Re: [ccp4bb] disinfecting keyboards

[Tristan Croll]

Posted semi-seriously (they look like they’d be awful to use, but maybe I’m 
being pessimistic): https://wiki.ezvid.com/best-virtual-keyboards. With a 
projection keyboard, all you have to worry about cleaning is the benchtop.
 

 

> On 29 Apr 2020, at 21:38, Crissy Lynette Tarver  wrote:
> 
> https://pdb101.rcsb.org/learn/videos/fighting-coronavirus-with-soap
> 
> 
> Crissy L Tarver
> Postdoctoral Researcher
> Department of Structural Biology
> Stanford University School of Medicine
> From: CCP4 bulletin board  on behalf of Tim Gruene 
> 
> Sent: Wednesday, April 29, 2020 11:53:32 AM
> 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 interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
> 
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
> 
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
> 
> But maybe there are other ways that won't require gloves?
> 
> Best regards,
> Tim
> 
> -- 
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
> 
> Phone: +43-1-4277-70202
> 
> GPG Key ID = A46BEE1A
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] 2fofc maps from refmac twinned refinement - clarify?

[Petrus Zwart]

I am not quite sure how it is done in Refmac, but in phenix it works as
follows

- difference maps are gradient maps for a least squares target and they do
not contain any amplitude contamination from twinning.

- Fo type maps are computed either via classic detwinning (solving the
linear equations) or this is done using some proportionality rule like
James and Eleanor allude to.

An alternative way would be use something like this relation

Map coefficients we want: 2Fo-Fc

Realize that 2Fo - Fc = Fc + 2(Fo-Fc)

and compute

Fcalc + 2*difference map*magic scale factor

It is a bit of a hack, no FOM's etc and I worry about bias. It would be far
better to get map coefficients from the joint distribution of the structure
factors that take into account twinning. In this way, you can handle
experimental error as well in a proper fashion. I wouldn't be surprised if
this happens in Refmac, it doesn't in Phenix (yet).

My PhD supervisor's advice always holds btw: "Grow better crystals"

Regards
Peter





On Wed, Apr 29, 2020 at 12:40 PM James Holton  wrote:

> Yes, they are "de-twinned".  There is really no other way to do it.
> Without de-twinning you'd be looking at a map of two overlapping
> structures.  How do you turn a single observation of the sum of
> intensities from two different hkls into two different Iobs values? You
> need to know the ratio.  The twin fraction is one way, but once it gets
> close to 0.5 the "de-twinning" gets very noisy.  I believe what the
> refinement programs do is use the ratio of the two Fcalc^2 values in
> order to "split" the Iobs value. Doesn't that introduce "bias"?  Yes, of
> course it does.  That's one of the many reasons why twinning sucks.
>
> Now, of course, there are probably fancy weighting schemes that make
> things a bit better, but rather than speculate I'd ask the program
> authors themselves.  The best thing, of course, is to refine until Icalc
> becomes more accurate than Iobs, which is the typical result of
> small-molecule refinements.  I expect that is why they are not nearly as
> afraid of twinning as we are.
>
> -James Holton
> MAD Scientist
>
>
> On 4/28/2020 2:19 PM, Frank von Delft wrote:
> > Hi all - feel free to point me to the docs if it's already clear
> > somewhere:
> >
> > When refmac generates 2mFo-DFc maps after twinned refinement, are they
> > the "untwinned" view of the electron density?  I.e. with the twinnig
> > convoluted out by his statistical magic?
> >
> > I remember Garib mentioning the ambition a few years ago;  but I've
> > not been paying enough attention to remember if it's actually
> > implemented, or still in progress (because it's hard).
> >
> >
> > Thanks
> > Frank
> >
> > 
> >
> > 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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-- 

P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246

PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
-



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Re: [ccp4bb] disinfecting keyboards

[Crissy Lynette Tarver]

https://pdb101.rcsb.org/learn/videos/fighting-coronavirus-with-soap


Crissy L Tarver
Postdoctoral Researcher
Department of Structural Biology
Stanford University School of Medicine

From: CCP4 bulletin board  on behalf of Tim Gruene 

Sent: Wednesday, April 29, 2020 11:53:32 AM
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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] disinfecting keyboards

[Lukasz Sobala]

You can find tutorials for everything on YouTube, and one prominently
featured >>tech tip<< uses a dishwasher on a selection of cheap to
expensive keyboards. Interestingly, all keyboards worked after drying.

Good luck,
Lukasz

On Wed, 29 Apr 2020, 22:12 DUMAS Philippe (IGBMC), <
p.du...@ibmc-cnrs.unistra.fr> wrote:

> I got a good advice about it: inject WhiteHouse disinfectant right into
> the cpu.
> Good to repeat it a couple of times, but wear mask and gloves against
> possible Cotrump-16-20 last attacks !
> Hope it will be helpful.
> Philippe Dumas
> (#SupportFauci)
>
>
>
> - Mail original -
> De: "Jurgen Bosch" 
> À: "CCP4BB" 
> Envoyé: Mercredi 29 Avril 2020 21:35:06
> Objet: Re: [ccp4bb] disinfecting keyboards
>
> You really just need two keyboards per computer, every user change, just
> add the used keyboards into the hutch, the rest should take care of itself
> then.
>
> You are at the source to successfully blast these little viruses
>
> Jürgen
> > On Apr 29, 2020, at 3:30 PM, James Holton  wrote:
> >
> > Keyboards are cheap.  Why not everyone get their own?
> >
> > Then we can all stop fighting about whether the  key should be
> shaped like an "L" or not.
> >
> > -James Holton
> > MAD Scientist
> >
> > On 4/29/2020 11:53 AM, Tim Gruene wrote:
> >> 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 interface will be the computer keyboards, as well
> >> as the door of our X-ray diffractometer and the mounting of the
> >> crystals.
> >>
> >> The keyboard labels may not like alcohols (and the efficiency of
> >> injecting disinfecting through the USB cable is also under discussion,
> >> so I heard).
> >>
> >> One way would be to use individual keyboards, and wearing gloves for
> >> replugging, and to use gloves for mounting crystals.
> >>
> >> But maybe there are other ways that won't require gloves?
> >>
> >> Best regards,
> >> Tim
> >>
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> 
>
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Re: [ccp4bb] disinfecting keyboards

[Bernhard Rupp]

>This email was not typed but spoken by Siri on my laptop.

Outing yourself?
https://www.youtube.com/watch?v=7-SVvtxHJGU

HTH BR


> On Apr 29, 2020, at 2:59 PM, Sravya Mounika Kantamneni 
>  wrote:
> 
> How about using keyboard guards and dissecting them as usual?
> 
> Regards,
> Sravya
> 
>> On Apr 29, 2020, at 8:53 PM, Tim Gruene  wrote:
>> 
>> 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 interface will be the computer keyboards, as 
>> well as the door of our X-ray diffractometer and the mounting of the 
>> crystals.
>> 
>> The keyboard labels may not like alcohols (and the efficiency of 
>> injecting disinfecting through the USB cable is also under 
>> discussion, so I heard).
>> 
>> One way would be to use individual keyboards, and wearing gloves for 
>> replugging, and to use gloves for mounting crystals.
>> 
>> But maybe there are other ways that won't require gloves?
>> 
>> Best regards,
>> Tim
>> 
>> --
>> --
>> Tim Gruene
>> Head of the Centre for X-ray Structure Analysis Faculty of Chemistry 
>> University of Vienna
>> 
>> Phone: +43-1-4277-70202
>> 
>> GPG Key ID = A46BEE1A
>> 
>> #
>> ###
>> 
>> 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] disinfecting keyboards

[Matthew Bick]

Even better - UV "inside the computer".  Hasn't been done, but we're
testing it and it looks promising.

Matthew Bick

On Wed, Apr 29, 2020 at 1:12 PM DUMAS Philippe (IGBMC) <
p.du...@ibmc-cnrs.unistra.fr> wrote:

> I got a good advice about it: inject WhiteHouse disinfectant right into
> the cpu.
> Good to repeat it a couple of times, but wear mask and gloves against
> possible Cotrump-16-20 last attacks !
> Hope it will be helpful.
> Philippe Dumas
> (#SupportFauci)
>
>
>
> - Mail original -
> De: "Jurgen Bosch" 
> À: "CCP4BB" 
> Envoyé: Mercredi 29 Avril 2020 21:35:06
> Objet: Re: [ccp4bb] disinfecting keyboards
>
> You really just need two keyboards per computer, every user change, just
> add the used keyboards into the hutch, the rest should take care of itself
> then.
>
> You are at the source to successfully blast these little viruses
>
> Jürgen
> > On Apr 29, 2020, at 3:30 PM, James Holton  wrote:
> >
> > Keyboards are cheap.  Why not everyone get their own?
> >
> > Then we can all stop fighting about whether the  key should be
> shaped like an "L" or not.
> >
> > -James Holton
> > MAD Scientist
> >
> > On 4/29/2020 11:53 AM, Tim Gruene wrote:
> >> 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 interface will be the computer keyboards, as well
> >> as the door of our X-ray diffractometer and the mounting of the
> >> crystals.
> >>
> >> The keyboard labels may not like alcohols (and the efficiency of
> >> injecting disinfecting through the USB cable is also under discussion,
> >> so I heard).
> >>
> >> One way would be to use individual keyboards, and wearing gloves for
> >> replugging, and to use gloves for mounting crystals.
> >>
> >> But maybe there are other ways that won't require gloves?
> >>
> >> Best regards,
> >> Tim
> >>
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> 
>
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Re: [ccp4bb] disinfecting keyboards

[David Briggs]

Have you considered autoclaving the keyboards in between users?

Or maybe autoclave the users?

That'll work, right?

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of Bernhard Rupp 

Sent: Wednesday, April 29, 2020 9:19:57 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] disinfecting keyboards


>I do not know if any of the equipment may suffer damage in the medium or long 
>term due to the incidence of UV light.



Hmm….everything made of cheap plastic….i.e. almost everything made in 
China…that must be the true conspiracy behind the virus!



Cheers, BR



On Wed, Apr 29, 2020 at 2:53 PM Tim Gruene 
mailto:tim.gru...@univie.ac.at>> wrote:

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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
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--

Eduardo Rodríguez-Román, PhD

ASM, eLIFE & USERN Ambassador

Biotechnology and Plant Virology Lab

Center for Microbiology and Cell Biology

Instituto Venezolano de Investigaciones Científicas

PO Box 20632, Caracas 1020A, Venezuela.

ORCiD: 
orcid.org/-0001-8717-7527

Phone: +58 (212) 504 1189/1366/1500

Cell phone: +58 (424) 111 0375

E-mail: ejrodrig...@ivic.gob.ve,

or erodriguezro...@gmail.com

Twitter: 
@erodriguezroman

 
[https://docs.google.com/uc?export=download=1_MmmlkLEEx67-CUSQYLGHM9eAuWKgHX0=0B7ogjC4ootvrUi9ITGpVWEd4S01rVnBVTjVvd3p0OUN5d1hRPQ]
 

  
[https://drive.google.com/uc?id=1rHts30EjUWzlunzrJxVquEu_aYsfYmHE=download]
 


[https://docs.google.com/uc?export=download=1eQDqlB4kvjK2qLYX3htqhh54b-l76rcs=0B7ogjC4ootvrNy9vbGtQb0h4YkhUK2J5MmZvczhMK0NBbks0PQ]
 
[https://docs.google.com/uc?export=download=1CekoNvw6Til3qV0zBn5Vohz05SD-nyTR=0B7ogjC4ootvrRFhPTzJiMFBrZ1ZqRUpJYTRDZ0FBRDFkT28wPQ]






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Re: [ccp4bb] disinfecting keyboards

[Bernhard Rupp]

>I do not know if any of the equipment may suffer damage in the medium or long 
>term due to the incidence of UV light.

 

Hmm….everything made of cheap plastic….i.e. almost everything made in 
China…that must be the true conspiracy behind the virus!

 

Cheers, BR

 

On Wed, Apr 29, 2020 at 2:53 PM Tim Gruene mailto:tim.gru...@univie.ac.at> > wrote:

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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
 =1




 

-- 

Eduardo Rodríguez-Román, PhD

ASM, eLIFE & USERN Ambassador

Biotechnology and Plant Virology Lab

Center for Microbiology and Cell Biology

Instituto Venezolano de Investigaciones Científicas

PO Box 20632, Caracas 1020A, Venezuela.

ORCiD:   orcid.org/-0001-8717-7527

Phone:   +58 (212) 504 1189/1366/1500

Cell phone:   +58 (424) 111 0375

E-mail: ejrodrig...@ivic.gob.ve  ,

or erodriguezro...@gmail.com  

Twitter: @erodriguezroman  

      

     


 

  _  

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Re: [ccp4bb] disinfecting keyboards

[Frank Von Delft]

Make your users wear masks.

Sent from tiny silly touch screen

From: David Schuller 
Sent: Wednesday, 29 April 2020 21:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] disinfecting keyboards

If you are going that route, it would make sense to locate the UV lamps in the 
X-ray hutch, since those already have safety interlocks, etc. The X-ray beam 
itself is too directional to uniformly cover much.


On 2020-04-29 15:48, Eduardo Rodríguez-Román wrote:
Hi Tim,
It may be convenient to install a UV light lamp in the room. Have you thought 
about that?
I do not know if any of the equipment may suffer damage in the medium or long 
term due to the incidence of UV light. You must evaluate this.
UV light is used in different microbiology laboratories around the world to 
sterilize the work area.
Just turn on the UV light about ten min before entering the room, then turn off 
the UV light, and wait another 15 min to enter. When leaving, turn on the UV 
light for 10 min, and then turn off.
The UV light on/off switch should be located outside the room.
Best,
Eduardo.

On Wed, Apr 29, 2020 at 2:53 PM Tim Gruene 
mailto:tim.gru...@univie.ac.at>> wrote:
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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


--
Eduardo Rodríguez-Román, PhD
ASM, eLIFE & USERN Ambassador
Biotechnology and Plant Virology Lab
Center for Microbiology and Cell Biology
Instituto Venezolano de Investigaciones Científicas
PO Box 20632, Caracas 1020A, Venezuela.
ORCiD: orcid.org/-0001-8717-7527
Phone: +58 (212) 504 1189/1366/1500
Cell phone: +58 (424) 111 0375
E-mail: ejrodrig...@ivic.gob.ve,
or erodriguezro...@gmail.com
Twitter: @erodriguezroman
 
[https://docs.google.com/uc?export=download=1_MmmlkLEEx67-CUSQYLGHM9eAuWKgHX0=0B7ogjC4ootvrUi9ITGpVWEd4S01rVnBVTjVvd3p0OUN5d1hRPQ]
   
[https://drive.google.com/uc?id=1rHts30EjUWzlunzrJxVquEu_aYsfYmHE=download]
 
[https://docs.google.com/uc?export=download=1eQDqlB4kvjK2qLYX3htqhh54b-l76rcs=0B7ogjC4ootvrNy9vbGtQb0h4YkhUK2J5MmZvczhMK0NBbks0PQ]
 
[https://docs.google.com/uc?export=download=1CekoNvw6Til3qV0zBn5Vohz05SD-nyTR=0B7ogjC4ootvrRFhPTzJiMFBrZ1ZqRUpJYTRDZ0FBRDFkT28wPQ]




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--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu



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Re: [ccp4bb] disinfecting keyboards

[DUMAS Philippe (IGBMC)]

I got a good advice about it: inject WhiteHouse disinfectant right into the cpu.
Good to repeat it a couple of times, but wear mask and gloves against possible 
Cotrump-16-20 last attacks !
Hope it will be helpful.
Philippe Dumas 
(#SupportFauci)



- Mail original -
De: "Jurgen Bosch" 
À: "CCP4BB" 
Envoyé: Mercredi 29 Avril 2020 21:35:06
Objet: Re: [ccp4bb] disinfecting keyboards

You really just need two keyboards per computer, every user change, just add 
the used keyboards into the hutch, the rest should take care of itself then.

You are at the source to successfully blast these little viruses

Jürgen 
> On Apr 29, 2020, at 3:30 PM, James Holton  wrote:
> 
> Keyboards are cheap.  Why not everyone get their own?
> 
> Then we can all stop fighting about whether the  key should be shaped 
> like an "L" or not.
> 
> -James Holton
> MAD Scientist
> 
> On 4/29/2020 11:53 AM, Tim Gruene wrote:
>> 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 interface will be the computer keyboards, as well
>> as the door of our X-ray diffractometer and the mounting of the
>> crystals.
>> 
>> The keyboard labels may not like alcohols (and the efficiency of
>> injecting disinfecting through the USB cable is also under discussion,
>> so I heard).
>> 
>> One way would be to use individual keyboards, and wearing gloves for
>> replugging, and to use gloves for mounting crystals.
>> 
>> But maybe there are other ways that won't require gloves?
>> 
>> Best regards,
>> Tim
>> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] disinfecting keyboards

[David Schuller]

If you are going that route, it would make sense to locate the UV lamps 
in the X-ray hutch, since those already have safety interlocks, etc. The 
X-ray beam itself is too directional to uniformly cover much.



On 2020-04-29 15:48, Eduardo Rodríguez-Román wrote:

Hi Tim,
It may be convenient to install a UV light lamp in the room. Have you 
thought about that?
I do not know if any of the equipment may suffer damage in the medium 
or long term due to the incidence of UV light. You must evaluate this.
UV light is used in different microbiology laboratories around the 
world to sterilize the work area.
Just turn on the UV light about ten min before entering the room, then 
turn off the UV light, and wait another 15 min to enter. When leaving, 
turn on the UV light for 10 min, and then turn off.

The UV light on/off switch should be located outside the room.
Best,
Eduardo.

On Wed, Apr 29, 2020 at 2:53 PM Tim Gruene > wrote:


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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

-- 
--

Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



--
*Eduardo Rodríguez-Román, PhD*
ASM, eLIFE & USERN Ambassador
Biotechnology and Plant Virology Lab
Center for Microbiology and Cell Biology
Instituto Venezolano de Investigaciones Científicas
PO Box 20632, Caracas 1020A, Venezuela.
ORCiD: orcid.org/-0001-8717-7527 


Phone: +58 (212) 504 1189/1366/1500 
Cell phone: +58 (424) 111 0375 
E-mail: ejrodrig...@ivic.gob.ve ,
or erodriguezro...@gmail.com 
Twitter: @erodriguezroman 
 





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--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu




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Re: [ccp4bb] disinfecting keyboards

[Crissy Lynette Tarver]

Hello,

I agree with wiping instruments down with 75-80% ethanol (as used to clean 
during cell culture). However, the BEST precaution is simply not touching your 
face and washing your hands for 20-30 seconds after touching anything. I made 
it a habit of scrubbing my hands with Hibiclens after every shift when I worked 
in ER, and I was ill only 3 times in 12 years.

Crissy L Tarver
Postdoctoral Researcher
Department of Structural Biology
Stanford University School of Medicine

From: CCP4 bulletin board  on behalf of Andrea Thorn 

Sent: Wednesday, April 29, 2020 12:41:57 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] disinfecting keyboards


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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



UT Southwestern

Medical Center


The future of medicine, today.



To unsubscribe from the CCP4BB list, click the 

Re: [ccp4bb] disinfecting keyboards

[Eduardo Rodríguez-Román]

Hi Tim,
It may be convenient to install a UV light lamp in the room. Have you
thought about that?
I do not know if any of the equipment may suffer damage in the medium or
long term due to the incidence of UV light. You must evaluate this.
UV light is used in different microbiology laboratories around the world to
sterilize the work area.
Just turn on the UV light about ten min before entering the room, then turn
off the UV light, and wait another 15 min to enter. When leaving, turn on
the UV light for 10 min, and then turn off.
The UV light on/off switch should be located outside the room.
Best,
Eduardo.

On Wed, Apr 29, 2020 at 2:53 PM Tim Gruene  wrote:

> 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 interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
>
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
>
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
>
> But maybe there are other ways that won't require gloves?
>
> Best regards,
> Tim
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
*Eduardo Rodríguez-Román, PhD*
ASM, eLIFE & USERN Ambassador
Biotechnology and Plant Virology Lab
Center for Microbiology and Cell Biology
Instituto Venezolano de Investigaciones Científicas
PO Box 20632, Caracas 1020A, Venezuela.
ORCiD: orcid.org/-0001-8717-7527
Phone: +58 (212) 504 1189/1366/1500 <%2B58%20%28212%29%20504%201366>
Cell phone: +58 (424) 111 0375
E-mail: ejrodrig...@ivic.gob.ve,
or erodriguezro...@gmail.com
Twitter: @erodriguezroman 
    





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Re: [ccp4bb] disinfecting keyboards

[Andrea Thorn]

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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



UTSouthwestern

Medical Center


The future of medicine, today.




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CAUTION: This email originated from outside UTSW. Please be cautious
of links or attachments, and validate the sender's email address
before replying.




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--
Dr. Andrea Thorn | group leader
andrea.th...@uni-wuerzburg.de
+49 931 31-83677

Rudolf Virchow Center, University of Wuerzburg
Josef-Schneider-Str. 2 | 97080 Wuerzburg | Germany
https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/




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Re: [ccp4bb] disinfecting keyboards

[James Holton]

Because as soon as I put on gloves my nose starts to itch.

On 4/29/2020 12:37 PM, gianluca.sant...@esrf.fr wrote:

ISO keyboards are bad.
But why not just using disposable gloves to operate the instruments?

On April 29, 2020 9:30:19 PM GMT+02:00, James Holton 
 wrote:


Keyboards are cheap.  Why not everyone get their own?

Then we can all stop fighting about whether the  key should be
shaped like an "L" or not.

-James Holton
MAD Scientist

On 4/29/2020 11:53 AM, Tim Gruene wrote:

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 interface will be the computer keyboards, as
well as the door of our X-ray diffractometer and the mounting
of the crystals. The keyboard labels may not like alcohols
(and the efficiency of injecting disinfecting through the USB
cable is also under discussion, so I heard). One way would be
to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals. But maybe
there are other ways that won't require gloves? Best regards, Tim 





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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


--
Sent from my Android device with K-9 Mail. Please excuse my brevity. 





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Re: [ccp4bb] 2fofc maps from refmac twinned refinement - clarify?

[James Holton]

Yes, they are "de-twinned".  There is really no other way to do it. 
Without de-twinning you'd be looking at a map of two overlapping 
structures.  How do you turn a single observation of the sum of 
intensities from two different hkls into two different Iobs values? You 
need to know the ratio.  The twin fraction is one way, but once it gets 
close to 0.5 the "de-twinning" gets very noisy.  I believe what the 
refinement programs do is use the ratio of the two Fcalc^2 values in 
order to "split" the Iobs value. Doesn't that introduce "bias"?  Yes, of 
course it does.  That's one of the many reasons why twinning sucks.


Now, of course, there are probably fancy weighting schemes that make 
things a bit better, but rather than speculate I'd ask the program 
authors themselves.  The best thing, of course, is to refine until Icalc 
becomes more accurate than Iobs, which is the typical result of 
small-molecule refinements.  I expect that is why they are not nearly as 
afraid of twinning as we are.


-James Holton
MAD Scientist


On 4/28/2020 2:19 PM, Frank von Delft wrote:
Hi all - feel free to point me to the docs if it's already clear 
somewhere:


When refmac generates 2mFo-DFc maps after twinned refinement, are they 
the "untwinned" view of the electron density?  I.e. with the twinnig 
convoluted out by his statistical magic?


I remember Garib mentioning the ambition a few years ago;  but I've 
not been paying enough attention to remember if it's actually 
implemented, or still in progress (because it's hard).



Thanks
Frank



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Re: [ccp4bb] disinfecting keyboards

[Ankita Singla]

Injecting the disinfectant might not be much functional. Maybe the Royal
Society of London have thoughts to add to this. Can we publish it and call
it a computer hazard! *laughs*


Ankita Singla
Masters student
All India Institute of medical sciences
New Delhi

On Thu 30 Apr, 2020, 12:54 AM , <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:

> Re: injecting disinfect[ing]ant[?] through the USB cable [port?].
>
> Dear Tim
>
> I am intrigued, seriously.
>
> Best wishes.
>
> Jon Cooper
>
> On 29 Apr 2020 19:53, Tim Gruene  wrote:
>
> 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 interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
>
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
>
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
>
> But maybe there are other ways that won't require gloves?
>
> Best regards,
> Tim
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> On 29 Apr 2020 19:53, Tim Gruene  wrote:
>
> 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 interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
>
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
>
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
>
> But maybe there are other ways that won't require gloves?
>
> Best regards,
> Tim
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> On 29 Apr 2020 19:53, Tim Gruene  wrote:
>
> 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 interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
>
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
>
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
>
> But maybe there are other ways that won't require gloves?
>
> Best regards,
> Tim
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
> 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] disinfecting keyboards

[Gianluca Santoni]

ISO keyboards are bad.
But why not just using disposable gloves to operate the instruments?

On April 29, 2020 9:30:19 PM GMT+02:00, James Holton  wrote:
>Keyboards are cheap.  Why not everyone get their own?
>
>Then we can all stop fighting about whether the  key should be 
>shaped like an "L" or not.
>
>-James Holton
>MAD Scientist
>
>On 4/29/2020 11:53 AM, Tim Gruene wrote:
>> 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 interface will be the computer keyboards, as
>well
>> as the door of our X-ray diffractometer and the mounting of the
>> crystals.
>>
>> The keyboard labels may not like alcohols (and the efficiency of
>> injecting disinfecting through the USB cable is also under
>discussion,
>> so I heard).
>>
>> One way would be to use individual keyboards, and wearing gloves for
>> replugging, and to use gloves for mounting crystals.
>>
>> But maybe there are other ways that won't require gloves?
>>
>> Best regards,
>> Tim
>>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
Sent from my Android device with K-9 Mail. Please excuse my brevity.



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Re: [ccp4bb] disinfecting keyboards

[Jurgen Bosch]

You really just need two keyboards per computer, every user change, just add 
the used keyboards into the hutch, the rest should take care of itself then.

You are at the source to successfully blast these little viruses

Jürgen 
> On Apr 29, 2020, at 3:30 PM, James Holton  wrote:
> 
> Keyboards are cheap.  Why not everyone get their own?
> 
> Then we can all stop fighting about whether the  key should be shaped 
> like an "L" or not.
> 
> -James Holton
> MAD Scientist
> 
> On 4/29/2020 11:53 AM, Tim Gruene wrote:
>> 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 interface will be the computer keyboards, as well
>> as the door of our X-ray diffractometer and the mounting of the
>> crystals.
>> 
>> The keyboard labels may not like alcohols (and the efficiency of
>> injecting disinfecting through the USB cable is also under discussion,
>> so I heard).
>> 
>> One way would be to use individual keyboards, and wearing gloves for
>> replugging, and to use gloves for mounting crystals.
>> 
>> But maybe there are other ways that won't require gloves?
>> 
>> Best regards,
>> Tim
>> 
> 
> 
> 
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Re: [ccp4bb] disinfecting keyboards

[James Holton]

Keyboards are cheap.  Why not everyone get their own?

Then we can all stop fighting about whether the  key should be 
shaped like an "L" or not.


-James Holton
MAD Scientist

On 4/29/2020 11:53 AM, Tim Gruene wrote:

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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim





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Re: [ccp4bb] disinfecting keyboards

[00000c2488af9525-dmarc-request]

Re: injecting disinfect[ing]ant[?] through the USB cable [port?].Dear TimI am intrigued, seriously.Best wishes.Jon CooperOn 29 Apr 2020 19:53, Tim Gruene  wrote: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 interface will be the computer keyboards, as well

as the door of our X-ray diffractometer and the mounting of the

crystals.



The keyboard labels may not like alcohols (and the efficiency of

injecting disinfecting through the USB cable is also under discussion,

so I heard).



One way would be to use individual keyboards, and wearing gloves for

replugging, and to use gloves for mounting crystals.



But maybe there are other ways that won't require gloves?



Best regards,

Tim



-- 

--

Tim Gruene

Head of the Centre for X-ray Structure Analysis

Faculty of Chemistry

University of Vienna



Phone: +43-1-4277-70202



GPG Key ID = A46BEE1A







To unsubscribe from the CCP4BB list, click the following link:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


On 29 Apr 2020 19:53, Tim Gruene  wrote: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 interface will be the computer keyboards, as well

as the door of our X-ray diffractometer and the mounting of the

crystals.



The keyboard labels may not like alcohols (and the efficiency of

injecting disinfecting through the USB cable is also under discussion,

so I heard).



One way would be to use individual keyboards, and wearing gloves for

replugging, and to use gloves for mounting crystals.



But maybe there are other ways that won't require gloves?



Best regards,

Tim



-- 

--

Tim Gruene

Head of the Centre for X-ray Structure Analysis

Faculty of Chemistry

University of Vienna



Phone: +43-1-4277-70202



GPG Key ID = A46BEE1A







To unsubscribe from the CCP4BB list, click the following link:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


On 29 Apr 2020 19:53, Tim Gruene  wrote: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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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] disinfecting keyboards

[Jurgen Bosch]

Somehow this reminds me of the scene of Scotty talking into the mouse when he 
is instructed to use the keyboard to interact with the computer.

How is voice recognition these days on Linux?

This email was not typed but spoken by Siri on my laptop.

Jürgen 


> On Apr 29, 2020, at 2:59 PM, Sravya Mounika Kantamneni 
>  wrote:
> 
> How about using keyboard guards and dissecting them as usual?
> 
> Regards,
> Sravya
> 
>> On Apr 29, 2020, at 8:53 PM, Tim Gruene  wrote:
>> 
>> 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 interface will be the computer keyboards, as well
>> as the door of our X-ray diffractometer and the mounting of the
>> crystals.
>> 
>> The keyboard labels may not like alcohols (and the efficiency of
>> injecting disinfecting through the USB cable is also under discussion,
>> so I heard).
>> 
>> One way would be to use individual keyboards, and wearing gloves for
>> replugging, and to use gloves for mounting crystals.
>> 
>> But maybe there are other ways that won't require gloves?
>> 
>> Best regards,
>> Tim
>> 
>> -- 
>> --
>> Tim Gruene
>> Head of the Centre for X-ray Structure Analysis
>> Faculty of Chemistry
>> University of Vienna
>> 
>> Phone: +43-1-4277-70202
>> 
>> GPG Key ID = A46BEE1A
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] disinfecting keyboards

[Sravya Mounika Kantamneni]

How about using keyboard guards and dissecting them as usual?

Regards,
Sravya

> On Apr 29, 2020, at 8:53 PM, Tim Gruene  wrote:
> 
> 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 interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
> 
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
> 
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
> 
> But maybe there are other ways that won't require gloves?
> 
> Best regards,
> Tim
> 
> -- 
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
> 
> Phone: +43-1-4277-70202
> 
> GPG Key ID = A46BEE1A
> 
> 
> 
> 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] disinfecting keyboards

[Ethan A Merritt]

On Wednesday, 29 April 2020 11:53:32 PDT Tim Gruene wrote:
> Dear all,
> 
> can you make suggestions for how to disinfect computer keyboards, and
> instrument panels?

The consensus here is that the keyboards must have a cover that can be
washed/disinfected.  They are not [usually] that hard to find. Sometimes
they are called "skins" rather than covers.

Instrument panels - no idea.  Labs here have discussed instituting a strict
tagging system with a log.  One user per instrument, separated by
[72 hours? not sure if there is a consensus] between users. 

Ethan

> 
> Our facility is going to reboot next week, with shifts so that people
> don't meet. The main interface will be the computer keyboards, as well
> as the door of our X-ray diffractometer and the mounting of the
> crystals.
> 
> The keyboard labels may not like alcohols (and the efficiency of
> injecting disinfecting through the USB cable is also under discussion,
> so I heard).
> 
> One way would be to use individual keyboards, and wearing gloves for
> replugging, and to use gloves for mounting crystals.
> 
> But maybe there are other ways that won't require gloves?
> 
> Best regards,
> Tim
> 
> 


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] disinfecting keyboards

[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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
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UT Southwestern


Medical Center



The future of medicine, today.




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CAUTION: This email originated from outside UTSW. Please be cautious of links 
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Re: [ccp4bb] disinfecting keyboards

[Diana Tomchick]

?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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



UT Southwestern


Medical Center



The future of medicine, today.




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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] disinfecting keyboards

[Dominika Borek]

http://www.viziflex.com/disposables/universal-disposable-50-pack/

D.


On 2020-04-29 01:53 PM, Tim Gruene wrote:

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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


--
Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-9577 (phone) *** 214-645-6353 (fax)



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Re: [ccp4bb] disinfecting keyboards

[Tristan Croll]

I once knew a particularly germaphobic IT manager who used to absolutely 
*everything* via ssh or remote desktop from his own laptop, even when he 
was physically in front of the user's computer. If feasible, that 
approach would actually seem quite smart in the current environment.


On 2020-04-29 19:53, Tim Gruene wrote:

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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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] disinfecting keyboards

[Tim Gruene]

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 interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

The keyboard labels may not like alcohols (and the efficiency of
injecting disinfecting through the USB cable is also under discussion,
so I heard).

One way would be to use individual keyboards, and wearing gloves for
replugging, and to use gloves for mounting crystals.

But maybe there are other ways that won't require gloves?

Best regards,
Tim

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


pgp1PC7XeJlSP.pgp
Description: OpenPGP digital signature

[ccp4bb] Sanofi Postdoctoral Fellowship: Computational Scientist for Antibody Engineering (Framingham, MA)

[Qiu, Yu PH/US]

To the ccp4bb community,

If you have Ph. D. in data science, artificial intelligence, machine learning, 
deep learning, computer sciences, bioinformatics, mathematics, computational 
biology, or related field, and interested in applying cutting-edge technology 
to antibody/protein engineering, please check this postdoc opportunity.
https://sanofi.wd3.myworkdayjobs.com/en-US/StudentPrograms/job/Framingham-MA/Sanofi-Postdoctoral-Fellowship--Computational-Scientist-for-Antibody-Engineering--Framingham--MA-_R2552646

Yu Qiu
Principal Scientist, Protein Engineering, Biologics Research
TEL.: (+1)508-270-2555
49 New York Avenue - Framingham, MA 01701 - USA
[cid:image003.jpg@01D61E24.7DCCD480]

Please consider the environment before printing this email!




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[ccp4bb] Micro-ED "pushing the frontiers" again ... but which frontiers?

[Gerard Bricogne]

Dear all,

 There have been warnings circulating for quite some time now about the
possible impact of SARS-CoV-2 on the cognitive abilities of patients who
have recovered from Covid-19, and I fear that I have reasons to worry about
possibly having fallen victim to these ... .

 I came across a remarkable piece of work published in 

https://doi.org/10.1016/j.str.2020.01.008

entitled "Experimental Phasing of MicroED Data Using Radiation Damage". I
will follow my notes, in order to ensure that I do not stray even further
from the logic of this paper than I may have done already in writing them
down.

 The subject matter of this article is a famous seven-residue peptide of
exceptional structural stability (which is why it is associated with severe
pathologies), giving radiation-hard microcrystals capable of yielding 1.0
Angs resolution electron diffraction data enabling the solution of this (in
effect, small-molecule) structure by direct methods (PDB code 6CLI) from
such data. A thorough study of radiation damage had been conducted on these
crystals in a previous paper (https://doi.org/10.1016/j.str.2018.03.021),
revealing a detailed picture of site-specific radiation damage affecting in
particular the fully-occupied Zn atom co-crystallised with the peptide.

 The material presented in this new paper is a by-product of the earlier
analysis at 1.0 Angs resolution, whereby two datasets were assembled to
correspond to two substantially different stages of radiation damage (PDB
codes 6CLI and 6CLJ) and were truncated to 1.4 Angs to make direct methods
ineffective. The question is then whether this differential radiation damage
can be exploited as a source of experimental phase information, as has been
done successfully with the so-called RIP method in X-ray crystallography,
the implication being that this could then constitute a generally applicable
method for experimentally phasing electron diffraction data. This ambition
is clearly articulated in the last paragraph of the Introduction: "Here, we
demonstrate that radiation damage from exposure to the electron beam can be
used to solve the phase problem in Micro-ED experiments".

 Enough to get you sitting on the edge of your seat ... .

 The delicate scaling between the two datasets (the first called "low
dose" and the second called "damaged" was accomplished by the DSCA method in
SHELXC so that the difference Patterson showed a single peak, interpreted as
being due to radiation damage on the Zn atom between the two datasets. As we
are in P1 this Zn atom could have been placed at the origin, but for the
sake of comparability, a difference Fourier map was computed by combining
the amplitude differences corresponding to the scaled intensities with the
phases from 6CLI, in which the highest peak corresponded to the position of
the Zn atom in 6CLI. 

 Now the heart of the matter. The maps produced from this single Zn as
sole source of phase information were uninterpretable. Density modification
did not help, presumably because these crystals are close-packed so that
there is no solvent to flatten. The method used instead in order to "solve
the phase problem" (sic) consists in placing atoms in trial positions and
applying some selection criteria to prune out the worst choices. None of
these criteria, however, can dispense with using the wMPE (weighted mean
phase error) from the known structure (6CLI) as a guide. In whatever way it
may be described, therefore, the procedure used seems depends on already
knowing the perfect structure from the previous work at 1.0 Angs resolution.

 This is where I began to question my own sanity, and to wonder whether,
like Rip van Winkle (https://en.wikipedia.org/wiki/Rip_Van_Winkle), I had
somehow fallen into a deep sleep and completely missed a revolution: I was
still clinging to the old-fashioned conception of experimental phasing as
the technique that has the power to produce three-dimensional electron
density maps for macromolecules with total objectivity; now, however, the
new paradigm is clearly that the "experimental" component in experimental
phasing consists in experimenting with the trial placement of atoms while
keeping an eye on the agreement between the corresponding phases and those
for ... the already known structure!

 The problem must obviously lie on my side, since this work has been
published not only in the highly-respected journal "Structure", but even
under the prestigious "Resource" label of this journal, reserved for
articles that are expected "to highlight significant technical advances,
exciting new methods [...] that are of value and interest to the broad
Structure readership and have high impact on the field of structural
biology". 

 I can see that it should indeed have some impact, in the sense of
reassuring Structure readers that if they too happen to have pathologically
stable crystals capable of diffracting to 1.0 Angs resolution (so that, when

Re: [ccp4bb] neg density/high B on sidechains

[Clemens Vonrhein]

Dear Len,

maybe a slight side-track, but you could consider taking one step back
and applying a slightly different approach to data-processing -
something we call "F(early)-F(late)" maps in autoPROC [1].

Why could that be useful here? Because it might allow you to

 (1) differentiate between radiation damage (atoms present at the
 beginning but "lost" or "somewhere else" at the end - which could
 be modelled through occupancy refinement) and genuine disorder
 (static throughout the experiment - probably best described
 through large B-factros);

 (2) generate and use a dataset of the least damaged subset of
 reflections to refine against;

 Note: this is different from just processing a subset of your
 images, since all data is still scaled together but merged
 separately.

Of course, this all assumes that data were collected on a modern
detector/beamline using a low-dose, high-multiplicity (and
fine-sliced) strategy - but that is nowadays usually the case anyway
due to fast detectors and shutterless collection (and because it
allows for more flexibility and better data in the end).

There are other approaches to this (e.g. zero-dose extrapolation [2]
or RABDAM [3]), but if you have a set of diffraction images sitting on
disk it might be easy to just push them through our software.

If you want to have a look at some recent examples (of what you might
be able to learn about your data, collection strategy or model
refinement) also related to radiation damage:

  https://www.globalphasing.com/autoproc/wiki/index.cgi?Covid19
  https://www.globalphasing.com/buster/wiki/index.cgi?Covid19

Cheers

Clemens

[1] https://www.globalphasing.com/autoproc/
[2] Diederichs et al (2003). Acta D 59,903-909.
[3] Shelley et al (2018). J Appl. Cryst 51, 552-559.

On Tue, Apr 28, 2020 at 03:37:20PM +, Thomas, Leonard M. wrote:
> Hello all,
> 
> This is one of those issues that seems to come up now and then.  I have been 
> working on a structure that obviously has some radiation damage as indicted 
> by negative density and/or high thermal parameters.  Since we know that 
> residue X is in the sequence the sidechain should be there and is just 
> flopping around or has been damaged/removed by radiation exposure.  My 
> questions is what is the current thinking on presenting these residues for 
> deposition.  Remove the side chain atoms, drop the occupancy to zero, just 
> let them  behave as they want ie high B factors some negative density.
> 
> Cheers,
> Len
> 
> Leonard Thomas
> lmtho...@ou.edu
> 
> 
> 
> 
> 
> 
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-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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[ccp4bb] EMBL Online Course - Solution Scattering from Biological Macromolecules

[Clement Blanchet]

Dear Colleagues,

the EMBL SAXS group is offering a free online lecture course on Solution
Scattering from Biological Macromolecules.

Starting from Tuesday, May 5th, members of our group will give a total
of 8 live webinars at *9:20 AM (CEST) on Tuesdays and Thursdays*
(excluding public holidays).

This online course aims at young biochemists/biophysicists and
researchers active in related structural methods with little or no
experience in solution scattering. The course will cover the basics of
small angle scattering, instrumentation, sample preparation, modelling
techniques and complementary use with other methods. Participants are
encouraged to send their questions/comments through the text chat
during/after the lectures.

The course is open to everyone, please feel free to invite your colleagues.

To register your interest and see more information on the course
syllabus, please visit
https://www.embl-hamburg.de/biosaxs/courses/embl2020/

In case of any questions, please don’t hesitate to get in touch with us. 
We look forward to seeing you online!

Best wishes,
Clément, Al, Melissa and Dmitri

This course is supported by BIOSAXS GmbH http://biosaxs.com/



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