving your application!

Luca

--

Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se<mailto:luca.jov...@ki.se>
W3: http://jovinelab.org




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Re: [ccp4bb] mmciif pdb file editor.

[Luca Jovine]

https://pdbj.org/cif-editor/

HTH,
 Luca

From: CCP4 bulletin board  on behalf of Krishnan Raman 

Reply to: Krishnan Raman 
Date: Wednesday, 30 August 2023 at 15:06
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] mmciif pdb file editor.

You don't often get email from rkrish...@biocryst.com. Learn why this is 
important
How do I edit mmcif files from pdb?  Is there a editor for download from pdb 
website? Thanks krish



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Re: [ccp4bb] Mac M2 chip

[Luca Jovine]

Hi Firdous, for Phaser the solution is simple - just install any nightly 
version of PHENIX > 1.21rc1-5015 (from 
https://phenix-online.org/download/nightly_builds.cgi?show_all=1), and it 
should be fine.
-Luca

From: Firdous Tarique 
Date: Wednesday, 5 July 2023 at 18:33
To: Luca Jovine 
Cc: "CCP4BB@jiscmail.ac.uk" 
Subject: Re: [ccp4bb] Mac M2 chip

Hi

I too have an issue with my latest M2 Mac mini where the Phaser in Phenix runs 
extremely slow in comparision to my intel Mac laptop. I had also posted it on 
the phenix bulletin board but so far did not receive any suggestions how to fix 
it.

By any chance if you guys have the previous email threads where a similar 
problem was fixed and now it is very fast, then can you please share that with 
me?

Best

Firdous

On Wed, 5 Jul 2023, 10:54 Luca Jovine, 
<9d27029f2b4b-dmarc-requ...@jiscmail.ac.uk<mailto:9d27029f2b4b-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Hi Dan,
Please see yesterday's posts on phenixbb (thread 
https://phenix-online.org/pipermail/phenixbb/2023-July/025527.html): there was 
an issue with Phaser, but this has now been fixed in and it runs superfast. 
There may be others, but whatever I've been throwing at my M2 in recent times 
seemed to run just fine (or, if there were issues, these were not M2-specific) 
- including other PHENIX programs, XDS, autoPROC/BUSTER and quite a few CCP4 
programs of course.
HTH,
Luca

-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>> on behalf of 
Daniel Bonsor 
<a71eb7acd5aa-dmarc-requ...@jiscmail.ac.uk<mailto:a71eb7acd5aa-dmarc-requ...@jiscmail.ac.uk>
 
<mailto:a71eb7acd5aa-dmarc-requ...@jiscmail.ac.uk<mailto:a71eb7acd5aa-dmarc-requ...@jiscmail.ac.uk>>>
Reply to: Daniel Bonsor mailto:daniel.bon...@nih.gov> 
<mailto:daniel.bon...@nih.gov<mailto:daniel.bon...@nih.gov>>>
Date: Wednesday, 5 July 2023 at 17:22
To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>" 
mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>>>
Subject: [ccp4bb] Mac M2 chip


[You don't often get email from 
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Dear All,


Has anyone encountered problems with CCP4i/Phenix/XDS/etc on Macs with the M2 
chip? I saw a post from 2020 on the M1 chip, but was curious about if there are 
any issues between the M2 chip and our crystallographic software.


Thanks for any information.


Dan





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Re: [ccp4bb] Mac M2 chip

[Luca Jovine]

Hi Dan,
Please see yesterday's posts on phenixbb (thread 
https://phenix-online.org/pipermail/phenixbb/2023-July/025527.html): there was 
an issue with Phaser, but this has now been fixed in and it runs superfast. 
There may be others, but whatever I've been throwing at my M2 in recent times 
seemed to run just fine (or, if there were issues, these were not M2-specific) 
- including other PHENIX programs, XDS, autoPROC/BUSTER and quite a few CCP4 
programs of course.
HTH,
Luca

-Original Message-
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Daniel Bonsor 
>
Reply to: Daniel Bonsor mailto:daniel.bon...@nih.gov>>
Date: Wednesday, 5 July 2023 at 17:22
To: "CCP4BB@JISCMAIL.AC.UK " 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Mac M2 chip


[You don't often get email from a71eb7acd5aa-dmarc-requ...@jiscmail.ac.uk 
. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification 
 ]


Dear All,


Has anyone encountered problems with CCP4i/Phenix/XDS/etc on Macs with the M2 
chip? I saw a post from 2020 on the M1 chip, but was curious about if there are 
any issues between the M2 chip and our crystallographic software.


Thanks for any information.


Dan





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[ccp4bb] Two postdoctoral openings in structural biochemistry of fertilization at Karolinska Institutet

[Luca Jovine]

Our research group at Karolinska Institutet (http://jovinelab.org) is looking 
for two ambitious postdoctoral fellows who would like to spearhead our future 
steps towards unveiling the molecular basis of gamete recognition and fusion 
through the evolutionary tree.

For more information and to submit an application (deadline 31 July 2023), 
please visit:

Integrative Structural Biology of Fertilization
https://ki.varbi.com/se/what:job/jobID:637984

Biochemistry of Fertilization
https://ki.varbi.com/se/what:job/jobID:639567

Of course, you are also always welcome to contact me directly for informal 
queries.

We look forward to receiving your application!

With best regards,

Luca

--

Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org



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Re: [ccp4bb] Structure prediction - waiting to happen

[Luca Jovine]

This was published just recently and it's really informative:

https://pubmed.ncbi.nlm.nih.gov/36876433/

Best, Luca


From: CCP4 bulletin board  on behalf of Ian Tickle 

Sent: Sunday, April 2, 2023 3:30 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Structure prediction - waiting to happen


All, the first hurdle will of course be whether the AlphaFold model works as a 
MR model, even with the 100% completeness and sequence identity of a bespoke 
model.  The question is what B factors to use or which disordered bits to leave 
out, as that can strongly influence the result (perhaps use info from a similar 
structure).  If it doesn't work in MR that's a pretty good indication that it's 
too far from reality to be useful for looking at detailed interactions.

Does anyone know of a systematic investigation of the success rate of AlphaFold 
models in MR ?  That would be useful ammunition !

Cheers

-- Ian


On Sun, 2 Apr 2023 at 11:51, Gerard Bricogne 
mailto:g...@globalphasing.com>> wrote:
Dear all,

 I think that quoting general viewpoints and statements, however
knowledgeable and respected their authors may be, will only exacerbate the
climate of clashing prejudices between two camps and is bound to sustain a
war of opinions rather than lead to a rational acceptance that something has
changed. The frustration is that one camp (the AlphaFold believers) can be
viewed as in effect preventing experiments that could prove it wrong.

 One way to deal with this obstruction would be to provide, in each
particular case, evidence that the AlphaFold results "do not cut it" as the
sole provider of 3D information within the project at hand. This means that
every grant proposal requesting resources towards a crystallographic
structure solution should document the fact that AlphaFold predictions have
been performed (or, often, looked up in a database of pre-cooked results)
but do not provide the accuracy required for the proposed investigation. If
this step of writing up the "Background" section of the grant actually
delivers a useful result, then everyone will be happy; and if it doesn't,
then the case for the need to allocate resources to solving the structure by
crystallography will be unassailable. In this way, AlphaFold will be a game
changer (we have known that since July 2021) but not a game killer. Savvas
alluded to a similar approach, but it could be made a formal requirement
acceptable to both proposers and reviewers, who would then both be dealing
with the situation in a scientific rather than dogmatic manner.


 With best wishes,

  Gerard.

--
On Sat, Apr 01, 2023 at 06:54:33PM +, Goldman, Adrian wrote:
> I think this is all true - and I’ve been putting things like this into my 
> (failing) grants - but I get the dispiriting sense that the medics think (to 
> borrow a line from hamlet) “the applicant doth protest too much methinks”.
>
> Well if as per James H today ;), we deposit coordinates to 1sf, alphafold 
> will be just fine.
>
> Of course the coordinates won’t be of any use to anybody, but the pictures 
> will be nice.
>
> Adrian
>
> Sent from my iPhone
>
> > On 1 Apr 2023, at 21:39, Randy John Read 
> > mailto:rj...@cam.ac.uk>> wrote:
> >
> > There’s also this preprint with Tom Terwilliger as lead author: 
> > https://www.biorxiv.org/content/10.1101/2022.11.21.517405v1.
> >  The title is “AlphaFold predictions: great hypotheses but no match for 
> > experiment”.
> >
> > Best wishes,
> >
> > Randy
> >
> >> On 1 Apr 2023, at 18:18, Savvas Savvides 
> >> <9d24f7f13e09-dmarc-requ...@jiscmail.ac.uk>
> >>  wrote:
> >>
> >> Dear Rams,
> >>
> >> I salute you for sharing this.
> >>
> >> Just a week ago, I also received a remark along these lines on a declined 
> >> grant application. The remark was the only unfavourable point, which 
> >> suggested that it must have weighed disproportionally towards the negative 
> >> outcome. This was a two-stage evaluation process and the grant was cut in 
> >> stage-1 where it was evaluated by a small group of evaluators, none of 
> >> whom was a structural biologist/biochemist. Stage-2 would have involved 
> >> peer review by international experts.
> >>
> >> Despite my initial disbelief about what this remark might have caused and 
> >> upon reflection, I realized that it might be time to become proactive in 
> >> future applications in anticipation of the apparent growing trend towards 
> >> such remarks and perceptions.
> >>
> >> I think that a 

[ccp4bb] Postdoctoral position in structural biology of fertilization at Karolinska Institutet, Stockholm

[Luca Jovine]

Our group has an opening for an enthusiastic postdoctoral fellow to investigate 
the molecular basis of gamete interaction using cryo-EM/X-ray crystallography.

Join our team to shed light on a biological event that is not only fundamental 
from a basic science point of view, but has also major implications for the 
future of human reproductive medicine!

The position is available immediately, with application deadline 31 August 2021.

For detailed information and to apply, please see:

https://ki.varbi.com/en/what:job/jobID:402203/type:job/where:4/apply:1

Looking forward to receiving your application,

Luca

--
Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition
SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org
--




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Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Luca Jovine]

Dear Dale and Robbie,

I agree with your comments! But may I stir back the discussion to the original 
issue, which is that one-residue N-glycans are now treated differently from 
multi-residue N-glycans (although they are both covalently linked to a protein 
chain)? This inconsistency is independent of the file format…

Best, Luca

On 4 Dec 2020, at 18:30, Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:

Dear Dale,

Yes, good point. Let's stop bending over backwards to come up with faux PDB 
compatibility and focus on making mmCIF better.

There are struct_conn records that describe the linkages. This is enough to 
reconstruct the connectivity. There is an ongoing debate on how to capture the 
restraints for such linkages. But at least this can in principle be captured in 
mmCIF whereas this is pretty much undoable in PDB format.

Cheers,
Robbie

On 4 Dec 2020 18:01, Dale Tronrud 
mailto:de...@daletronrud.com>> wrote:

This suggestion violates a basic principle of data base theory.  A
single data item cannot encode two pieces of information.  The whole
structure of CIF falls apart if this is done.

Does the new PDB convention contain a CIF record of the link that
bridges between the protein chain and the, now separated, glycan chain?
  If not, I think this is the principle failing of their new scheme.

Dale Tronrud

On 12/4/2020 12:06 AM, Tristan Croll wrote:
> To go one step further: in large, heavily glycosylated multi-chain complexes 
> the assignment of a random new chain ID to each glycan will lead to headaches 
> for people building visualisations using existing viewers, because it loses 
> the easy name-based association of glycan to parent protein chain. A 
> suggestion: why not take full advantage of the mmCIF capability for 
> multi-character chain IDs, and name them by appending characters to the 
> parent chain ID? Using chain A as an example, perhaps the glycans could 
> become Ag1, Ag2, etc.?
>
>> On 4 Dec 2020, at 07:48, Luca Jovine 
>> mailto:luca.jov...@ki.se>> wrote:
>>
>> CC: pdb-l
>>
>> Dear Zhijie and Robbie,
>>
>> I agree with both of you that the new carbohydrate chain assignment 
>> convention that has been recently adopted by PDB introduces confusion, not 
>> just for PDB-REDO but also - and especially - for end users.
>>
>> Could we kindly ask PDB to improve consistency by either assigning a 
>> separate chain to all covalently attached carbohydrates (regardless of 
>> whether one or more residues have been traced), or reverting to the old 
>> system (where N-/O-glycans inherited the same chain ID of the protein to 
>> which they are attached)? The current hybrid solution hardly seems optimal...
>>
>> Best regards,
>>
>> Luca
>>
>>> On 3 Dec 2020, at 20:17, Robbie Joosten 
>>> mailto:robbie_joos...@hotmail.com>> wrote:
>>>
>>> Dear Zhijie,
>>>
>>> In generally I like the treatment of carbohydrates now as branched 
>>> polymers. I didn't realise there was an exception. It makes sense for 
>>> unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as 
>>> these might change during model building or, in my case, carbohydrate 
>>> rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.
>>>
>>> Cheers,
>>> Robbie
>>>
>>>> -Original Message-
>>>> From: CCP4 bulletin board 
>>>> mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Zhijie 
>>>> Li
>>>> Sent: Thursday, December 3, 2020 19:52
>>>> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
>>>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
>>>> PDB -- N-glycans are now separate chains if more than one residue
>>>>
>>>> Hi all,
>>>>
>>>> I was confused when I saw mysterious new glycan chains emerging during
>>>> PDB deposition and spent quite some time trying to find out what was
>>>> wrong with my coordinates.  Then it occurred to me that a lot of recent
>>>> structures also had tens of N-glycan chains.  Finally I realized that this
>>>> phenomenon is a consequence of this PDB policy announced here in July.
>>>>
>>>>
>>>> For future depositors who might also get puzzled, let's put it in a short
>>>> sentence:  O- and N-glycans are now separate chains if it they contain more
>>>> than one residue; single residues remain with the protein chain.
>>>>
>>>>
>>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcar

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Luca Jovine]

Yes Tristan, that would be even better - also because such an Ag1, Ag2,… system 
could conveniently fall back on a single-character chain A, when generating 
legacy PDB format files from the mmCIF ones.
Exactly for the reason that you pointed out, personally I do not understand the 
logic of assigning a different chain ID to covalently attached glycans (or any 
other covalent post-translational modification, for that matter). Aren't 
residue IDs enough to make it clear that such residues are not amino acids?
-Luca

> On 4 Dec 2020, at 09:06, Tristan Croll  wrote:
> 
> To go one step further: in large, heavily glycosylated multi-chain complexes 
> the assignment of a random new chain ID to each glycan will lead to headaches 
> for people building visualisations using existing viewers, because it loses 
> the easy name-based association of glycan to parent protein chain. A 
> suggestion: why not take full advantage of the mmCIF capability for 
> multi-character chain IDs, and name them by appending characters to the 
> parent chain ID? Using chain A as an example, perhaps the glycans could 
> become Ag1, Ag2, etc.?
> 
>> On 4 Dec 2020, at 07:48, Luca Jovine  wrote:
>> 
>> CC: pdb-l
>> 
>> Dear Zhijie and Robbie,
>> 
>> I agree with both of you that the new carbohydrate chain assignment 
>> convention that has been recently adopted by PDB introduces confusion, not 
>> just for PDB-REDO but also - and especially - for end users.
>> 
>> Could we kindly ask PDB to improve consistency by either assigning a 
>> separate chain to all covalently attached carbohydrates (regardless of 
>> whether one or more residues have been traced), or reverting to the old 
>> system (where N-/O-glycans inherited the same chain ID of the protein to 
>> which they are attached)? The current hybrid solution hardly seems optimal...
>> 
>> Best regards,
>> 
>> Luca
>> 
>>> On 3 Dec 2020, at 20:17, Robbie Joosten  wrote:
>>> 
>>> Dear Zhijie,
>>> 
>>> In generally I like the treatment of carbohydrates now as branched 
>>> polymers. I didn't realise there was an exception. It makes sense for 
>>> unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as 
>>> these might change during model building or, in my case, carbohydrate 
>>> rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.
>>> 
>>> Cheers,
>>> Robbie
>>> 
>>>> -Original Message-
>>>> From: CCP4 bulletin board  On Behalf Of Zhijie Li
>>>> Sent: Thursday, December 3, 2020 19:52
>>>> To: CCP4BB@JISCMAIL.AC.UK
>>>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
>>>> PDB -- N-glycans are now separate chains if more than one residue
>>>> 
>>>> Hi all,
>>>> 
>>>> I was confused when I saw mysterious new glycan chains emerging during
>>>> PDB deposition and spent quite some time trying to find out what was
>>>> wrong with my coordinates.  Then it occurred to me that a lot of recent
>>>> structures also had tens of N-glycan chains.  Finally I realized that this
>>>> phenomenon is a consequence of this PDB policy announced here in July.
>>>> 
>>>> 
>>>> For future depositors who might also get puzzled, let's put it in a short
>>>> sentence:  O- and N-glycans are now separate chains if it they contain more
>>>> than one residue; single residues remain with the protein chain.
>>>> 
>>>> 
>>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediationdata=04%7C01%7Cluca.jovine%40ki.se%7Ca3fed8eed9d94a481d6808d8982b731f%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426659666244613%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=BqPiPeexG0nLhUmaih2Bq8ppjkX%2F%2BbLP4SoBGL4u5%2Fw%3Dreserved=0
>>>> 
>>>> "Oligosaccharide molecules are classified as a new entity type, branched,
>>>> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF
>>>> category introduced to define the type of branching
>>>> (_pdbx_entity_branch.type) . "
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> I found the differential treatment of single-residue glycans and 
>>>> multi-residue
>>>> glycans not only bit lack of aesthetics but also misleading.  When a 
>>>> structure
>>>> contains both NAG-NAG... and single NAG on N-gly

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Luca Jovine]

CC: pdb-l

Dear Zhijie and Robbie,

I agree with both of you that the new carbohydrate chain assignment convention 
that has been recently adopted by PDB introduces confusion, not just for 
PDB-REDO but also - and especially - for end users.

Could we kindly ask PDB to improve consistency by either assigning a separate 
chain to all covalently attached carbohydrates (regardless of whether one or 
more residues have been traced), or reverting to the old system (where 
N-/O-glycans inherited the same chain ID of the protein to which they are 
attached)? The current hybrid solution hardly seems optimal...

Best regards,

Luca

> On 3 Dec 2020, at 20:17, Robbie Joosten  wrote:
>
> Dear Zhijie,
>
> In generally I like the treatment of carbohydrates now as branched polymers. 
> I didn't realise there was an exception. It makes sense for unlinked 
> carbohydrate ligands, but not for N- or O-glycosylation sites as these might 
> change during model building or, in my case, carbohydrate rebuilding in 
> PDB-REDO powered by Coot. Thanks for pointing this out.
>
> Cheers,
> Robbie
>
>> -Original Message-
>> From: CCP4 bulletin board  On Behalf Of Zhijie Li
>> Sent: Thursday, December 3, 2020 19:52
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
>> PDB -- N-glycans are now separate chains if more than one residue
>>
>> Hi all,
>>
>> I was confused when I saw mysterious new glycan chains emerging during
>> PDB deposition and spent quite some time trying to find out what was
>> wrong with my coordinates.  Then it occurred to me that a lot of recent
>> structures also had tens of N-glycan chains.  Finally I realized that this
>> phenomenon is a consequence of this PDB policy announced here in July.
>>
>>
>> For future depositors who might also get puzzled, let's put it in a short
>> sentence:  O- and N-glycans are now separate chains if it they contain more
>> than one residue; single residues remain with the protein chain.
>>
>>
>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediationdata=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=mBrkCJECFpZyCih4kOCcCvLT1GzQHxD5GD7bZDI9s1s%3Dreserved=0
>>
>> "Oligosaccharide molecules are classified as a new entity type, branched,
>> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF
>> category introduced to define the type of branching
>> (_pdbx_entity_branch.type) . "
>>
>>
>>
>>
>>
>> I found the differential treatment of single-residue glycans and 
>> multi-residue
>> glycans not only bit lack of aesthetics but also misleading.  When a 
>> structure
>> contains both NAG-NAG... and single NAG on N-glycosylation sites, it might
>> be because of lack of density for building more residues, or because that
>> some of the glycosylation sites are now indeed single NAGs (endoH etc.)
>> while some others are not cleaved due to accessibility issues.Leaving 
>> NAGs
>> on the protein chain while assigning NAG-NAG... to a new chain, feels like
>> suggesting something about their true oligomeric state.
>>
>>
>> For example, for cryoEM structures, when one only builds a single NAG at a
>> site does not necessarily mean that the protein was treated by endoH. In
>> fact all sites are extended to at least tri-Man in most cases. Then why
>> keeping some sites associated with the protein chain while others kicked
>> out?
>>
>> Zhijie
>>
>>
>>
>> 
>>
>> From: CCP4 bulletin board  on behalf of John
>> Berrisford 
>> Sent: Thursday, July 9, 2020 4:39 AM
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB
>>
>>
>> Dear CCP4BB
>>
>> PDB data will shortly incorporate a new data representation for
>> carbohydrates in PDB entries and reference data that improves the
>> Findability and Interoperability of these molecules in macromolecular
>> structures. In order to remediate and improve the representation of
>> carbohydrates across the archive, the wwPDB has:
>>
>> *standardized Chemical Component Dictionary nomenclature
>> following IUPAC-IUBMB recommendations
>> *provided uniform representation for oligosaccharides
>> *adopted Glycoscience-community commonly used linear descriptors
>> using community tools
>> *annotated glycosylation sites in PDB structures
>>
>> Starting July 29, 2020, users will be able to access the improved data via 
>> FTP
>> or wwPDB partner websites. Detailed information about this project is
>> available at the wwPDB website
>> 

[ccp4bb] Postdoctoral positions in structural biology of fertilization at Karolinska Institutet and Umeå University

[Luca Jovine]

gical event that 
is not only fundamental from a basic science point of view, but has also major 
implications for the future of human reproductive medicine!

With best wishes,

Luca

--
Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se<mailto:luca.jov...@ki.se>
W3: http://jovinelab.org
--






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[ccp4bb] Postdoctoral studies in structural biology of fertilization, Karolinska Institutet

[Luca Jovine]

Our research group at Karolinska Institutet 
(http://jovinelab.org<http://jovinelab.org/>) is looking for a postdoctoral 
fellow to investigate the molecular mechanism of egg-sperm interaction at 
fertilization by single-particle cryo-EM.

The position, funded by a long-term grant from the Knut and Alice Wallenberg 
foundation, will benefit from a close collaboration with Alexey Amunts 
laboratory at SciLifeLab (https://www.scilifelab.se/researchers/alexey-amunts/) 
as well as easy access to local cryo-EM facilities (Stockholm node of the 
Cryo-EM Swedish National Facility 
(https://www.scilifelab.se/facilities/cryo-em/) and KI 3D-EM 
(https://ki.se/en/research/3d-em)) that together include 3 x Titan Krios with 
K3 detectors, a Talos Arctica with K2 and a Talos L120C with Ceta-D. Joining 
our groups will thus provide a unique opportunity to build upon the strengths 
of two complementary labs and state-of-the-art technology, in order to tackle 
one of the most fundamental questions in biology and understand how life begins.

Candidates must hold (or be about to receive) a Ph.D. degree and have 
significant hands-on experience in structural biology. Although proven 
experience in single-particle cryo-EM and knowledge of helical reconstruction 
will constitute an advantage, excellent candidates with experience in X-ray 
crystallography and a strong interest in learning cryo-EM will also be taken 
into consideration. Additionally, previous experience in mammalian cell 
expression as well as purification and biochemical characterization of 
glycoproteins will be considered an asset. At least one first author paper in a 
high-quality international peer-reviewed journal, fluency in English (both 
written and oral), good team spirit and a very strong personal drive to excel 
in science are required.

For more information about this position and to submit an application through 
the KI MyNetwork recruitment system (deadline 3 March 2020), please visit:

https://ki.varbi.com/se/what:job/jobID:313955

We look forward to receiving your application!

With best wishes,

Luca

----
Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se<mailto:luca.jov...@ki.se>
W3: http://jovinelab.org




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kommer att behandla dina personuppgifter. Här finns information om hur KI 
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Re: [ccp4bb] Live stream of CCP4 Study Weekend?

[Luca Jovine]

From another tweet of just a few sec ago:

The live stream of this years #ccp4sw is now available at 
sas.stfc.ac.uk/p.jsp?i=2<http://sas.stfc.ac.uk/p.jsp?i=2>. Check out previous 
proceedings in @ActaCrystD at bit.ly/2CdGU2n<http://bit.ly/2CdGU2n> - papers 
from last year's meeting are appearing at bit.ly/2H5Nr51<http://bit.ly/2H5Nr51> 
pic.twitter.com/6tLLc53Cnh<http://pic.twitter.com/6tLLc53Cnh>

-Luca

----
Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Innovative Medicine
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se<mailto:luca.jov...@ki.se>
W3: http://jovinelab.org


On 9 Jan 2019, at 10:08, Tim Gruene 
mailto:tim.gru...@psi.ch>> wrote:

Hi Mark,

Seriously on Twitter only?
Sic transit gloria mundi.

Best,
Tim

On Wednesday, January 9, 2019 9:50:02 AM CET Mark J van Raaij wrote:
Good morning and happy 2019,

There was an announcement on Twitter yesterday:
https://twitter.com/ccp4_mx <https://twitter.com/ccp4_mx>
(second post as of writing this)

pointing here:
https://stfc.ukri.org/about-us/our-purpose-and-priorities/requesting-informa
tion-from-uk-research-and-innovation/webinars/

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/

On 9 Jan 2019, at 09:39, Kay Diederichs 
wrote:

Good morning everybody,

I haven't seen any announcement about the streaming of the Study Weekend
... I'd be really interested to watch and listen!

Any hints?

thanks,

Kay



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--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
Forschungsstrasse 111
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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Re: [ccp4bb] Non-specific disulfides in a secreted protein

[Luca Jovine]

Dear Tomas,

Along Radu’s comments, here’s another paper well worth looking into:

   Halff EF, Versteeg M, Brondijk TH, Huizinga EG
   When less becomes more: optimization of protein expression in HEK293-EBNA1 
cells using plasmid titration - a case study for NLRs
   https://www.ncbi.nlm.nih.gov/pubmed/24680733

We have also observed this phenomenon several times, and simply diluting the 
expression construct did indeed help in such cases.

Good luck!

Luca


Luca Jovine, Ph.D.
Professor of Structural Biology & EMBO Member
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Innovative Medicine
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se<mailto:luca.jov...@ki.se>
W3: http://jovinelab.org


On 14 Dec 2018, at 17:55, Tomas Malinauskas 
mailto:tomas.malinaus...@gmail.com>> wrote:

Dear All,

we are purifying a small secreted protein from conditioned media and
have a rather unusual problem.

It is a small ectodomain (~11 kDa, pI ~6, His-tagged) of the type 1
transmembrane receptor, crystal structures are known (of the protein
that was produced in E.coli and refolded; we are secreting the same
protein using mammalian cells) so we can design reasonable constructs.
The protein is expressed and secreted by transiently transfected
HEK293T cells that work very well for other ectodomains and
extracellular proteins in our hands (PMID 17001101). The target
protein has 10 cysteines that form 5 disulfides in the crystal
structure (of E.coli-expressed and refolded protein), there should be
no free cysteines and no non-specific disulfides. Unfortunately, once
the protein is secreted, it forms non-specific dimers and higher-order
oligomers in the media (standard DMEM/2% FBS) before purification
(confirmed by Western blotting under non-reducing conditions). Using
0.5 mM DTT during SEC gives a nice monomeric peak (however, the
protein suffers as suggested by weaker interactions with its binding
partners). We don't understand how a secreted protein (which passes
trafficking quality control in the cell) with a known disulfide
pattern forms non-specific disulfide linked oligomers in the
extracellular media. We tried expressing it at 37 C and 30 C, and have
sequenced our constructs (plasmids) multiple times.

If anyone has seen this kind of problem and successfully solved it
(purified homogeneous crystallisation quality protein), please let us
know if possible. I thank you for your help.

Best wishes,
Tomas


Dr. Tomas Malinauskas
University of Oxford
Wellcome Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
to...@strubi.ox.ac.uk<mailto:to...@strubi.ox.ac.uk>
tomas.malinaus...@gmail.com




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[ccp4bb] REMINDER - Postdoc position in structural biology of TGF-beta superfamily coreceptors, Karolinska Institutet (deadine 3 September 2017)

[Luca Jovine]

Dear all,

The research group of Luca Jovine at Karolinska Institutet has an opening for a 
postdoctoral fellow to study protein complexes involving TGF-beta superfamily 
coreceptors, with a focus on endoglin/CD105 - a key human glycoprotein involved 
in hereditary hemorrhagic telangiectasia type 1 (HHT1), preeclampsia and tumor 
angiogenesis. Parallel studies are also ongoing on a number of structurally 
related biological systems mediating fertilization as well as protection from 
bacterial infection.

For further information about our laboratory and recent examples, please see 
http://jovinelab.org<http://jovinelab.org/> and:

Saito et al. Cell Rep. 19(9):1917–28 (2017) [ 
http://www.cell.com/cell-reports/fulltext/S2211-1247(17)30636-8 ]

Raj et al. Cell 169(7):1315–26 (2017) [ 
http://www.cell.com/cell/fulltext/S0092-8674(17)30594-9 ]

Bokhove et al. Proc. Natl. Acad. Sci. USA 113(6):1552-7 (2016) [ 
http://www.pnas.org/content/113/6/1552.long ]

The Department of Biosciences and Nutrition of Karolinska Institutet has 
state-of-the-art equipment for protein expression and purification, sample 
characterization (microscale thermophoresis, SEC-MALS) and in house X-ray/EM 
data collection (Rigaku Compact HomeLab with PILATUS 200K detector; 
http://ki.se/en/bionut/center-for-high-resolution-electron-microscopy-em). 
Frequent access to various synchrotron sites, as well as access to the newly 
established Cryo-EM Swedish National Facility 
(https://www.scilifelab.se/facilities/cryo-em/), are also available. With their 
close integration of academic and clinical research, KI and the Center for 
Innovative Medicine (CIMED; http://cimed.ki.se<http://cimed.ki.se/> ) - to 
which our group also belongs - offer a highly international and collaborative 
environment for biomedical studies.

Candidates should have (or will be soon awarded) a PhD degree and must have 
significant experience in studying protein-protein interactions, both 
biochemically and using either X-ray crystallography or single-particle 
cryo-EM. Proven experience with the latter and/or protein expression in 
eukaryotic cells will be a significant advantage. At least one first author 
paper in a high quality international peer-reviewed journal, fluency in English 
(both written and oral), good team spirit and a very strong personal drive to 
excel in science are required.

For more information about this position and to submit an application through 
the KI MyNetwork recruitment system by 3 September, please see:

 https://ki.mynetworkglobal.com/en/what:job/jobID:156827

With best wishes,

Luca

----
Luca Jovine, Ph.D.
Professor of Structural Biology
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Innovative Medicine
Halsovagen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se<mailto:luca.jov...@ki.se>
W3: http://jovinelab.org<http://jovinelab.org/>

[ccp4bb] Postdoc position in structural biology of TGF-beta superfamily coreceptors, Karolinska Institutet

[Luca Jovine]

Dear all,

The research group of Luca Jovine at Karolinska Institutet has an opening for a 
postdoctoral fellow to study protein complexes involving TGF-beta superfamily 
coreceptors, with a focus on endoglin/CD105 - a key human glycoprotein involved 
in hereditary hemorrhagic telangiectasia type 1 (HHT1), preeclampsia and tumor 
angiogenesis. Parallel studies are also ongoing on a number of structurally 
related biological systems mediating fertilization as well as protection from 
bacterial infection.

For further information about our laboratory and recent examples, please see 
http://jovinelab.org and:

Saito et al. Cell Rep. 19(9):1917–28 (2017) [ 
http://www.cell.com/cell-reports/fulltext/S2211-1247(17)30636-8 ]

Raj et al. Cell 169(7):1315–26 (2017) [ 
http://www.cell.com/cell/fulltext/S0092-8674(17)30594-9 ]

Bokhove et al. Proc. Natl. Acad. Sci. USA 113(6):1552-7 (2016) [ 
http://www.pnas.org/content/113/6/1552.long ]

The Department of Biosciences and Nutrition of Karolinska Institutet has 
state-of-the-art equipment for protein expression and purification, sample 
characterization (microscale thermophoresis, SEC-MALS) and in house X-ray/EM 
data collection (Rigaku Compact HomeLab with PILATUS 200K detector; 
http://ki.se/en/bionut/center-for-high-resolution-electron-microscopy-em). 
Frequent access to various synchrotron sites, as well as access to the newly 
established Cryo-EM Swedish National Facility 
(https://www.scilifelab.se/facilities/cryo-em/), are also available. With their 
close integration of academic and clinical research, KI and the Center for 
Innovative Medicine (CIMED; http://cimed.ki.se ) - to which our group also 
belongs - offer a highly international and collaborative environment for 
biomedical studies.

Candidates should have (or will be soon awarded) a PhD degree and must have 
significant experience in studying protein-protein interactions, both 
biochemically and using either X-ray crystallography or single-particle 
cryo-EM. Proven experience with the latter and/or protein expression in 
eukaryotic cells will be a significant advantage. At least one first author 
paper in a high quality international peer-reviewed journal, fluency in English 
(both written and oral), good team spirit and a very strong personal drive to 
excel in science are required.

For more information about this position and to submit an application through 
the KI MyNetwork recruitment system, please see:

 https://ki.mynetworkglobal.com/en/what:job/jobID:156827

With best wishes,

Luca


Luca Jovine, Ph.D.
Professor of Structural Biology
Karolinska Institutet
Department of Biosciences and Nutrition & Center for Innovative Medicine
Halsovagen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se<mailto:luca.jov...@ki.se>
W3: http://jovinelab.org<http://jovinelab.org/>

Re: [ccp4bb] Crystallisation of a minority fraction monomers

[Luca Jovine]

Sure - crystallization selects what packs, which may constitute a very minor 
fraction of what you set up drops with. 1DUH is an example...
-Luca

 On Apr 8, 2015, at 15:08, Sebastiaan Werten 
 sebastiaan.wer...@uni-greifswald.de wrote:
 
 Dear all,
 
 we are currently working on a protein that is known to exist in a 
 monomer-dimer equilibrium. At the high concentrations used for 
 crystallisation assays, the dimer is predominant and the monomer practically 
 undetectable.
 
 Nevertheless, one of the crystal forms that we have obtained contains the 
 monomeric species, not the dimer.
 
 I was wondering if anyone is aware of similar (published) cases, and if the 
 phenomenon as such has been discussed in detail anywhere?
 
 I did literature searches but so far couldn't find anything.
 
 Any pointers would be much appreciated!
 
 Best wishes,
 
 Sebastiaan Werten.
 

[ccp4bb] Postdoctoral position at Karolinska Institutet

[Luca Jovine]

A postdoctoral position is available immediately on structural studies of 
protein-protein interactions at the core of the human Hedgehog signaling 
pathway, as part of a long-term collaboration between the laboratories of Rune 
Toftgård and Luca Jovine at the Department of Biosciences and Nutrition  
Center for Innovative Medicine at Karolinska Institutet.  

The Department of Biosciences and Nutrition has state-of-the-art equipment for 
protein expression in E. coli, insect and mammalian cells, purification, 
crystallization and in house X-ray diffraction data collection (including 
Mosquito robotics and a brand new Rigaku CompactHome Lab system with a Pilatus 
P200K detector). Frequent access to synchrotron sites and excellent 
computational facilities are also available. With their close integration of 
academic, clinical and industrial research, KI and the Center for Innovative 
Medicine offer a highly international and collaborative environment for 
biomedical studies.

To qualify, applicants must hold a Ph.D. or a foreign qualification deemed 
equivalent to a doctoral degree. The candidate must have significant experience 
in studying protein-protein interactions using both biochemical and 
crystallographic approaches. Previous experience with protein expression in 
mammalian cells will be a distinct advantage. Familiarity with SAXS data 
collection and processing will also be a plus. At least one first author paper 
in a high quality international peer-reviewed journal, fluency in english and a 
strong personal drive to excel in science are required.

For additional information and to apply please visit the Karolinska Institutet 
NetRecruiter system (deadline 29 June):

https://ki.mynetworkglobal.com/en/what:job/jobID:38811/where:4/

Further information may also be found here:

http://ki.se/people/rutoft

http://jovinelab.org

Cherry et al. Acta Cryst. D 69:2563-2579 (2013)
http://www.ncbi.nlm.nih.gov/pubmed/24311597

Teglund  Toftgard Biochim. Biophys. Acta 1805:181-208 (2010)
http://www.ncbi.nlm.nih.gov/pubmed/20085802

With best regards,

Luca Jovine  Rune Toftgård


Luca Jovine, Ph.D.
Professor of Structural Biology  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Halsovagen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org

Re: [ccp4bb] Molecular cloning software for linux

[Luca Jovine]

On Feb 8, 2013, at 05:16 , Theresa Hsu wrote:

Dear all

Is there any good molecular cloning software for linux? It should read plasmid 
constructs in Genbank format, do assembly of plasmid sequencing results, 
display the sequencing trace and highlight regions where there are mutations 
based on relative QV values, has a list of built-in restriction enzyme 
recognition sequences and also has a database holding all the constructs.

It does not have to be free as long as the price is reasonable for single users.

Thank you.

Theresa

Dear Theresa,

You may also want to look into SerialCloner:

http://serialbasics.free.fr/Serial_Cloner.html

We use the OS X version and it's great (and free)!

Best,

Luca


Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.semailto:luca.jov...@ki.se
W3: http://jovinelab.org

[ccp4bb] Postdoctoral position at Karolinska Institutet

[Luca Jovine]

As part of a long-term collaboration between the laboratories of Luca Jovine 
and Rune Toftgård at the Department of Biosciences and Nutrition  the Center 
for Biosciences of Karolinska Institutet, a postdoctoral position is available 
from January 2013 on structural studies of protein-protein interactions at the 
core of the human Hedgehog signaling pathway.

For further information, please see: http://jovinelab.org; 
http://ki.se/ki/jsp/polopoly.jsp?d=22596a=84967l=en ; Teglund  Toftgard 
Biochim. Biophys. Acta 1805:181-208 (2010); Briscoe  Rohatgi EMBO Rep. 
13:580-583 (2012).

The Department of Biosciences and Nutrition has state-of-the-art equipment for 
protein expression, purification and in house X-ray and EM data collection; 
frequent access to multiple synchrotron sites and excellent computational 
facilities are also available. With their close integration of academic, 
clinical and industrial research, KI and the Center for Biosciences offer a 
highly international and collaborative environment for biomedical studies.

The candidate must have significant experience in studying protein-protein 
interactions using both biochemical and crystallographic approaches. Previous 
experience with protein expression in mammalian and/or insect cells will be an 
advantage. Familiarity with SAXS data colection and processing will also be a 
plus. At least one first author paper in a high quality international 
peer-reviewed journal, fluency in english and a strong personal drive to excel 
in science are required.

Please apply by 16 December via the Karolinska Institutet NetRecruiter system: 
https://ki.netrecruiter.se/en/what:job/jobID:15431/where:4/

With best regards,

Luca Jovine  Rune Toftgård


Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.semailto:luca.jov...@ki.se
W3: http://jovinelab.org

Re: [ccp4bb] Various OSes and Crystallography

[Luca Jovine]

Yes, you can define 3 buttons on a MagicMouse with this free software:

http://magicprefs.com/

or simply attach a mouse with 3 real buttons...

-Luca


Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org


On Aug 9, 2012, at 17:29 , Jacob Keller wrote:

 Are there no closet windows-users on this list to respond? Shall we have a 
 coming-out day?
 
 Question--do macs have multiple-button mice? Last I checked they had only one 
 button, which seemed almost criminal.
 
 JPK
 
 On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre q...@hotmail.fr wrote:
 Le 09/08/2012 16:58, Nat Echols a écrit :
 
 On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
 j-kell...@fsm.northwestern.edu wrote:
 one. Are there any really reasonable arguments for preferring Mac over
 windows (or linux) with regard to crystallography? What can Mac/Linux do
 that windows cannot (especially considering that there is Cygwin)? What
 wonderful features am I missing?
 Mac vs. Linux: mostly a matter of personal preference, but I agree
 with Graeme.  Most programs run equally well on either - with Coot a
 partial exception, apparently due to problems with the X11
 implementation (but once you get used to these, it's not a big deal).
 
 Windows, on the other hand, simply doesn't support the full range of
 modern crystallography software.  And in my experience, it has
 crippling flaws that mean some programs will always work better on
 Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
 scientific computing unless you need to run an application that won't
 work on any other OS, and as far as I know there isn't a single
 (macromolecular) crystallography program that falls into this
 category.
 
 -Nat
 
 
 
 I have seen that in the last Mac Os, X11 have been removed... But can still 
 be used with some package installation.
 
 
 
 -- 
 ***
 Jacob Pearson Keller
 Northwestern University
 Medical Scientist Training Program
 email: j-kell...@northwestern.edu
 ***

Re: [ccp4bb] Off-topic His-Antibody

[Luca Jovine]

Our experience essentially agrees with QIAGEN's claim that you can detect 
proteins in the low nanogram range, i.e. 1-2 ng... so not a major improvement 
over your current antibody, I'm afraid. They also sell an HRP conjugate version:


http://www.qiagen.com/products/protein/detection/qiaexpressdetectionsystem/penta-hishrpconjugatekit.aspx

but we have never tried it... and now I'll stop here, otherwise you'll start 
thinking I own QIAGEN shares :-)

Luca

On Jun 26, 2012, at 09:54 , Juha Vahokoski wrote:

 I have been using an HRP conjugated antibody from Thermo that can detect 
 maybe 3-8ng of HisTagged protein from insect  cell lysates. Performance is 
 ok, but with the sensitivity I am not so happy with.
 
 How is the sensitivity with the Qiagen antibody? How many picograms you need 
 for a clear band?
 
 Does anyone know a good HRP conjugated antibody?
 
 Regards,
 Juha
 
 On 26 June 2012 06:59, Luca Jovine luca.jov...@ki.se wrote:
 We routinely use BSA-free anti-5His mAb from QIAGEN, and it works just fine 
 (at least using media and lysates of both insect and mammalian cells):
 

 http://www.qiagen.com/products/protein/detection/qiaexpressdetectionsystem/penta-hisantibody.aspx
 
 Good luck,
 
 Luca
 
 
 Luca Jovine, Ph.D.
 Assistant Professor  EMBO Young Investigator
 Karolinska Institutet
 Department of Biosciences and Nutrition  Center for Biosciences
 Hälsovägen 7, SE-141 83 Huddinge, Sweden
 Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
 E-mail: luca.jov...@ki.se
 W3: http://jovinelab.org
 
 
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of D Bonsor 
 [dbon...@ihv.umaryland.edu]
 Sent: Monday, June 25, 2012 23:33
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Off-topic His-Antibody
 
 Are there any good antibodies for His-tags on the market. I have never used 
 one and I heard several stories that they were poor and not worth the money, 
 over the past few years. The only post I could find on the BB was from 2008. 
 Have His-Antibodies improved or are they still rubbish.
 
 
 
 
 
 
 -- 
 Genius may have its limitations, but stupidity is not thus handicapped. 
 -Elbert Hubbard
 *

Re: [ccp4bb] Off-topic His-Antibody

[Luca Jovine]

We routinely use BSA-free anti-5His mAb from QIAGEN, and it works just fine (at 
least using media and lysates of both insect and mammalian cells):


http://www.qiagen.com/products/protein/detection/qiaexpressdetectionsystem/penta-hisantibody.aspx

Good luck,

Luca


Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of D Bonsor 
[dbon...@ihv.umaryland.edu]
Sent: Monday, June 25, 2012 23:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off-topic His-Antibody

Are there any good antibodies for His-tags on the market. I have never used one 
and I heard several stories that they were poor and not worth the money, over 
the past few years. The only post I could find on the BB was from 2008. Have 
His-Antibodies improved or are they still rubbish.

Re: [ccp4bb] Off topic: His-tag purification

[Luca Jovine]

…alternatively, depending on what is the source of your protein, you might have 
to dialyze the (concentrated) sample before applying it to IMAC. Insect cell 
media, in particular, can be pretty good at stripping off Ni2+ from IMAC 
supports. 

HTH, Luca

Re: [ccp4bb] is codon optimization worth it?

[Luca Jovine]

Have a look at this paper:

http://www.ncbi.nlm.nih.gov/pubmed?term=18289875

the bottom line appears to be that, in most cases, co-transforming with 
plasmids expressing rare tRNAs is just as good as codon optimizing the gene for 
your protein of interest. In addition to the financial aspects already touched 
upon by Tassos, we even had cases where codon optimizing a gene actually 
completely abolished its expression, presumably by causing havoc at the mRNA 
level. This obviously won't happen if you co-express rare codon tRNAs...

HTH, Luca
 

Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 57 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org


On Sep 30, 2011, at 19:13 , Segelke, Brent W. wrote:

 Is there a general consensus that this is true? I’ve heard exactly the 
 opposite, i.e., that codon optimization rarely gives you dramatically 
 improved yields of soluble protein. Are there any published studies on this 
 topic? This seems like something that might come out of one of the SG centers.
  
 Brent
  
 From: Anastassis Perrakis [mailto:abba...@gmail.com] On Behalf Of Anastassis 
 Perrakis
 Sent: Friday, September 30, 2011 10:08 AM
 To: Segelke, Brent W.
 Cc: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] is codon optimization worth it?
  
 Well, codon optimization is not really trouble, it's money. The money are 
 worth it usually anyway, since the optimized genes are easy to clone if you 
 make many constructs out of one gene, as you better do anyway ... Compared 
 with downstream expenses, optimized genes are these days almost always worth 
 the trouble...
  
 A. 
 
 Sent from my iPad
 
 On 30 Sep 2011, at 19:02, Segelke, Brent W. segel...@llnl.gov wrote:
 
 To me, the key question would seem to be, if I can’t win them all, how many 
 more do I win if I go to the trouble?
  
 Brent
  
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Keys
 Sent: Friday, September 30, 2011 8:29 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] is codon optimization worth it?
  
 We codon optimised a poorly expressed gene from neisseria meningitides based 
 on a codon usage table derived from the Welch (etal, 2009) paper below. The 
 optimisation is specifically for overexpression in BL21 (DE3). The optimised 
 gene increased protein expression by at least a factor of 10, and changed 
 (somewhat reduced) the degradation pattern we observed. Unfortunately it 
 didn't do anything to improve the folding (ie. we ended up with lots of 
 half-folded, semi-soluble protein).
 
 With other neisserial derived proteins we have had an almost undetectable 
 effect.
 
 You can't win 'em all.
 
 Cheers,
 Tim
 
 Design Parameters to Control Synthetic Gene Expression in Escherichia coli
 Welch et al, PlosONE 2009
 
 
 
 
 Medizinische Hochschule Hannover
 Zelluläre Chemie, OE 4330
 Zentrum Biochemie
 Carl-Neubergstr. 1
 30625 Hannover
 
 
 
 -Original Message-
 From: CCP4 bulletin board on behalf of Patrick Loll
 Sent: Fri 30.09.2011 16:49
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] is codon optimization worth it?
 
 Has anyone encountered a case in which a construct with the native sequence 
 expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding 
 construct with a codon-optimized sequence expressed well? (The gene in 
 question is from cerevesiae)
 Thanks,
 Pat
 
 ---
 Patrick J. Loll, Ph. D. 
 Professor of Biochemistry  Molecular Biology
 Director, Biochemistry Graduate Program
 Drexel University College of Medicine
 Room 10-102 New College Building
 245 N. 15th St., Mailstop 497
 Philadelphia, PA  19102-1192  USA
 
 (215) 762-7706
 pat.l...@drexelmed.edu
 
 
 

Re: [ccp4bb] Off topic: vector map editing and DNA sequence alignment software

[Luca Jovine]

Hi Florian,

Have a look at Serial Cloner - it's free, runs on OS X, Linux and Windows, and 
is really quite powerful - including the ability to export single or multiple 
sequences to FASTA format text files (however, it can only align two sequences 
at the time I'm afraid):

http://serialbasics.free.fr/Serial_Cloner.html

HTH, Luca


Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 83 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org


On 27 Sep 2011, at 17:42 , Florian Schmitzberger wrote:

 Dear All,
 
 What type of software are people commonly using these days for vector/plasmid 
 map editing, making/visualizing vector maps, and aligning (small to medium 
 size) DNA sequencing data? Preferably, it should not be too expensive and be 
 able to write text files, readable by other programs.
 
 I am familiar with VectorNTI, which is great for vector visualization and 
 editing; but I find it somewhat expensive. Sequencher seems good to quickly 
 align DNA sequences (such as from DNA sequencing) with templates, but is not 
 free. I have been using ApE for while for alignments, but aligning many 
 sequences is more cumbersome than in Sequencher; I have not tested if 
 Sequencher is good at visualizing and editing plasmid maps.
 
 Ideally, I would like to have a single program for both purposes (vector 
 editing and DNA sequence comparison). Does something like that exist? What 
 are the alternatives to above programs?
 
 Thank you in advance.
 
 Florian
 
 ---
 Florian Schmitzberger, PhD
 Biological Chemistry and Molecular Pharmacology
 Harvard Medical School
 250 Longwood Avenue, Seeley G. Mudd 123 
 Boston, MA 02115, US
 Tel: 001 617 432 5603
 
 
 
 
 
 
 
 
 
 
 
 
 

Re: [ccp4bb] Setup pymol in Mac OS X 10.7

[Luca Jovine]

On Sep 21, 2011, at 14:57 , Xiaoguang Xue wrote:

 And It is impossible to install MacPorts and Fink at the same time.

...not at all! We have both Fink and MacPorts installed on our machines (in /sw 
and /opt/local, respectively), and they happily coexist.

HTH, Luca


Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 57 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org

Re: [ccp4bb] metal binds?

[Luca Jovine]

On Mar 25, 2011, at 08:39 , Careina Edgooms wrote:

 Dear ccp4 users
 
 I would like to know, is there a way to check that heavy metal has bound to 
 crystals before I take it to synchrotron which is far away?
 
 thanks
 Careina

Here's a useful reference:

Boggon TJ, Shapiro L
Screening for phasing atoms in protein crystallography
Structure. 2000 Jul 15;8(7):R143-9
http://www.ncbi.nlm.nih.gov/pubmed/10903954

HTH,

Luca


Luca Jovine, Ph.D.
Assistant Professor  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 57 Huddinge, Sweden
Voice: +46.(0)8.524-81136  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org

[ccp4bb] Postdoctoral position in structural biology of fertilization proteins at Karolinska Institutet

[Luca Jovine]

A postdoctoral position is available immediately at Karolinska Institutet to 
investigate the 
structure of mammalian proteins that mediate egg-sperm interaction at the 
beginning of 
fertilization.

The project will combine X-ray crystallographic and electron microscopic 
studies, performed 
in collaboration with the group of Prof. Hans Hebert. Thus, the position is 
particularly suited 
to a protein crystallographer who would like to expand his/her knowledge to 
single particle 
cryo-EM, or viceversa. Moreover, previous experience in protein expression 
using 
mammalian cells will be a significant advantage.

For further information, please see http://jovinelab.org as well as Monne' et 
al. Nature 
456:653-657 (2008) (http://www.ncbi.nlm.nih.gov/pubmed/19052627)

The KI Department of Biosciences and Nutrition, located just outside Stockholm, 
has state-
of-the-art equipment for protein expression, purification and in house X-ray 
and EM data 
collection; frequent access to synchrotron sites and excellent computational 
facilities are also 
available. With their close integration of academic, clinical and industrial 
research, KI and the 
Department of Biosciences and Nutrition offer a highly international and 
collaborative 
environment for biomedical studies.

Highly motivated candidates are encouraged to apply by e-mailing a curriculum 
vitae, 
summary of research experience and interests, and names and contact information 
for two 
references to Luca Jovine (luca.jov...@ki.se).

Please note that, in order to be eligible for this position, candidates should 
be non-Swedish 
citizens who have obtained a doctorate or the equivalent outside Sweden no 
longer than 3 
years ago. Deadline for application is 30 June 2010.


Luca Jovine, Ph.D.
Group Leader  EMBO Young Investigator
Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
Hälsovägen 7, SE-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6081-501
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org

[ccp4bb] Postdoctoral position in protein crystallography at Karolinska Institutet

[Luca Jovine]

POSTDOCTORAL FELLOWSHIP IN PROTEIN CRYSTALLOGRAPHY AT KAROLINSKA INSTITUTET

As part of a collaboration between the laboratories of Rune Toftgård and Luca 
Jovine at the 
KI Department of Biosciences and Nutrition and the Center for Biosciences, a 
postdoctoral 
position is immediately available on structural studies of key players in the 
Hedgehog 
signaling pathway.

The Department of Biosciences and Nutrition has state-of-the-art equipment for 
protein 
expression, purification and in house X-ray data collection; frequent access to 
synchrotron 
sites and excellent computational facilities are also available. With their 
close integration of 
academic, clinical and industrial research, KI and the Center for Biosciences 
offer a highly 
international and collaborative environment for biomedical studies.

Highly motivated candidates with experience in protein expression (particularly 
in insect 
and/or mammalian cells), purification, crystallization and structure 
determination, are 
encouraged to apply by e-mailing a curriculum vitae, summary of research 
experience and 
interests, and names and contact information for two references to Luca Jovine 
(luca.jov...@ki.se). Please note that, in order to be eligible for this 
scholarship, candidates 
should be non-Swedish citizens who have obtained a doctorate or the equivalent 
outside 
Sweden. Deadline for application is 1 October 2009.


Luca Jovine, Ph.D.
Group Leader, Protein Crystallography Unit
Karolinska Institutet
Department of Biosciences and Nutrition
Hälsovägen 7, SE-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org

Re: [ccp4bb] generating omit maps

[Luca Jovine]

Subject: generating omit maps
From: Kathleen Frey [EMAIL PROTECTED]
Reply-To: Kathleen Frey [EMAIL PROTECTED]
Date: Wed, 10 Dec 2008 10:30:47 -0500

Hi Everyone,

Can anyone tell me a relatively easy way to generate an omit density  
map for
a ligand? I know that CNS can do this, but I was wondering if  
there's a CCP4

related program to generate omit maps.
Thanks,
Kathleen

Hi Kathleen,

Not CCP4, I know, but this can be done very easily in PHENIX:

   http://www.phenix-online.org/documentation/autobuild.htm#anch159

HTH,

Luca


Luca Jovine, Ph.D.
Group Leader, Protein Crystallography Unit
Karolinska Institutet
Department of Biosciences and Nutrition
Hälsovägen 7, SE-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290
E-mail: [EMAIL PROTECTED]
W3: http://jovinelab.org

[ccp4bb] Postdoctoral position in protein crystallography at Karolinska Institutet

[Luca Jovine]

POSTDOCTORAL POSITION IN PROTEIN CRYSTALLOGRAPHY AT KAROLINSKA  
INSTITUTET


As part of a collaboration between the laboratories of Rune Toftgård  
and Luca Jovine at the KI Department of Biosciences and Nutrition at  
Novum, a postdoctoral position is immediately available to study the  
structure of a key player within the Hedgehog signaling pathway.  
Crystals and initial maps are available.


The Department of Biosciences and Nutrition has state-of-the-art  
equipment for protein expression, purification and in house X-ray  
data collection; frequent access to synchrotron sites and excellent  
computational facilities are also available. With its close  
integration of academic, clinical and industrial research, Novum  
offers a highly international and collaborative environment for  
biomedical studies.


Highly motivated candidates with experience in protein  
crystallisation and structure determination are encouraged to apply  
by e-mailing a curriculum vitae, summary of research experience and  
interests, and names and contact information for two references to  
Luca Jovine ([EMAIL PROTECTED]) and Rune Toftgård  
([EMAIL PROTECTED]).



Luca Jovine, Ph.D.
Karolinska Institutet
Department of Biosciences and Nutrition
Hälsovägen 7, S-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290
E-mail: [EMAIL PROTECTED]
W3: http://www.ki.se

[ccp4bb] Postdoctoral position in protein crystallography at Karolinska Institutet (correction)

[Luca Jovine]

Apologies for sending this again, but I forgot to specify an important detail 
about the position: in 
order to be eligible for this scholarship, candidates should be non-Swedish 
citizens who have 
obtained a doctorate or the equivalent outside Sweden.


POSTDOCTORAL POSITION IN PROTEIN CRYSTALLOGRAPHY AT KAROLINSKA INSTITUTET 

As part of a collaboration between the laboratories of Rune Toftgård and Luca 
Jovine at the KI 
Department of Biosciences and Nutrition at Novum, a postdoctoral position is 
immediately available 
to study the structure of a key player within the Hedgehog signaling pathway. 
Crystals and initial 
maps are available. 

The Department of Biosciences and Nutrition has state-of-the-art equipment for 
protein 
expression, purification and in house X-ray data collection; frequent access to 
synchrotron sites and 
excellent computational facilities are also available. With its close 
integration of academic, clinical 
and industrial research, Novum offers a highly international and collaborative 
environment for 
biomedical studies.

Highly motivated candidates with experience in protein crystallisation and 
structure determination 
are encouraged to apply by e-mailing a curriculum vitae, summary of research 
experience and 
interests, and names and contact information for two references to Luca Jovine 
([EMAIL PROTECTED]) 
and Rune Toftgård ([EMAIL PROTECTED]). 

 
Luca Jovine, Ph.D. 
Karolinska Institutet 
Department of Biosciences and Nutrition 
Hälsovägen 7, S-141 57 Huddinge, Sweden 
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290 
E-mail: [EMAIL PROTECTED] 
W3: http://www.ki.se 
 

[ccp4bb] C3b, validation, deposition diffraction images

[Luca Jovine]

Dear fellow crystallographers,

I'd like to add yet another piece to the ongoing discussion about C3b  
 Co., and the importance of submitting diffraction images in  
addition to structure factors.


Partly in response to some letters that had just appeared in the same  
journal, on 16 July together with some colleagues I sent a one-page  
comment to the editor of Science exactly on this matter. You can read  
it here:


http://www.biosci.ki.se/groups/ljo/tmp/diffraction_images.pdf

As you will see, what we wrote very much mirrors the general opinions  
that have been expressed on ccp4bb during the last couple of days.  
However, Science declined to publish our letter; on 2 August we  
therefore sent it to Nature Structural and Molecular Biology, which  
after a few days also deemed it unsuitable for the journal. Uhm!


I will not elaborate as to why such an issue should not concern these  
journals, considering how many crystallographic structures have been  
debated recently. But I felt compelled to bring this up again in this  
occasion, since it is quite clear that we (almost) all agree on the  
fact that availability of raw images would improve things. And  
indeed, this was the take-home message of the communication in Nature  
by Janssen/Read/Brünger/Gros. So I have a simple suggestion: if we  
are convinced that this is an idea worth pursuing, why don't we come  
up with a common statement concerning this issue, undersigned by all  
that agree on the need of making available raw diffraction images in  
addition to structure factors? This could be sent to RCSB, to editors  
of scientific journals publishing structure papers, as well as -  
perhaps - to an open-access journal, so that it would also be  
formally published and made available for free to the whole  
community. Hopefully, the latter might help bring the issue to the  
attention of funding bodies (after all, someone would eventually have  
to pay for the required storage media).


One last (but important) point: as it should hopefully be obvious  
from the tone of our original letter, our main reason for suggestion  
image submission was not at all to start checking everyone else's  
data in search for faults! In fact, it was exactly the opposite: we  
wanted to help saving information, not destroying it. Should we  
decide to go ahead and make our voice heard as a community, it would  
be nice if we kept this disposition...


Awaiting comments!

With best regards,

Luca

PS: Since we are talking about fabricated - oops, suspect -  
structures, I thought I should provide some evidence that our  
submissions actually took place:


http://www.biosci.ki.se/groups/ljo/tmp/science.pdf
http://www.biosci.ki.se/groups/ljo/tmp/nsmb.pdf

See, they actually happened :-)


PS2: My colleagues E. Morgunova and R. Ladenstein are currently away,  
so I am the only person to be blamed for the above considerations.



Luca Jovine, Ph.D.
Karolinska Institutet
Department of Biosciences and Nutrition
Hälsovägen 7, S-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290
E-mail: [EMAIL PROTECTED]
W3: http://www.ki.se/

Re: [ccp4bb] MarView on OSX

[Luca Jovine]

On 25 Jan 2007, at 23:15, Michael McCormick wrote:


Hi Everyone,

Has anyone ever run the .mccd diffraction image viewing/editing  
program MarView on Mac OSX?  You can download it free form  
MarResearch (http://www.marresearch.com/), and I can get it to  
execute fine in Linux, but not on my Mac.  The main problem is I  
can't get the marView file to execute from a terminal, from X11,  
or simply by double-clicking on it in the Finder.  MarResearch  
claims that it runs in OSX X11, but thier tech support had no  
suggestions as how to get it running exactly.  I have the same  
problem with EMPR in OSX.  Maybe this is a unix path issue  
(?)...  Any help anyone can provide will be greatly appreciated.


MSM


Hi Michael,

It runs OK on my machine! But, did you make the file executable  
before running it? Try:


OSX chmod 755 marView
OSX  open /Applications/Utilities/X11.app
OSX ./marView

HTH,

Luca

-
Luca Jovine, Ph.D.
Karolinska Institutet
Department of Biosciences and Nutrition
Center for Structural Biochemistry (CSB)
Hälsovägen 7, S-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290
E-mail: [EMAIL PROTECTED]
W3: http://www.biosci.ki.se/groups/ljo/
-