Re: [ccp4bb] why does Coot ignore CONECT?

[Paul Emsley]

On 04/11/2019 17:06, Pavel Mader wrote:

Hi Paul,

thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids, 
the side chains of which are linked by click chemistry... I know how to make modified amino acids that will 
make peptide bonds with their neighbors in the polypeptide chain, but I don't know how to make a covalent 
link between side chains of amino acids say No. 3 and 12 for example (of a 15 AA long chain).


OK...

I was trying 
to solve the issue by making a CONECT record in the pdb file,


That's not the way to do it.

but Coot ignored it. 


Indeed.

LINK "sort of" worked, 


But not really, right?

but it was not possible to control the geometry (bond length and angles), often the real space refinement 
simply "explodes" probably in a attempt to avoid clashes. 


Yeah...

My current workaround is to make a cif file for the whole 15 AA long polypeptide 


Blimey!

(the bonds and angles now behave more or less as expected), but I don't 
consider this as a good general practice for building long polypeptide chains...


Hmm! Your scepticism is well placed, I feel.

The way to do it is to use the Coot (Modules -> CCP4 -> Acedrg Link) or CCP4i2 interface (Ligands -> Make a 
Link (?)) so that Acedrg is used to make a link between the specified atoms of the specified residue types 
(monomers).


Note: to self: make a YouTube vid to explain how to do this...

Paul.



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Re: [ccp4bb] why does Coot ignore CONECT?

[Pavel Mader]

Hello Eleanor,




We tried to follow your suggestion.



The atoms to be linked were 1.46A apart in the input pdb model and we ran 10
cycles of refinement in Refmac with the "make link between" option chosen in
either "defined in the file or residues are close". After the refinement we
saw the linkage as dotted line and the distance between the atoms was 2.2A
(in other words they moved apart instead of forming a covalent bond).



Thanks in advance for any further suggestions,


Pavel






-- Původní e-mail --
Od: Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Komu: CCP4BB@JISCMAIL.AC.UK
Datum: 4. 11. 2019 12:16:38
Předmět: Re: [ccp4bb] why does Coot ignore CONECT?
"

What does refmac do if you feed it the coordinates with side chains close 
enough to bond? In some cases it makes a full link dictionary with bonds 
angles planes etc. But can coot read such a dictionary entry?





On Mon, 4 Nov 2019 at 17:06, Pavel Mader mailto:mader.pa...@seznam.cz)> wrote:

"
Hi Paul,

thank you for your answer. My problem is that I am building a cyclic peptide
with non-standard amino acids, the side chains of which are linked by click
chemistry... I know how to make modified amino acids that will make peptide
bonds with their neighbors in the polypeptide chain, but I don't know how to
make a covalent link between side chains of amino acids say No. 3 and 12 for
example (of a 15 AA long chain). I was trying to solve the issue by making a
CONECT record in the pdb file, but Coot ignored it. LINK "sort of" worked,
but it was not possible to control the geometry (bond length and angles), 
often the real space refinement simply "explodes" probably in a attempt to
avoid clashes. My current workaround is to make a cif file for the whole 15
AA long polypeptide (the bonds and angles now behave more or less as
expected), but I don't consider this as a good general practice for building
long polypeptide chains...

Thanks in advance for any hints guiding me in the right direction.

Pavel
-- Původní e-mail --
Od: Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk)
>
Komu: CCP4BB@JISCMAIL.AC.UK(mailto:CCP4BB@jiscmail.ac.uk)
Datum: 1. 11. 2019 21:16:11
Předmět: Re: [ccp4bb] why does Coot ignore CONECT?
"On 01/11/2019 20:17, Pavel Mader wrote:
> Hello,

Hello.

>
> I have a question, can anyone explain, why does Coot not display a
covalent bond manually specified by
> CONECT line in a pdb file?

Because I have never thought them necessary. Using SSBOND, LINK and residue
dictionaries seemed to me to
cover the bases for which CONECT would be used.

Paul.

 

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[ccp4bb] RapiData at SSRL 2020 reminder - just over a week left to apply!

[Smith, Clyde]

Hi all,

A reminder that there is only a week left to apply for a place at the RapiData 
2020 @ SSRL workshop. Applications close the middle of this month, November 15 
2019. 

The workshop will be held from March 30 - April 4  2020 on the SLAC campus in 
Menlo Park, California. The course will comprise hands-on experiments at the 
SSRL beamlines, software tutorials, and lectures on the following topics: 
Specimen preparation, data collection strategies, X-ray light sources, X-ray 
detectors, data reduction, structure solution by MAD, SAD and molecular 
replacement, complementary methods (spectroscopy, small angle scattering and 
cryoEM).

Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use 
the links on the "registration" page to apply for the course. Successful 
applicants will be notified early in December 2019 and invited to register at 
that time. A limited amount of travel support funding may be available.

We look forward to seeing you all out in sunny California in March 2020!

Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) 
sru...@slac.stanford.edu 
jwier...@slac.stanford.edu 
csm...@slac.stanford.edu



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Re: [ccp4bb] why does Coot ignore CONECT?

[Eleanor Dodson]

What does refmac do if you feed it the coordinates with side chains close
enough to bond? In some cases it makes a full link dictionary with bonds
angles planes etc. But can coot read such a dictionary entry?

On Mon, 4 Nov 2019 at 17:06, Pavel Mader  wrote:

> Hi Paul,
>
> thank you for your answer. My problem is that I am building a cyclic
> peptide with non-standard amino acids, the side chains of which are linked
> by click chemistry... I know how to make modified amino acids that will
> make peptide bonds with their neighbors in the polypeptide chain, but I
> don't know how to make a covalent link between side chains of amino acids
> say No. 3 and 12 for example (of a 15 AA long chain). I was trying to solve
> the issue by making a CONECT record in the pdb file, but Coot ignored it.
> LINK "sort of" worked, but it was not possible to control the geometry
> (bond length and angles), often the real space refinement simply "explodes"
> probably in a attempt to avoid clashes. My current workaround is to make a
> cif file for the whole 15 AA long polypeptide (the bonds and angles now
> behave more or less as expected), but I don't consider this as a good
> general practice for building long polypeptide chains...
>
> Thanks in advance for any hints guiding me in the right direction.
>
> Pavel
> -- Původní e-mail --
> Od: Paul Emsley 
> Komu: CCP4BB@JISCMAIL.AC.UK
> Datum: 1. 11. 2019 21:16:11
> Předmět: Re: [ccp4bb] why does Coot ignore CONECT?
>
> On 01/11/2019 20:17, Pavel Mader wrote:
> > Hello,
>
> Hello.
>
> >
> > I have a question, can anyone explain, why does Coot not display a
> covalent bond manually specified by
> > CONECT line in a pdb file?
>
> Because I have never thought them necessary. Using SSBOND, LINK and
> residue dictionaries seemed to me to
> cover the bases for which CONECT would be used.
>
> Paul.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
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Re: [ccp4bb] why does Coot ignore CONECT?

[Pavel Mader]

Hi Paul,

thank you for your answer. My problem is that I am building a cyclic peptide
with non-standard amino acids, the side chains of which are linked by click
chemistry... I know how to make modified amino acids that will make peptide
bonds with their neighbors in the polypeptide chain, but I don't know how to
make a covalent link between side chains of amino acids say No. 3 and 12 for
example (of a 15 AA long chain). I was trying to solve the issue by making a
CONECT record in the pdb file, but Coot ignored it. LINK "sort of" worked,
but it was not possible to control the geometry (bond length and angles), 
often the real space refinement simply "explodes" probably in a attempt to
avoid clashes. My current workaround is to make a cif file for the whole 15
AA long polypeptide (the bonds and angles now behave more or less as
expected), but I don't consider this as a good general practice for building
long polypeptide chains...

Thanks in advance for any hints guiding me in the right direction.

Pavel
-- Původní e-mail --
Od: Paul Emsley 
Komu: CCP4BB@JISCMAIL.AC.UK
Datum: 1. 11. 2019 21:16:11
Předmět: Re: [ccp4bb] why does Coot ignore CONECT?
"On 01/11/2019 20:17, Pavel Mader wrote:
> Hello,

Hello.

>
> I have a question, can anyone explain, why does Coot not display a
covalent bond manually specified by
> CONECT line in a pdb file?

Because I have never thought them necessary. Using SSBOND, LINK and residue
dictionaries seemed to me to
cover the bases for which CONECT would be used.

Paul.

 

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Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

[Jrh Gmail]

Dear Michael
The Rmerge in the strong intensity bin of 0.079 is untypically high it seems to 
me. 
Were the diffraction images underexposed? 
Best wishes
John

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 



> On 3 Nov 2019, at 23:19, Michael Jarva  wrote:
> 
> 
> Hi CCP4BB,
> 
> I have some unusual crystal diffraction data I'd like to get your input on.
> 
> Almost a year ago I shot some small rods sticking out of a loop, so basically 
> no liquid around them - using the microfocus MX2 beamline at the australian 
> synchrotron, collected on an EIGER 16M detector.
> 
> The crystals diffracted weakly and was seemingly not viable at first glance 
> because of high Rmerge/Rpims. See the aimless summary at the bottom of this 
> post. This seemed to stem from a low spot intensity at low resolutions 
> (I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.
> 
> Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 
> 8.02 Å^2.
> 
> Density maps looked great and the build refined easily enough (R/Rfree 
> 0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is 
> lower than any other structure deposited in that resolution bin. Furthermore, 
> the molprobity score is 0.83, and overall real-space correlation CC is 0.855.
> 
> So my question is, can I feel comfortable depositing this? 
> 
> best regards
> Michael
> 
> Chosen Solution:space group P 1 21 1
> Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
> Number of batches in file:   1659
> The data do not appear to be twinned, from the L-test
> Overall InnerShell OuterShell
> Low resolution limit   41.34 41.34  2.49
> High resolution limit   2.40  8.98  2.40
> 
> Rmerge  (within I+/I-) 0.231 0.084 0.782
> Rmerge  (all I+ and I-)0.266 0.099 0.983
> Rmeas (within I+/I-)   0.323 0.118 1.091
> Rmeas (all I+ & I-)0.317 0.118 1.167
> Rpim (within I+/I-)0.225 0.084 0.759
> Rpim (all I+ & I-) 0.171 0.063 0.623
> Rmerge in top intensity bin0.079- - 
> Total number of observations   19901   362  2067
> Total number unique 6054   126   611
> Mean((I)/sd(I))  2.7   4.6   1.0
> Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
> Completeness98.6  98.2  97.3
> Multiplicity 3.3   2.9   3.4
> Mean(Chi^2) 0.48  0.33  0.50
> 
> Anomalous completeness  81.7  92.2  75.1
> Anomalous multiplicity   1.5   1.8   1.9
> DelAnom correlation between half-sets -0.003 0.041 0.045
> Mid-Slope of Anom Normal Probability   0.704   - -  
> 
> The anomalous signal appears to be weak so anomalous flag was left OFF
> 
> Estimates of resolution limits: overall
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.67A 
>from Mn(I/sd) >  2.00: limit =  2.87A 
> 
> Estimates of resolution limits in reciprocal lattice directions:
>   Along0.96 a* - 0.28 c*
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
> resolution
>   Along k axis
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.86A 
>   Along   -0.17 a* + 0.99 c*
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.98A 
> 
> Anisotropic deltaB (i.e. range of principal components), A^2:  8.62
> 
> Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00
> Space group: P 1 21 1
> Average mosaicity:   0.05
> 
> Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   
> 0.00   0.00
> 
> 
> 
> 
> Michael Jarva, PhD
> ACRF Chemical Biology Division
> The Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade
> Parkville Victoria 3052
> Australia
> Phone: +61 3 9345 2493 
> Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/
> The ACRF Chemical Biology Division is supported by the
> Australian Cancer Research Foundation
> 
> ___ 
> 
> The information in this email is confidential and intended solely for the 
> addressee.
> You must not disclose, forward, print or use it without the permission of the 
> sender.
> 
> The Walter and Eliza Hall Institute 

Re: [ccp4bb] crysalis pro from rigaku

[Almudena Ponce Salvatierra]

Dear all,

indeed, crysalis can import multiple image formats. I was having trouble
with finding a dummy parameter file that would allow me to import my
dataset. Once this was done, a real parameter file was created with the
info from my dataset's image headers.

Thank you very much for your input.

Best,

Almu

El lun., 4 nov. 2019 a las 16:47, SHEPARD William (<
william.shep...@synchrotron-soleil.fr>) escribió:

> Hi Everybody,
>
> I am also interested in this, but the current version of CrystalisPro that
> we have does not read HDF5 data files from EIGER detectors. Currently we
> convert to CBF, but Crystalis still has issues… Does anybody have a
> sure-fire script to convert HDF5 to Esperanto?
>
> Cheers,
> Bill
>
>
> De : Roger Rowlett 
> Répondre à : Roger Rowlett 
> Date : Monday 4 November 2019 16:02
> À : "CCP4BB@JISCMAIL.AC.UK" 
> Objet : Re: [ccp4bb] crysalis pro from rigaku
>
> The current version of CrysalisPro will directly import several image
> formats, or you can convert images to Esperanto format to import. The
> latter is a bit clumsy but does work.
>
> __
> Roger Rowlett
>
> On Mon, Nov 4, 2019, 9:54 AM Almudena Ponce Salvatierra <
> maps.fa...@gmail.com> wrote:
>
>> Dear all,
>>
>> does any of you have experience with using Crysalis Pro software from
>> Rigaku with data that were not collected on a Rigaku instrument?
>>
>> Any help will be much appreciated.
>>
>> All the best,
>>
>> Almudena
>>
>> --
>>
>> 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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Re: [ccp4bb] crysalis pro from rigaku

[SHEPARD William]

Hi Everybody,

I am also interested in this, but the current version of CrystalisPro that we 
have does not read HDF5 data files from EIGER detectors. Currently we convert 
to CBF, but Crystalis still has issues… Does anybody have a sure-fire script to 
convert HDF5 to Esperanto?

Cheers,
Bill


De : Roger Rowlett mailto:rrowl...@colgate.edu>>
Répondre à : Roger Rowlett mailto:rrowl...@colgate.edu>>
Date : Monday 4 November 2019 16:02
À : "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Objet : Re: [ccp4bb] crysalis pro from rigaku

The current version of CrysalisPro will directly import several image formats, 
or you can convert images to Esperanto format to import. The latter is a bit 
clumsy but does work.

__
Roger Rowlett

On Mon, Nov 4, 2019, 9:54 AM Almudena Ponce Salvatierra 
mailto:maps.fa...@gmail.com>> wrote:
Dear all,

does any of you have experience with using Crysalis Pro software from Rigaku 
with data that were not collected on a Rigaku instrument?

Any help will be much appreciated.

All the best,

Almudena



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Re: [ccp4bb] crysalis pro from rigaku

[Roger Rowlett]

The current version of CrysalisPro will directly import several image
formats, or you can convert images to Esperanto format to import. The
latter is a bit clumsy but does work.

__
Roger Rowlett

On Mon, Nov 4, 2019, 9:54 AM Almudena Ponce Salvatierra <
maps.fa...@gmail.com> wrote:

> Dear all,
>
> does any of you have experience with using Crysalis Pro software from
> Rigaku with data that were not collected on a Rigaku instrument?
>
> Any help will be much appreciated.
>
> All the best,
>
> Almudena
>
> --
>
> 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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[ccp4bb] crysalis pro from rigaku

[Almudena Ponce Salvatierra]

Dear all,

does any of you have experience with using Crysalis Pro software from
Rigaku with data that were not collected on a Rigaku instrument?

Any help will be much appreciated.

All the best,

Almudena



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Re: [ccp4bb] Sodium Ion Binding?

[Sarah Bowman]

Hi Jacob,

An additional technique to identify sodium is microPIXE, which can be used for 
elemental mapping. I'm not sure if the sulfur signal would be strong enough to 
be quantitative.

A ref: https://www.cell.com/structure/pdf/S0969-2126(00)88335-5.pdf

Hope that helps,
Sarah

Sarah EJ Bowman, PhD

Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center
Research Associate Professor, Department of Biochemistry, University at Buffalo

Research Webpage
www.getacrystal.org

sbow...@hwi.buffalo.edu



From: CCP4 bulletin board  on behalf of Artem Evdokimov 

Reply-To: Artem Evdokimov 
Date: Sunday, November 3, 2019 at 9:20 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: Sodium Ion Binding?

Hi Jacob

Not the easiest task... Based on past experience your major issue will be the 
incredible abundance of sodium ions in everything.

So assuming you have high quality sodium free solutions and are willing to work 
exclusively in plastic, quartz or fused silica - here are a few thoughts:

1. Na-22 isotope binding. An oldie but goodie.
2. Sodium-reactive dye equilibrium (see e.g. reference I put at the end)
3. Flame or ion coupled plasma spectroscopy. Very nice to do given the 
marvellous sodium band.
4. Sodium selective glass electrode (requires more solution of your analyte 
than the other methods)

Overall the key component to these methods is your ability to displace the 
sodium with something else prior to measuring the effect of titration the ion 
back. Isotopic Na is easier in this regard - but at a cost...

Hope this helps.

Artem

https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-6-556

https://www.google.com/url?sa=t=web=j=http://clinchem.aaccjnls.org/content/clinchem/24/4/580.full.pdf=2ahUKEwis5KL_vM_lAhXCmuAKHY2cAVQQFjAFegQIARAB=AOvVaw0Yhz23Yr_ulB85MDQspIFl=1572833723049


On Sun, Nov 3, 2019, 20:41 Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:
Dear Crystallographers,

Does anyone know of a good biophysical way to identify or quantify sodium ion 
binding to a protein, besides crystallography and ITC? Is this possible with 
SPR, perhaps? Mass spec? Gel shifts? Examples would be greatly appreciated!

All the best,

Jacob Keller


+
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
+

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Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

[Eleanor Dodson]

My first check would be to inspect the data processing plots -
Wilson Plot? Is it normal? predicted B factor of 8 - why?

Then the plot from  refmac  and  v resolution?
Is there a scaling abnormality?

B of 8 is surprisingly low for that resolution  but maybe the crystals just
did not have enough oomph to go to their limit..

Eleanor




On Mon, 4 Nov 2019 at 07:00, Anastassis Perrakis  wrote:

> Dear Michael,
>
> Exactly because the B factor is only 8, the intensity as function of
> resolution is droping really slowly, and thus the I/sigI 4.7 at low
> resolution drops so slowly to 1.0.
>
> I would almost bet you have a low solvent content.
>
> The data are fine imo.
>
> Best,
>
> Tassos
>
> On Nov 4, 2019, at 0:18, Michael Jarva  wrote:
>
> Hi CCP4BB,
>
> I have some unusual crystal diffraction data I'd like to get your input on.
>
> Almost a year ago I shot some small rods sticking out of a loop, so
> basically no liquid around them - using the microfocus MX2 beamline at the
> australian synchrotron, collected on an EIGER 16M detector.
>
> The crystals diffracted weakly and was seemingly not viable at first
> glance because of high Rmerge/Rpims. See the aimless summary at the bottom
> of this post. This seemed to stem from a low spot intensity at low
> resolutions (I/sd(I)=4.6), but since the CC1/2 was fine I went with it
> anyway.
>
> Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors,
> 8.02 Å^2.
>
> Density maps looked great and the build refined easily enough (R/Rfree 
> 0.1939/0.2259)
> with a mean B-factor of 19.85, which according to phenix is lower than any
> other structure deposited in that resolution bin. Furthermore, the
> molprobity score is 0.83, and overall real-space correlation CC is 0.855.
>
> So my question is, can I feel comfortable depositing this?
>
> best regards
> Michael
>
> Chosen Solution:space group P 1 21 1
> Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
> Number of batches in file:   1659
> The data do not appear to be twinned, from the L-test
> Overall InnerShell OuterShell
>
> Low resolution limit   41.34 41.34  2.49
>
> High resolution limit   2.40  8.98  2.40
>
>
> Rmerge  (within I+/I-) 0.231 0.084 0.782
>
> Rmerge  (all I+ and I-)0.266 0.099 0.983
>
> Rmeas (within I+/I-)   0.323 0.118 1.091
>
> Rmeas (all I+ & I-)0.317 0.118 1.167
>
> Rpim (within I+/I-)0.225 0.084 0.759
>
> Rpim (all I+ & I-) 0.171 0.063 0.623
>
> Rmerge in top intensity bin0.079- -
>
> Total number of observations   19901   362  2067
>
> Total number unique 6054   126   611
>
> Mean((I)/sd(I))  2.7   4.6   1.0
>
> Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
>
> Completeness98.6  98.2  97.3
>
> Multiplicity 3.3   2.9   3.4
>
> Mean(Chi^2) 0.48  0.33  0.50
>
>
> Anomalous completeness  81.7  92.2  75.1
>
> Anomalous multiplicity   1.5   1.8   1.9
>
> DelAnom correlation between half-sets -0.003 0.041 0.045
>
> Mid-Slope of Anom Normal Probability   0.704   - -
>
>
> The anomalous signal appears to be weak so anomalous flag was left OFF
>
>
> Estimates of resolution limits: overall
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.67A
>
>from Mn(I/sd) >  2.00: limit =  2.87A
>
>
> Estimates of resolution limits in reciprocal lattice directions:
>
>   Along0.96 a* - 0.28 c*
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
> resolution
>
>   Along k axis
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.86A
>
>   Along   -0.17 a* + 0.99 c*
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>
>from Mn(I/sd) >  1.50: limit =  2.98A
>
>
> Anisotropic deltaB (i.e. range of principal components), A^2:  8.62
>
>
> Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00
>
> Space group: P 1 21 1
>
> Average mosaicity:   0.05
>
>
> Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   
> 0.00   0.00
>
>
>
>
>
> Michael Jarva, PhD
> ACRF Chemical Biology Division
> The Walter and Eliza Hall Institute of Medical Research
> 

[ccp4bb] First CCP4 Study Weekend illustration competition

[Jon Agirre]

Dear colleagues,

We are pleased to announce the opening of the first CCP4 Study Weekend
illustration competition, made possible by CCP4’s long standing
collaboration with IUCr Journals.

Getting your science out to the public requires more than good research.
You need to make it memorable! And what better way to do it than with
excellent figures? We invite you to make a figure that tells a structural
biology story in a creative and informative way. The submitted figures will
be showcased during the Study Weekend at several locations at the
conference venue.

*Prize*
The creator of the winning illustration gets to design the cover
illustration of the Study Weekend’s proceedings to be published early 2021.
Apart from this commission there may be another (sur)prize.

*Format*
Illustrations, along with a short description of content and methods used,
are to be sent to jon.agi...@york.ac.uk before December 15th 2019.

Images must have a resolution of 1920x1080 (16:9) in order to fit the
format of the screens and main room projector. Any combination of graphics
and (if any) post-processing software may be used, as long as details are
given with the submission. The format of the illustration should be PNG.

*Judges*
As you may know, Dr Jeroen Claus (founder of Phospho Biomedical Animation)
will give the closing talk at the 2020 edition of the CCP4 Study Weekend.
He, along with Louise Jones (managing editor of Acta Crystallographica
sections D & F) will judge the submitted figures based on their graphical
quality as well as their ability to convey a complex structural message
clearly.

*Decision*
The winner will be announced on January 8th at the dinner - before the
céilidh.

Up to date information and registration:
http://www.cvent.com/d/fyq0g9/4K?cpc=FCNF5V7H4B4

Looking forward to receiving your images!

Jon Agirre, Alan Roseman, Robbie Joosten and Karen McIntyre
-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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[ccp4bb] Senior Scientist and Research Associate Structural Biology Positions Open at Confo Therapeutics Gent/Brussels, Belgium

[Veli-Pekka Jaakola]

Senior Scientist Structural Biology (GPCR; cryo-EM; Xrays; SBDD; Biophysics)
(Senior) Research Associate Structural Biology (GPCR; cryo-EM, protein tool 
generation, biophysical/biochemical screening)

We are looking for a highly motivated individuals to join our growing 
structural biology team as a specialist to lead and support our GPCR cryo-EM 
efforts. Confo has a unique technology which makes use of antibody VHH 
fragments or ConfoBodies(tm) to stabilize GPCRs in a particular biologically 
active conformation of interest as a superior starting point for protein 
structure determination and innovative H2L/SBDD process. Recently, Confo 
secured an exclusive license to the Megabody(tm) technology. Megabodies enable 
to produce high resolution cryo-EM structures of membrane proteins, overcoming 
current protein size limitations and potential preferential orientation issues 
in the study of GPCRs via cryo-EM. Confo is currently located on the Technology 
Park in Zwijnaarde/Ghent and on the VUB campus in Brussels. More information 
about Confo's technology and strategy can be found on 
www.confotherapeutics.com.

Senior Scientist Structural Biology (Gent/Brussels)
http://confotherapeutics.com/career-201907-scientist-struct-biol.html

You should have Ph.D. in a field related to structural biology such as cell 
biology, biochemistry or biophysics. Experience in the membrane protein 
structural biology -- either or both x-ray crystallography and electron 
microscopy -- ideally at the postdoctoral level and/or industrial experience. 
Moderate or extensive EM experience is preferred. You should be an energetic 
team player with the ability to model enthusiasm and motivate others to 
excellence. Ambitious in growing to cryo-EM expert in the membrane protein 
field and a project leader in drug discovery projects.

(Senior) Research Associate Structural Biology (Brussels)
http://confotherapeutics.com/career-201901-RA-structural-biology.html

You should have an advanced degree (BSc/MSc) and at least 3 year experience in 
a related field in a biotech environment. You should be an expert in molecular 
biology, recombinant protein expression using insect/mammalian systems and 
purification methods. The ideal candidate would have also extensive experience 
in biochemical/biophysical characterization/screening and protein engineering. 
You should be highly collaborative, self-motivated and team-oriented individual.

Our offer is a competitive compensation package with extensive benefits; an 
entrepreneurial and stimulating working environment in a growing and ambitious 
biotech company; excellent career development opportunity, with exposure to all 
aspects of R in the company, with external collaborators and partners.

Do you have the right qualifications and are you up to the challenge of joining 
our team? Then forward a short motivation letter and your CV to 
veli-pekka.jaak...@confotherapeutics.com

Cheerio,

Veli Jaakola

--
Veli-Pekka Jaakola
Head of Structural Biology
Confo Therapeutics
Technologiepark 94
9052 Zwijnaarde
Belgium
+32 471 80 01 56
www.confotherapeutics.com
veli-pekka.jaak...@confotherapeutics.com
https://www.linkedin.com/in/vpjaakol
--



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addressee. If you have received this transmission in error, please contact the 
sender immediately and return it to the sender without retaining a copy. 
Electronic communications are not secure and may be intercepted, manipulated, 
infected, delayed or misdirected, e.g. by viruses and spam filters. Confo 
Therapeutics is not liable on any legal ground for damage resulting from any 
such event.



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