Re: [ccp4bb] disinfecting keyboards

[Gloria Borgstahl]

We were looking at these, they look like fun.

https://www.wetkeys.com/Soft-touch-Comfort-Hygienic-Washable-Keyboard-USB-p/kbstfc106-w.htm



On Tue, May 5, 2020, 7:20 PM 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 encountered a keyboard that suffered from having the writing removed
> with that or 100% ethanol. Both work and as long as they are 100% (no
> water), the keyboard and mouse have no issues.
>
>
> 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 Tim Gruene 
> 
> *Sent:* Wednesday, April 29, 

Re: [ccp4bb] disinfecting keyboards

[James Holton]

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 encountered a keyboard that suffered from having the 
writing removed with that or 100% ethanol. Both work and as long as 
they are 100% (no water), the keyboard and mouse have no issues.



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 Tim 
Gruene 

*Sent:* Wednesday, April 29, 2020 1:53 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] disinfecting keyboards
Dear all,

can you make suggestions for how to disinfect computer keyboards, and
instrument panels?

Our facility is going to reboot next week, with shifts so that people
don't meet. The main 

[ccp4bb] LCLS Project Scientist for Sample Delivery Posting

[Hunter, Mark Steven]

Job ID 
4077
SLAC National Accelerator Laboratory (SLAC) is one of the world’s premier 
research laboratories, providing an internationally leading capability in the 
form of its accelerator based light sources and its science programs. The Linac 
Coherent Light Source (LCLS), a directorate of SLAC and the world’s first hard 
x-ray free electron laser, seeks a Research Associate with a background in 
sample introduction for serial data collection to join the Sample Environment 
and Delivery group within the LCLS Hard X-Ray department. Members of this 
department are responsible for developing new instrumentation and methods as 
well as performing innovative ultrafast experiments using hard x-ray beams from 
LCLS. The SED Department specifically focuses on sample preparation, 
characterization and delivery.
Please Note – due to COVID-19 related curtailment of on-site activities, the 
job duties for this position will be required to be performed from home until 
full site-access is restored.
In this position, you will primarily support the development and integration of 
methods for sample introduction of biological samples at LCLS and will also 
support the user experiment program. You will participate in and contribute to 
efforts involving the characterization and testing of sample introduction 
methods for solutions and suspensions as well as help to automate sample 
introduction at the LCLS beam lines. You will have the opportunity to 
collaborate with researchers at SLAC and Stanford University working on 
simulations and theoretical frameworks of the underlying physics. The 
successful candidate should be curious, motivated and self-driven.
Note: The position is a 2 year fixed term with the possibility of renewal. 
Assignment duration is contingent upon project needs and funding.
To be successful in this position you will bring:

  *   A Ph.D. (or its equivalent in research skill and subject knowledge) in 
physics, engineering, biochemistry, or related field in demonstrated coursework 
and research experience with sample preparation, characterization and delivery. 
(Candidates currently pursuing a PhD or recently graduated with relevant 
post-graduate research background are encouraged to apply)
  *   Experience with sample introduction for serial data collection at x-ray 
sources.
  *   Demonstrated experience as evidenced by a publication record commensurate 
with level of work experience.
  *   Ability to carry out independent research.
  *   Strong analytical and experimental skills.
  *   Effective written and verbal communication skills.
  *   Ability to work and communicate effectively with a diverse population.
In addition, preferred requirements and experience include:

  *   User facility operations and research.
  *   X-ray crystallography, especially serial methods.
  *   X-ray scattering techniques.
  *   Script writing and data analysis using Python
  *   Experience in automation
SLAC employee competencies:

  *   Effective Decisions: Uses job knowledge and solid judgment to make 
quality decisions in a timely manner.
  *   Self-Development: Pursues a variety of venues and opportunities to 
continue learning and developing.
  *   Dependability: Can be counted on to deliver results with a sense of 
personal responsibility for expected outcomes.
  *   Initiative: Pursues work and interactions proactively with optimism, 
positive energy, and motivation to move things forward.
  *   Adaptability: Flexes as needed when change occurs, maintains an open 
outlook while adjusting and accommodating changes.
  *   Communication: Ensures effective information flow to various audiences 
and creates and delivers clear, appropriate written, spoken, presented messages.
  *   Relationships: Builds relationships to foster trust, collaboration, and a 
positive climate to achieve common goals.
Physical requirements and working conditions:

  *   Consistent with its obligations under the law, the University will 
provide reasonable accommodation to any employee with a disability who requires 
accommodation to perform the essential functions of the job. May work extended 
hours during peak business cycles. The ability to travel to synchrotron and 
XFEL facilities around the world to perform experiments
Work standards:

  *   Interpersonal Skills: Demonstrates the ability to work well with Stanford 
colleagues and clients and with external organizations.
  *   Promote Culture of Safety: Demonstrates commitment to personal 
responsibility and value for environment, safety and security; communicates 
related concerns; uses and promotes safe behaviors based on training and 
lessons learned.  Meets the applicable roles and responsibilities as described 
in the ESH Manual, Chapter 1—General Policy and Responsibilities:  
http://www-group.slac.stanford.edu/esh/eshmanual/pdfs/ESHch01.pdf
  

Re: [ccp4bb] Fusion proteins to solubilize your protein

[Artem Evdokimov]

Probably the easiest would be blasting sequences all by all and extracting
peaks above certain height with a filter of some sorts. Not entirely
trivial.

I can add to your list, although not all of these proteins are in the PDB -
some are from my own collection :)

Lysozyme (s) several are used
Artificial helix bundles
GS
SUMO
Ubq
NusA
Fc and other mAb domains
Nanobodies (as fusions)
Cyt b562
Rubredoxin
Flavodoxin
VLR
Barnase
MHC proteins


Bostjan Kobe wrote a paper in 2015 which you probably saw already.

Artem




On Tue, May 5, 2020, 2:45 PM Murpholino Peligro 
wrote:

> 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
>
>
>
>
> --
>
> 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] Dose in diffraction patterns?

[Murpholino Peligro]

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



Thanks



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[ccp4bb] Fusion proteins to solubilize your protein

[Murpholino Peligro]

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] Arp/wARP

[Reza Khayat]

Hi,


I've installed the entire CCP4 7.1 package (ShelX and arpWarp); however, I 
can't find the arp/Warp binaries/scripts (e.g. auto_em.sh). Are these not 
included with the CCP4 package? If not, why not? Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031



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