Re: [ccp4bb] Dose in diffraction patterns?

[James Holton]

In general?  No.

I believe a few places put "flux" into the header, but as Andreas just 
mentioned that is only one of the bits of information you need to 
calculate dose.  If all you want is a rough estimate, then the numbers 
you need are:

f = flux (photons/s)
t = exposure time (s)
w = wavelength (A)
a = beam area (um^2)

The dose (D) to a sample of protein/water/plastic under a given beam 
will be roughly:

D = f*t*w^2/a/2000  (in Gy)

For example: a crystal under a square 100 um x 100 um beam at 1 A 
wavelength with flux 1e12 ph/s will get 1 MGy dose in 20 s.


The 2000/w^2 is a fudge factor that fits the true curve of metal-free 
protein crystals to within 15% for the wavelength range 0.5 < w < 3.  
The error induced by not knowing if the beam was round or square and 
just multiplying together the width and height to get the area (a), is 
21%.  The error from not realizing you had 100 mM uranium in your sample 
is about a factor of two at 1 A. Smaller concentrations and lighter 
atoms have less impact on accuracy.


If you don't know the flux, or beam size, you can try looking them up at 
http://biosync.sbkb.org/ . I scraped these for my little dose calculator 
here:

bl831.als.lbl.gov/xtallife.html
Some of the biosync numbers are more accurate than others, however, 
depending on how often beamline scientists remember to update the site, 
and how well they know themselves.  And attenuation is not always 
written into the header either.


In a pinch, you can estimate the flux by the total number of photons on 
the image (P).  This is assuming that you know the sample thickness (L) 
in microns.  You must also assume that the total scattering cross 
section of the atoms in the sample is close to that of oxygen (0.2 
cm^2/g), that the sample density is 1.2 g/cm^3 and that about 50% of the 
scattered photons reach the detector.  None of these are terrible 
assumptions. The equation then becomes:


f = P/t/L*1.2e-5

Where 1.2e-5 = 0.2 cm^2/g * 1.2 g/cm^3 * 1e-4 cm/micron * 50%, f=flux 
and t=exposure (as above).


Getting P from a pixel array is easy: you just add up all the pixel 
values.  From a CCD you want to be careful to subtract the baseline 
value from each pixel first (40 on ADSC, 10 on Mar/Rayonix), and then 
divide by the "gain", which near 1 A is ~1 on Mar/Rayonix, 0.6 for ADSC 
Q315 (swbin) and 1.8 for Q315r (hwbin).  A few considerations, yes, but 
it can be a good sanity check.


-James Holton
MAD Scientist


On 5/5/2020 11:48 AM, Murpholino Peligro wrote:
Do diffraction patterns publicly accessible contain information about 
the x-ray absorbed dose?




Thanks



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Re: [ccp4bb] CCP4 source code

[Fischmann, Thierry]

Thank you for making the  7.1 source available !

For those interested, http://www.ccp4.ac.uk/download/index.php#os=src

Thierry

From: CCP4 bulletin board  On Behalf Of Fischmann, 
Thierry
Sent: Monday, May 4, 2020 3:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 source code

EXTERNAL EMAIL – Use caution with any links or file attachments.
Hello,

This question is addressed to the CCP4 staff, but the answer may be of general 
interest:

Do you have a projection for when the 7.1 source code will be available? Is 
there a way to access the source code for 7.0 in the mean time?

Of course it is understood that the source code availability may be delayed due 
to the current COVID-19 crisis: safety of the CCP4 staff first! But it would be 
useful to have an estimate if you can provide one.

Thank you!

Thierry

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.



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for affiliates is available at 
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[ccp4bb] PhD Position in Structural Biology

[Roman Fedorov]

The research group headed by Prof. Dr. Dietmar Manstein invites applications 
for a PhD position funded by the Health Research Framework Programme of the 
German Federal Government and the European Joint Programme on Rare Diseases 
under the call "Transnational Research to Accelerate the Diagnosis and/or 
Investigation of Disease Processes and Mechanisms in Rare Diseases"
The work is performed in the context of a multidisciplinary, international 
research team that includes participants from France, Italy, Hungary and 
Germany.

The PhD project involves structural studies of actin mutants, molecular motors 
and their complexes.   The Manstein laboratory is offering excellent working 
conditions and a stimulating research environment. We typically use hybrid 
approaches that combine X-ray crystallography, serial crystallography, electron 
microscopy, time-resolved spectroscopy, and in silico modelling.  The work is 
in part conducted at synchrotron facilities in Germany and France. The salary 
is in accordance to the German Public Sector Collective Agreement (TV-L 
E13/58%). The position is available from July 1, 2020.

Related References:
Chinthalapudi, K., Heissler, S. M., Preller, M., Sellers, J. R. & Manstein, D. 
J. 2017. Mechanistic insights into the active site and allosteric communication 
pathways in human nonmuscle myosin-2C. Elife, 6(e32742), DOI: 
10.7554/eLife.32742.
Latham, S. L., Ehmke, N., Reinke, P. Y. A., Taft, M. H., et al.., Manstein, D. 
J. & Di Donato, N. 2018. Variants in exons 5 and 6 of ACTB cause syndromic 
thrombocytopenia. Nat Commun, 9(1), pp 4250, DOI: 10.1038/s41467-018-06713-0.
Radke, M. B., Taft, M. H., Stapel, B., Hilfiker-Kleiner, D., Preller, M. & 
Manstein, D. J. 2014. Small molecule-mediated refolding and activation of 
myosin motor function. Elife, 3(e01603), DOI: 10.7554/eLife.01603.
von der Ecken, J., Heissler, S. M., Pathan-Chhatbar, S., Manstein, D. J. & 
Raunser, S. 2016. Cryo-EM structure of a human cytoplasmic actomyosin complex 
at near-atomic resolution. Nature, 534(7609), pp 724-8, DOI: 
10.1038/nature18295.

For more information, please refer to the website:
https://www.mhh.de/en/bpc/prof-dr-dietmar-manstein


Please send your application by electronic mail and preferably in one single 
pdf-document to
Joanna D. Schille, BA

E-Mail:  schille.joa...@mh-hannover.de
Medizinische Hochschule Hannover, Fritz-Hartmann-Centre for Medical Research
Institute for Biophysical Chemistry and Structural Biochemistry OE 4350

30625 Hannover

Carl-Neuberg-Str. 1

Germany

For full consideration, the application should include a cover letter, a 
detailed CV, copies of all educational certificates and transcripts of records, 
a summary of previous research, and the address details of two academic 
advisors who can provide letters of recommendation. The deadline for 
application is June 30, 2020. Early applications are encouraged; applications 
may be processed as they are received.
MHH is an equal opportunity employer. Qualified women are therefore 
particularly encouraged to apply. Applicants with disabilities are treated with 
preference given comparable qualification.





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Re: [ccp4bb] disinfecting keyboards

[Jurgen Bosch]

Must have been wearing a traditional Scottish outfit :-)

Jürgen 

> On May 6, 2020, at 11:19 AM, Tristan Croll  wrote:
> 
> You got off lucky. An old friend of mine learned this lesson when on a 
> particularly sunny day he spent an hour out on a New Zealand glacier in 
> shorts with no underwear...
> 
> On 2020-05-06 16:17, James Holton wrote:
>> I feel I should correct you on one thing Tim: UV _can_ go around
>> corners because it scatters.  I learned this the hard way as a younger
>> man after a fine day of skiing.  I had put sunscreen everywhere except
>> the bottom of my nose.
>> You are right, however, that the intensity after scattering is quite a
>> bit less than tha main illumination.  This is true for all kinds of
>> light.
>> -James Holton
>> MAD Scientist
>> On 5/5/2020 11:59 PM, Tim Gruene wrote:
>>> Hi James,
>>> for us, the suggestions of cling film / plastic wrap or just swapping
>>> keyboards and mice per person is the simplest - thanks to everyone for
>>> the many suggestions. Especially the latter, since only two people will
>>> operate the instruments.
>>> UV light does not go around corners. It might be useful for fume hoods,
>>> but for most places, door handles and other curved surfaces are
>>> probably much more the infecting parts, while they escape the UV light.
>>> And vira are transported in water droplets, which are larger than 1um.
>>> Best,
>>> Tim
>>>  On Tue, 5 May 2020 17:19:56 -0700
>>> James Holton  wrote:
 All joking aside, there has been a furor of attention on UV-based
 disinfection of late.  Some of it is not entirely crazy.  I.E.
 Columbia University’s Center for Radiological Research has put
 forward the idea of illuminating occupied public areas with
 ultra-narrow-band UV-C (222 nm).
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552051/
 Mind you, UV-C normally covers 100 - 280 nm, and the PPE requirements
 for that (at LBNL at least) are extensive: polycarbonate safety
 glasses and face shield with a mark U6 (UV protection), long-sleeved
 clothing, and gloves.  Basically: do not expose skin!
 The idea behind using monochromatic 222 nm radiation is that it is at
 the edge of a very steep increase in the absorption of water,
 protein, and other biologicals.  Penetration depths are hard to
 estimate because of the steep slope, but they are on the order of 1
 micron.  So, smaller than a typical mamalian cell, but bigger than a
 bacterium or virus.  The paper above did not have any human subjects,
 nor did it discuss how to deal with all the ozone, but the results
 are intruiging. Needs further study.
 Personally, I think this would probably fog your corneas and perhaps
 burn the thin skin on lips and other exposed mucosa. Hair I'd expect
 to embrittle and fall apart eventually. Yes, hair is 40 microns thick
 and the penetration depth is 1 micron, but photon's don't "stop" at
 the penetration depth.  36% of them go deeper. Plastic in keyboards
 too would probably bleach and flake with prolonged exposure.  Ever
 seen a keyboard left out in the sun for a few weeks?  I'd worry a bit
 about this micro-damage creating crevices where bugs could hide.
 I encourage you to bring this up with your Health and Safety people,
 but make sure they are sitting down first.
 -James Holton
 MAD Scientist
 On 4/29/2020 12:41 PM, Andrea Thorn wrote:
> Hi Tim!
> 100% alcohol is less effective than 80%, and in order to completely
> be sure, the keyboard needs not only to be wiped. One can buy
> keyboards that can be disinfected because they are waterproof, such
> as the Cherry JK-1068DE-2 for about 50 €.
> We clean the keyboards in our lab occasionally anyway, and have
> used 70% alcohol on them without problem. Disinfectant wipes, a
> detergent cleaner (such as Viss Glass & Flächen) and cotton swabs
> also offer some help. We wipe our mobile phones with a disinfectant
> wipe after washing our hands when arriving home/at work.
> I would also be really interested in what could be done with a UV
> light, if someone knows?
> If the computer is used by one person during the shift, individual
> keyboards for each person could be a solution. If people sit down,
> the desk surface, which may be touched, should likely also be wiped
> at the beginning and end of the shift I would say.
> Stay save and best wishes,
> Andrea.
> Am 29/04/2020 um 21:04 schrieb Diana Tomchick:
>> ​100% ethanol or isopropanol work really well on the microscopes,
>> I soak a Kimwipe and then clean the eyepieces and the knobs for
>> changing magnification and focus, as well as the door handles,
>> bench tops, etc.
>> Diana
>> **
>> Diana R. Tomchick
>> Professor
>> Departments of Biophysics and Biochemistry
>> UT Southwestern Medical 

Re: [ccp4bb] disinfecting keyboards

[Tristan Croll]

You got off lucky. An old friend of mine learned this lesson when on a 
particularly sunny day he spent an hour out on a New Zealand glacier in 
shorts with no underwear...


On 2020-05-06 16:17, James Holton wrote:

I feel I should correct you on one thing Tim: UV _can_ go around
corners because it scatters.  I learned this the hard way as a younger
man after a fine day of skiing.  I had put sunscreen everywhere except
the bottom of my nose.

You are right, however, that the intensity after scattering is quite a
bit less than tha main illumination.  This is true for all kinds of
light.

-James Holton
MAD Scientist

On 5/5/2020 11:59 PM, Tim Gruene wrote:

Hi James,

for us, the suggestions of cling film / plastic wrap or just swapping
keyboards and mice per person is the simplest - thanks to everyone for
the many suggestions. Especially the latter, since only two people 
will

operate the instruments.

UV light does not go around corners. It might be useful for fume 
hoods,

but for most places, door handles and other curved surfaces are
probably much more the infecting parts, while they escape the UV 
light.


And vira are transported in water droplets, which are larger than 1um.

Best,
Tim

  On Tue, 5 May 2020 17:19:56 -0700
James Holton  wrote:


All joking aside, there has been a furor of attention on UV-based
disinfection of late.  Some of it is not entirely crazy.  I.E.
Columbia University’s Center for Radiological Research has put
forward the idea of illuminating occupied public areas with
ultra-narrow-band UV-C (222 nm).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552051/

Mind you, UV-C normally covers 100 - 280 nm, and the PPE requirements
for that (at LBNL at least) are extensive: polycarbonate safety
glasses and face shield with a mark U6 (UV protection), long-sleeved
clothing, and gloves.  Basically: do not expose skin!

The idea behind using monochromatic 222 nm radiation is that it is at
the edge of a very steep increase in the absorption of water,
protein, and other biologicals.  Penetration depths are hard to
estimate because of the steep slope, but they are on the order of 1
micron.  So, smaller than a typical mamalian cell, but bigger than a
bacterium or virus.  The paper above did not have any human subjects,
nor did it discuss how to deal with all the ozone, but the results
are intruiging. Needs further study.

Personally, I think this would probably fog your corneas and perhaps
burn the thin skin on lips and other exposed mucosa. Hair I'd expect
to embrittle and fall apart eventually. Yes, hair is 40 microns thick
and the penetration depth is 1 micron, but photon's don't "stop" at
the penetration depth.  36% of them go deeper. Plastic in keyboards
too would probably bleach and flake with prolonged exposure.  Ever
seen a keyboard left out in the sun for a few weeks?  I'd worry a bit
about this micro-damage creating crevices where bugs could hide.

I encourage you to bring this up with your Health and Safety people,
but make sure they are sitting down first.

-James Holton
MAD Scientist

On 4/29/2020 12:41 PM, Andrea Thorn wrote:

Hi Tim!


100% alcohol is less effective than 80%, and in order to completely
be sure, the keyboard needs not only to be wiped. One can buy
keyboards that can be disinfected because they are waterproof, such
as the Cherry JK-1068DE-2 for about 50 €.


We clean the keyboards in our lab occasionally anyway, and have
used 70% alcohol on them without problem. Disinfectant wipes, a
detergent cleaner (such as Viss Glass & Flächen) and cotton swabs
also offer some help. We wipe our mobile phones with a disinfectant
wipe after washing our hands when arriving home/at work.

I would also be really interested in what could be done with a UV
light, if someone knows?

If the computer is used by one person during the shift, individual
keyboards for each person could be a solution. If people sit down,
the desk surface, which may be touched, should likely also be wiped
at the beginning and end of the shift I would say.

Stay save and best wishes,



Andrea.



Am 29/04/2020 um 21:04 schrieb Diana Tomchick:

​100% ethanol or isopropanol work really well on the microscopes,
I soak a Kimwipe and then clean the eyepieces and the knobs for
changing magnification and focus, as well as the door handles,
bench tops, etc.


Diana


**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

*From:* CCP4 bulletin board  on behalf of
Diana Tomchick 
*Sent:* Wednesday, April 29, 2020 2:00 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] disinfecting keyboards

EXTERNAL MAIL

​You could try doing what my technician does with her keyboard;
she wraps it in a clear, thin food wrap 

Re: [ccp4bb] disinfecting keyboards

[James Holton]

I feel I should correct you on one thing Tim: UV _can_ go around corners 
because it scatters.  I learned this the hard way as a younger man after 
a fine day of skiing.  I had put sunscreen everywhere except the bottom 
of my nose.


You are right, however, that the intensity after scattering is quite a 
bit less than tha main illumination.  This is true for all kinds of light.


-James Holton
MAD Scientist

On 5/5/2020 11:59 PM, Tim Gruene wrote:

Hi James,

for us, the suggestions of cling film / plastic wrap or just swapping
keyboards and mice per person is the simplest - thanks to everyone for
the many suggestions. Especially the latter, since only two people will
operate the instruments.

UV light does not go around corners. It might be useful for fume hoods,
but for most places, door handles and other curved surfaces are
probably much more the infecting parts, while they escape the UV light.

And vira are transported in water droplets, which are larger than 1um.

Best,
Tim

  On Tue, 5 May 2020 17:19:56 -0700
James Holton  wrote:


All joking aside, there has been a furor of attention on UV-based
disinfection of late.  Some of it is not entirely crazy.  I.E.
Columbia University’s Center for Radiological Research has put
forward the idea of illuminating occupied public areas with
ultra-narrow-band UV-C (222 nm).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552051/

Mind you, UV-C normally covers 100 - 280 nm, and the PPE requirements
for that (at LBNL at least) are extensive: polycarbonate safety
glasses and face shield with a mark U6 (UV protection), long-sleeved
clothing, and gloves.  Basically: do not expose skin!

The idea behind using monochromatic 222 nm radiation is that it is at
the edge of a very steep increase in the absorption of water,
protein, and other biologicals.  Penetration depths are hard to
estimate because of the steep slope, but they are on the order of 1
micron.  So, smaller than a typical mamalian cell, but bigger than a
bacterium or virus.  The paper above did not have any human subjects,
nor did it discuss how to deal with all the ozone, but the results
are intruiging. Needs further study.

Personally, I think this would probably fog your corneas and perhaps
burn the thin skin on lips and other exposed mucosa. Hair I'd expect
to embrittle and fall apart eventually. Yes, hair is 40 microns thick
and the penetration depth is 1 micron, but photon's don't "stop" at
the penetration depth.  36% of them go deeper. Plastic in keyboards
too would probably bleach and flake with prolonged exposure.  Ever
seen a keyboard left out in the sun for a few weeks?  I'd worry a bit
about this micro-damage creating crevices where bugs could hide.

I encourage you to bring this up with your Health and Safety people,
but make sure they are sitting down first.

-James Holton
MAD Scientist

On 4/29/2020 12:41 PM, Andrea Thorn wrote:

Hi Tim!


100% alcohol is less effective than 80%, and in order to completely
be sure, the keyboard needs not only to be wiped. One can buy
keyboards that can be disinfected because they are waterproof, such
as the Cherry JK-1068DE-2 for about 50 €.


We clean the keyboards in our lab occasionally anyway, and have
used 70% alcohol on them without problem. Disinfectant wipes, a
detergent cleaner (such as Viss Glass & Flächen) and cotton swabs
also offer some help. We wipe our mobile phones with a disinfectant
wipe after washing our hands when arriving home/at work.

I would also be really interested in what could be done with a UV
light, if someone knows?

If the computer is used by one person during the shift, individual
keyboards for each person could be a solution. If people sit down,
the desk surface, which may be touched, should likely also be wiped
at the beginning and end of the shift I would say.

Stay save and best wishes,



Andrea.



Am 29/04/2020 um 21:04 schrieb Diana Tomchick:

​100% ethanol or isopropanol work really well on the microscopes,
I soak a Kimwipe and then clean the eyepieces and the knobs for
changing magnification and focus, as well as the door handles,
bench tops, etc.


Diana


**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

*From:* CCP4 bulletin board  on behalf of
Diana Tomchick 
*Sent:* Wednesday, April 29, 2020 2:00 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] disinfecting keyboards

EXTERNAL MAIL

​You could try doing what my technician does with her keyboard;
she wraps it in a clear, thin food wrap that can be taped to the
back of the keyboard. This is usually done to keep food and other
things (liquids) from damaging the keyboard, but you could simply
replace the wrap every time someone else uses it.


Personally 

[ccp4bb] IMCA-CAT beam time is available for proprietary experiments

[Jesse Yoder]

Dear Colleagues,



The IMCA-CAT beamline at the Advanced Photon Source (APS) is continuing to
operate and collect crystallography data during the current
restricted-access operations at Argonne National Laboratory.  Experiments
are limited to (1) critical research related to COVID-19 or (2) critical
proprietary research related to drug development.



The current APS run cycle (2020-1) has been extended through May 31, 2020
in order to best provide structural biology data to fight COVID-19. The
next APS run cycle (2020-2) has also been shifted and will now begin on
June 10, 2020.



All pharmaceutical companies and research entities conducting either
COVID-19 related research or critical, proprietary research in drug
discovery are invited to inquire about access to IMCA-CAT for beam time.
All experiments must be either remote access or mail-in.



IMCA-CAT is committed to accelerating drug discovery through
synchrotron-based structural biology research.  The insertion device
beamline is optimized for delivering exceptional quality data, collecting
data at high-throughput rates, and ensuring data security for proprietary
experiments.  Streamlined pathways for establishing proprietary agreements
have been implemented for new industrial users to begin conducting
experiments without delay.



For more information about accessing IMCA-CAT, please contact Dr. Lisa
Keefe (email is keefe [at] imca-cat.org).



Work safely and stay healthy,

Jesse Yoder

-- 
Jesse Yoder, PhD
Macromolecular Crystallographer
IMCA-CAT | Argonne National Laboratory
(630) 252-0529



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[ccp4bb] PDBe-KB COVID-19 pages: more download options and antibody annotations

[John Berrisford]

We recently announced the new PDBe-KB COVID-19 data portal
(pdbe.org/covid19), allowing users to easily access a wealth of structural
data from the SARS-CoV-2 virus. We have now added annotations on antibody
classifications and details of peptide inhibitor molecules to the
interactions section. In addition, we have also extended the bulk download
options to entries with specific ligands or macromolecular interactions.

 

The interactions section of the PDBe-KB protein aggregated views previously
only identified macromolecules based on Uniprot accession. We have now
extended this for the COVID-19 pages to include antibody chains so that
these interactions are highlighted.

 

We recently introduced a new bulk file download service to the PDBe-KB
COVID-19 pages, and have now extended this to allow download for subsets of
entries containing macromolecular complexes or entries with similar
structures.

 

For full details see our news release (pdbe.org/news).

 

Regards

 

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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[ccp4bb] Structural Biology- researcher position available

[Elżbieta Nowak]

Dear All,


posted on behalf of Dr. Marcin Nowotny, IIMCB


Laboratory of Protein Structure at the International Institute of Molecular and 
Cell Biology in Warsaw (http://bit.ly/nowotny-lab) seeks a researcher (full 
time position) to work in a large multinational consortium project that aims at 
the development of antiviral substances for treatment of COVID-19. The position 
is available in frame of EXSCALATE4CoV project funded by the European 
Commission 
(www.iimcb.gov.pl/en/press-office/news/news/1112-developing-sars-cov-2-antiviral-drugs).
 The person in this position will be responsible for the determination of 
crystal and cryo-EM structures of viral protein in complex with inhibitors 
(potential antiviral drugs).

More details can be found here:

https://www.iimcb.gov.pl/en/new-jobs-positions/314-researcher


Best wishes,

Elzbieta Nowak Ph.D.



***

Laboratory of Protein Structure

International Institute of Molecular and Cell Biology

4 Ks. Trojdena Street,

02-109 Warsaw, Poland

Telephone: (+48 22) 597 07 21

Fax: (+48 22) 597 07 15






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Re: [ccp4bb] Fusion proteins to solubilize your protein

[Jose Artur Brito]

Dear Murpholino,
a portuguese company called NZYtech has a collection of fusion tag pHTP 
expression vectors 
(https://www.nzytech.com/wp-content/uploads/2019/04/nzyeasy-cloning-expression-system_userguide_v1901.pdf), 
some of them designed for increased protein's solubilization.


We have a recent example of using a Ketosteroid isomerase (KSI) tag that 
highly increased solubility and crystallizability of one of our tagets 
(a kinase). No news on phasing and phase extension since crystals were 
not screened yet due to this long lock-down.


HTH, best,
Jose




Subject Fusion proteins to solubilize your protein
FromMurpholino Peligro
DateTue 19:44
I was wondering how many proteins that help to crystallize the protein 
of interest are out there...


and how effective is the phase extension method (i.e. use MR to get the 
structure of the fusion protein into its density and the density of the 
protein of interest...)


Is there a way to get this data from the PDB?

Here is my list so far:
- MBP
- GFP
- TRX
- Lysozyme
- GST

Thanks


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[ccp4bb] Structural Biology-researcher position available

[Elżbieta Nowak]

Dear All,


posted on behalf of Dr. Marcin Nowotny, IIMCB


Laboratory of Protein Structure at the International Institute of Molecular and 
Cell Biology in Warsaw (http://bit.ly/nowotny-lab) seeks a researcher (full 
time position) to work in a large multinational consortium project that aims at 
the development of antiviral substances for treatment of COVID-19. The position 
is available in frame of EXSCALATE4CoV project funded by the European 
Commission 
(www.iimcb.gov.pl/en/press-office/news/news/1112-developing-sars-cov-2-antiviral-drugs).
 The person in this position will be responsible for the determination of 
crystal and cryo-EM structures of viral protein in complex with inhibitors 
(potential antiviral drugs).

More details can be found here:

https://www.iimcb.gov.pl/en/new-jobs-positions/314-researcher


Best wishes,

Elzbieta Nowak Ph.D.



***

Laboratory of Protein Structure

International Institute of Molecular and Cell Biology

4 Ks. Trojdena Street,

02-109 Warsaw, Poland

Telephone: (+48 22) 597 07 21

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Re: [ccp4bb] disinfecting keyboards

[Tim Gruene]

Hi James,

for us, the suggestions of cling film / plastic wrap or just swapping
keyboards and mice per person is the simplest - thanks to everyone for
the many suggestions. Especially the latter, since only two people will
operate the instruments.

UV light does not go around corners. It might be useful for fume hoods,
but for most places, door handles and other curved surfaces are
probably much more the infecting parts, while they escape the UV light.

And vira are transported in water droplets, which are larger than 1um.

Best,
Tim

 On Tue, 5 May 2020 17:19:56 -0700
James Holton  wrote:

> All joking aside, there has been a furor of attention on UV-based 
> disinfection of late.  Some of it is not entirely crazy.  I.E.
> Columbia University’s Center for Radiological Research has put
> forward the idea of illuminating occupied public areas with
> ultra-narrow-band UV-C (222 nm).
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552051/
> 
> Mind you, UV-C normally covers 100 - 280 nm, and the PPE requirements 
> for that (at LBNL at least) are extensive: polycarbonate safety
> glasses and face shield with a mark U6 (UV protection), long-sleeved
> clothing, and gloves.  Basically: do not expose skin!
> 
> The idea behind using monochromatic 222 nm radiation is that it is at 
> the edge of a very steep increase in the absorption of water,
> protein, and other biologicals.  Penetration depths are hard to
> estimate because of the steep slope, but they are on the order of 1
> micron.  So, smaller than a typical mamalian cell, but bigger than a
> bacterium or virus.  The paper above did not have any human subjects,
> nor did it discuss how to deal with all the ozone, but the results
> are intruiging. Needs further study.
> 
> Personally, I think this would probably fog your corneas and perhaps 
> burn the thin skin on lips and other exposed mucosa. Hair I'd expect
> to embrittle and fall apart eventually. Yes, hair is 40 microns thick
> and the penetration depth is 1 micron, but photon's don't "stop" at
> the penetration depth.  36% of them go deeper. Plastic in keyboards
> too would probably bleach and flake with prolonged exposure.  Ever
> seen a keyboard left out in the sun for a few weeks?  I'd worry a bit
> about this micro-damage creating crevices where bugs could hide.
> 
> I encourage you to bring this up with your Health and Safety people,
> but make sure they are sitting down first.
> 
> -James Holton
> MAD Scientist
> 
> On 4/29/2020 12:41 PM, Andrea Thorn wrote:
> >
> > Hi Tim!
> >
> >
> > 100% alcohol is less effective than 80%, and in order to completely
> > be sure, the keyboard needs not only to be wiped. One can buy
> > keyboards that can be disinfected because they are waterproof, such
> > as the Cherry JK-1068DE-2 for about 50 €.
> >
> >
> > We clean the keyboards in our lab occasionally anyway, and have
> > used 70% alcohol on them without problem. Disinfectant wipes, a
> > detergent cleaner (such as Viss Glass & Flächen) and cotton swabs
> > also offer some help. We wipe our mobile phones with a disinfectant
> > wipe after washing our hands when arriving home/at work.
> >
> > I would also be really interested in what could be done with a UV 
> > light, if someone knows?
> >
> > If the computer is used by one person during the shift, individual 
> > keyboards for each person could be a solution. If people sit down,
> > the desk surface, which may be touched, should likely also be wiped
> > at the beginning and end of the shift I would say.
> >
> > Stay save and best wishes,
> >
> >
> >
> > Andrea.
> >
> >
> >
> > Am 29/04/2020 um 21:04 schrieb Diana Tomchick:  
> >>
> >> ​100% ethanol or isopropanol work really well on the microscopes,
> >> I soak a Kimwipe and then clean the eyepieces and the knobs for 
> >> changing magnification and focus, as well as the door handles,
> >> bench tops, etc.
> >>
> >>
> >> Diana
> >>
> >>
> >> **
> >> Diana R. Tomchick
> >> Professor
> >> Departments of Biophysics and Biochemistry
> >> UT Southwestern Medical Center
> >> 5323 Harry Hines Blvd.
> >> Rm. ND10.214A
> >> Dallas, TX 75390-8816
> >> diana.tomch...@utsouthwestern.edu
> >> (214) 645-6383 (phone)
> >> (214) 645-6353 (fax)
> >> 
> >> *From:* CCP4 bulletin board  on behalf of 
> >> Diana Tomchick 
> >> *Sent:* Wednesday, April 29, 2020 2:00 PM
> >> *To:* CCP4BB@JISCMAIL.AC.UK
> >> *Subject:* Re: [ccp4bb] disinfecting keyboards
> >>
> >> EXTERNAL MAIL
> >>
> >> ​You could try doing what my technician does with her keyboard;
> >> she wraps it in a clear, thin food wrap that can be taped to the
> >> back of the keyboard. This is usually done to keep food and other
> >> things (liquids) from damaging the keyboard, but you could simply
> >> replace the wrap every time someone else uses it.
> >>
> >>
> >> Personally I like using a Kimwipe soaked with 100% isopropanol,
> >> I've never yet 

Re: [ccp4bb] Dose in diffraction patterns?

[Andreas Förster]

Dear Murpholino,

all diffraction patterns contain information on absorbed dose in the form
of radiation damage.

You might be more interested in a quantitative description of dose.  For
this, you need information on the size and shape of your crystal; the
sequence of your protein + cofactors, ligands, metals and crystallization
buffer; the size, shape and flux of your beam; and the position of the
rotation axis relative to the beam (does the crystal rotate or wobble in
the beam?).  In a perfect world, all this information would be part of the
metadata that's saved with your diffraction data.  Currently, none of this
is.  (Correct me if I'm wrong.  I'd like to know.)  With it, you can
estimate dose with the current or future versions of Raddose 3D.

All best.


Andreas



On Tue, May 5, 2020 at 8:49 PM Murpholino Peligro 
wrote:

> Do diffraction patterns publicly accessible contain information about the
> x-ray absorbed dose?
>
>
>
> Thanks
>
> --
>
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>


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