Re: [ccp4bb] Words to avoid

[Marko Hyvonen]

“The word free still existed in Newspeak, but it could only be used in such 
statements as 'This dog is free from lice' or 'This field is free from weeds'. 
It could not be used in its old sense of 'politically free' or 'intellectually 
free' since political and intellectual freedom no longer existed even as 
concepts, and were therefore of necessity nameless.”

Nineteen Eighty-Four – George Orwell (1949)


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Herbert J. Bernstein mailto:yaya...@gmail.com>>
Sent: Tuesday, March 11, 2025 11:05:38 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Words to avoid

Sorry the prior message lost the attachment.  Here is a complete version:

Dear Colleagues,
  When I got home today, Frances presented me with an article from the
NY Times which contained the attached list of words and the explanation,
 "As President Trump seeks to purge the federal government of "woke"
initiatives, agencies have flagged hundreds of words to limit or avoid,
according to a compilation of government documents."
  For this audience in particular, please note that "Mx", "polarization",
"orientation", "status", "systemic". "discrimination", "equality", "expression",
"barriers", and  "bias" are among the words to avoid.  Care should be
taken in writing proposals and reports since AIs may be used for screening
and they are' likely to miss explanatory context.
  Regard,
 Herbert

From: f...@marbuta.pair.com 
mailto:f...@marbuta.pair.com>>
Sent: Tuesday, March 11, 2025 6:29:06 PM (UTC-05:00) Eastern Time (US & Canada)
To: Bernstein, Herbert
Subject: words not to use (NYT Imes)

accessible
activism
activists
advocacy
advocate
advocates
affirming care
all-inclusive
allyship
anti-racism
antiracist
assigned at birth
assigned female at birth
assigned male at birth
at risk
barrier
barriers
belong
bias
biased
biased toward
biases
biases towards
biologically female
biologically male
BIPOC
Black
breastfeed + people
breastfeed + person
chestfeed + people
chestfeed + person
clean energy
climate crisis
climate science
commercial sex worker
community diversity
community equity
confirmation bias
cultural competence
cultural differences
cultural heritage
cultural sensitivity
culturally appropriate
culturally responsive
DEI
DEIA
DEIAB
DEIJ
disabilities
disability
discriminated
discrimination
discriminatory
disparity
diverse
diverse backgrounds
diverse communities
diverse community
diverse group
diverse groups
diversified
diversify
diversifying
diversity
enhance the diversity
enhancing diversity
environmental quality
equal opportunity
equality
equitable
equitableness
equity
ethnicity
excluded
exclusion
expression
female
females
feminism
fostering inclusivity
GBV
gender
gender based
gender based violence
gender diversity
gender identity
gender ideology
gender-affirming care
genders
Gulf of Mexico
hate speech
health disparity
health equity
hispanic minority
historically
identity
immigrants
implicit bias
implicit biases
inclusion
inclusive
inclusive leadership
inclusiveness
inclusivity
increase diversity
increase the diversity
indigenous community
inequalities
inequality
inequitable
inequities
inequity
injustice
institutional
intersectional
intersectionality
key groups
key people
key populations
Latinx
LGBT
LGBTQ
marginalize
marginalized
men who have sex with men
mental health
minorities
minority
most risk
MSM
multicultural
Mx
Native American
non-binary
nonbinary
oppression
oppressive
orientation
people + uterus
people-centered care
person-centered
person-centered care
polarization
political
pollution
pregnant people
pregnant person
pregnant persons
prejudice
privilege
privileges
promote diversity
promoting diversity
pronoun
pronouns
prostitute
race
race and ethnicity
racial
racial diversity
racial identity
racial inequality
racial justice
racially
racism
segregation
sense of belonging
sex
sexual preferences
sexuality
social justice
sociocultural
socioeconomic
status
stereotype
stereotypes
systemic
systemically
they/them
trans
transgender
transsexual
trauma
traumatic
tribal
unconscious bias
underappreciated
underprivileged
underrepresentation
underrepresented
underserved
undervalued
victim
victims
vulnerable populations
women
women and underrepresented


On Tue, Mar 11, 2025 at 6:59 PM Herbert J. Bernstein 
mailto:yaya...@gmail.com>> wrote:
Dear Colleagues,
  When I got home today, Frances presented me with an article from the
NY Times which contained the attached list of words and the explanation,
 "As President Trump seeks to purge the federal government of "woke" 
initiatives, agencies have flagged hundreds of words to limit or avoid,
according to a compilation of government documents."
  For this audience in particular, please note that "Mx", "polarization", 
"orientation", "status", "systemic". "discrimination", "equality", 
"expression", "barriers", and  "bias" a

Re: [ccp4bb] 3 alternate position of metal ion

[Martin Malý]

PS: It may also help you to check the typical distances from zinc to 
other elements - these data are collected here:

https://github.com/MonomerLibrary/monomers/blob/master/metals.json
as explained here:
https://github.com/MonomerLibrary/monomers/wiki/Dealing-with-metals#typical-interatomic-distances
Cheers,
Martin

On 12/03/2025 10:10, Martin Malý wrote:

Dear Shikha,

We recently released and published program MetalCoord which analyses 
coordination geometry of metal sites and generate restraints to 
stabilise refinement.


My suggestion would be to model there just a single zinc and refine 
the structure. Then put that structure as an input to MetalCoord and 
analyse zinc (monomer code ZN).
Then refine the structure with updated links which MetalCoord gives 
you and with the restraints generated. After refinement, check the 
atom distance and angle outliers.
When modelling of this tricky region became clearer, you can consider 
to use anisotropic ADP just for the zinc.


There is a tutorial for MetalCoord available:
https://github.com/Lekaveh/MetalCoordAnalysis/blob/master/tutorial/tutorial.rst

Good luck! Please let me know how is it going.
Cheers,
Martin

On 12/03/2025 09:34, Shikha Gupta wrote:

Dear all,

I have a complex structure where zinc

metal ion is present in the active site (evidence from several PDBs). 
However, despite multiple efforts, I am getting lot of positive 
densities close to the metal ion (please see image attached). I have 
also tried to place water or two zinc ions but that also doesn’t seem 
to work. The last and overall best solution I came up with was by 
positioning three zinc ions with combined occupancy of 1 
(0.3+0.2+0.3). Although I still see positive densities around but 
this is best I have achieved.


This was a soaked crystals, any suggestions on this. Is this the 
right way to do this. The resolution of the structure is 1.7 angs.


Thanks,
Shikha



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] 3 alternate position of metal ion

[Martin Malý]

Dear Shikha,

We recently released and published program MetalCoord which analyses 
coordination geometry of metal sites and generate restraints to 
stabilise refinement.


My suggestion would be to model there just a single zinc and refine the 
structure. Then put that structure as an input to MetalCoord and analyse 
zinc (monomer code ZN).
Then refine the structure with updated links which MetalCoord gives you 
and with the restraints generated. After refinement, check the atom 
distance and angle outliers.
When modelling of this tricky region became clearer, you can consider to 
use anisotropic ADP just for the zinc.


There is a tutorial for MetalCoord available:
https://github.com/Lekaveh/MetalCoordAnalysis/blob/master/tutorial/tutorial.rst

Good luck! Please let me know how is it going.
Cheers,
Martin

On 12/03/2025 09:34, Shikha Gupta wrote:

Dear all,

I have a complex structure where zinc

metal ion is present in the active site (evidence from several PDBs). 
However, despite multiple efforts, I am getting lot of positive 
densities close to the metal ion (please see image attached). I have 
also tried to place water or two zinc ions but that also doesn’t seem 
to work. The last and overall best solution I came up with was by 
positioning three zinc ions with combined occupancy of 1 
(0.3+0.2+0.3). Although I still see positive densities around but this 
is best I have achieved.


This was a soaked crystals, any suggestions on this. Is this the right 
way to do this. The resolution of the structure is 1.7 angs.


Thanks,
Shikha



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







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[ccp4bb] Protein engineering scientist position

[Patricia Langan]

Dear all,

For those of you on the job market, here is an industry protein engineering and 
structural biology position in the DC area, that we just opened up: 
https://www.miltenyibiotec.com/US-en/about-us/careers/open-positions/job-details/show/E75F4BB0-D186-463B-A97E-8CF005B99454_xx

Scientist I, Protein & Structural Biology *PC 1455
This Scientist-I role is for those with demonstrated education, training, 
and/or work experience in protein engineering, computational structural 
biology, AI/ML, and its application in cell therapy, including CAR-T therapy, 
medicine, or a related field, as specified. The position reports to the group 
leader, and the duties include leading and assisting the group leader in 
executing projects and developing products in the cell and gene therapy area.

Thank you!
Patricia Langan 




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Re: [ccp4bb] Inappropriate

[Harry Powell]

bingo.

But now everone knows…

Harry

> On 11 Mar 2025, at 22:38, Gloria Borgstahl  wrote:
> 
> Thanks for the help everyone,  I found them.  Harry my buddy Wolfie was at a 
> pub in Darmstat if I remember right!
> 
> On Tue, Mar 11, 2025, 8:02 PM Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hmmm. I think if Gloria actually sent this, it might have come from her work 
> address…
> 
> If I’m wrong, the sender would be able to tell me where we met Wolfie…
> 
> Harry
> 
> > On 11 Mar 2025, at 07:42, Gloria Borgstahl  wrote:
> > 
> > Trying to find Tom Peat and Janet
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/



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Re: [ccp4bb] Words to avoid

[Harry Powell]

I am reminded that this diktat has come in the “Land of the Free”

Harry

> On 12 Mar 2025, at 07:12, Marko Hyvonen 
>  wrote:
> 
> “The word free still existed in Newspeak, but it could only be used in such 
> statements as 'This dog is free from lice' or 'This field is free from 
> weeds'. It could not be used in its old sense of 'politically free' or 
> 'intellectually free' since political and intellectual freedom no longer 
> existed even as concepts, and were therefore of necessity nameless.”
> 
>  
> 
> Nineteen Eighty-Four – George Orwell (1949)
> 
>   
> 
> From: CCP4 bulletin board  on behalf of Herbert J. 
> Bernstein 
> Sent: Tuesday, March 11, 2025 11:05:38 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Words to avoid
> 
>  
> 
> Sorry the prior message lost the attachment.  Here is a complete version:
> 
>  
> 
> Dear Colleagues,
> 
>   When I got home today, Frances presented me with an article from the 
> 
> NY Times which contained the attached list of words and the explanation,
> 
>  "As President Trump seeks to purge the federal government of "woke" 
> 
> initiatives, agencies have flagged hundreds of words to limit or avoid, 
> 
> according to a compilation of government documents."
> 
>   For this audience in particular, please note that "Mx", "polarization", 
> 
> "orientation", "status", "systemic". "discrimination", "equality", 
> "expression", 
> 
> "barriers", and  "bias" are among the words to avoid.  Care should be 
> 
> taken in writing proposals and reports since AIs may be used for screening 
> 
> and they are' likely to miss explanatory context.
> 
>   Regard,
> 
>  Herbert
> 
>  
> 
> From: f...@marbuta.pair.com 
> Sent: Tuesday, March 11, 2025 6:29:06 PM (UTC-05:00) Eastern Time (US & 
> Canada)
> To: Bernstein, Herbert
> Subject: words not to use (NYT Imes)
> 
> accessible
> activism
> activists
> advocacy
> advocate
> advocates
> affirming care
> all-inclusive
> allyship
> anti-racism
> antiracist
> assigned at birth
> assigned female at birth
> assigned male at birth
> at risk
> barrier
> barriers
> belong
> bias
> biased
> biased toward
> biases
> biases towards
> biologically female
> biologically male
> BIPOC
> Black
> breastfeed + people
> breastfeed + person
> chestfeed + people
> chestfeed + person
> clean energy
> climate crisis
> climate science
> commercial sex worker
> community diversity
> community equity
> confirmation bias
> cultural competence
> cultural differences
> cultural heritage
> cultural sensitivity
> culturally appropriate
> culturally responsive
> DEI
> DEIA
> DEIAB
> DEIJ
> disabilities
> disability
> discriminated
> discrimination
> discriminatory
> disparity
> diverse
> diverse backgrounds
> diverse communities
> diverse community
> diverse group
> diverse groups
> diversified
> diversify
> diversifying
> diversity
> enhance the diversity
> enhancing diversity
> environmental quality
> equal opportunity
> equality
> equitable
> equitableness
> equity
> ethnicity
> excluded
> exclusion
> expression
> female
> females
> feminism
> fostering inclusivity
> GBV
> gender
> gender based
> gender based violence
> gender diversity
> gender identity
> gender ideology
> gender-affirming care
> genders
> Gulf of Mexico
> hate speech
> health disparity
> health equity
> hispanic minority
> historically
> identity
> immigrants
> implicit bias
> implicit biases
> inclusion
> inclusive
> inclusive leadership
> inclusiveness
> inclusivity
> increase diversity
> increase the diversity
> indigenous community
> inequalities
> inequality
> inequitable
> inequities
> inequity
> injustice
> institutional
> intersectional
> intersectionality
> key groups
> key people
> key populations
> Latinx
> LGBT
> LGBTQ
> marginalize
> marginalized
> men who have sex with men
> mental health
> minorities
> minority
> most risk
> MSM
> multicultural
> Mx
> Native American
> non-binary
> nonbinary
> oppression
> oppressive
> orientation
> people + uterus
> people-centered care
> person-centered
> person-centered care
> polarization
> political
> pollution
> pregnant people
> pregnant person
> pregnant persons
> prejudice
> privilege
> privileges
> promote diversity
> promoting diversity
> pronoun
> pronouns
> prostitute
> race
> race and ethnicity
> racial
> racial diversity
> racial identity
> racial inequality
> racial justice
> racially
> racism
> segregation
> sense of belonging
> sex
> sexual preferences
> sexuality
> social justice
> sociocultural
> socioeconomic
> status
> stereotype
> stereotypes
> systemic
> systemically
> they/them
> trans
> transgender
> transsexual
> trauma
> traumatic
> tribal
> unconscious bias
> underappreciated
> underprivileged
> underrepresentation
> underrepresented
> underserved
> undervalued
> victim
> victims
> vulnerable populations
> women
> women and underrepresented
> 
>  
> 
>  
> 
> On Tue, Mar 11, 2025 at 6:59 PM Herbert J. Bernstein  
> wrote:
> 
> Dear Colleagues,
> 
>   W

Re: [ccp4bb] Words to avoid

[Eta A Isiorho]

Time to break out the thesaurus…

From: CCP4 bulletin board  on behalf of Herbert J. 
Bernstein 
Date: Tuesday, March 11, 2025 at 7:06 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Words to avoid
Sorry the prior message lost the attachment.  Here is a complete version:

Dear Colleagues,
  When I got home today, Frances presented me with an article from the
NY Times which contained the attached list of words and the explanation,
 "As President Trump seeks to purge the federal government of "woke"
initiatives, agencies have flagged hundreds of words to limit or avoid,
according to a compilation of government documents."
  For this audience in particular, please note that "Mx", "polarization",
"orientation", "status", "systemic". "discrimination", "equality", "expression",
"barriers", and  "bias" are among the words to avoid.  Care should be
taken in writing proposals and reports since AIs may be used for screening
and they are' likely to miss explanatory context.
  Regard,
 Herbert

From: f...@marbuta.pair.com 
mailto:f...@marbuta.pair.com>>
Sent: Tuesday, March 11, 2025 6:29:06 PM (UTC-05:00) Eastern Time (US & Canada)
To: Bernstein, Herbert
Subject: words not to use (NYT Imes)

accessible
activism
activists
advocacy
advocate
advocates
affirming care
all-inclusive
allyship
anti-racism
antiracist
assigned at birth
assigned female at birth
assigned male at birth
at risk
barrier
barriers
belong
bias
biased
biased toward
biases
biases towards
biologically female
biologically male
BIPOC
Black
breastfeed + people
breastfeed + person
chestfeed + people
chestfeed + person
clean energy
climate crisis
climate science
commercial sex worker
community diversity
community equity
confirmation bias
cultural competence
cultural differences
cultural heritage
cultural sensitivity
culturally appropriate
culturally responsive
DEI
DEIA
DEIAB
DEIJ
disabilities
disability
discriminated
discrimination
discriminatory
disparity
diverse
diverse backgrounds
diverse communities
diverse community
diverse group
diverse groups
diversified
diversify
diversifying
diversity
enhance the diversity
enhancing diversity
environmental quality
equal opportunity
equality
equitable
equitableness
equity
ethnicity
excluded
exclusion
expression
female
females
feminism
fostering inclusivity
GBV
gender
gender based
gender based violence
gender diversity
gender identity
gender ideology
gender-affirming care
genders
Gulf of Mexico
hate speech
health disparity
health equity
hispanic minority
historically
identity
immigrants
implicit bias
implicit biases
inclusion
inclusive
inclusive leadership
inclusiveness
inclusivity
increase diversity
increase the diversity
indigenous community
inequalities
inequality
inequitable
inequities
inequity
injustice
institutional
intersectional
intersectionality
key groups
key people
key populations
Latinx
LGBT
LGBTQ
marginalize
marginalized
men who have sex with men
mental health
minorities
minority
most risk
MSM
multicultural
Mx
Native American
non-binary
nonbinary
oppression
oppressive
orientation
people + uterus
people-centered care
person-centered
person-centered care
polarization
political
pollution
pregnant people
pregnant person
pregnant persons
prejudice
privilege
privileges
promote diversity
promoting diversity
pronoun
pronouns
prostitute
race
race and ethnicity
racial
racial diversity
racial identity
racial inequality
racial justice
racially
racism
segregation
sense of belonging
sex
sexual preferences
sexuality
social justice
sociocultural
socioeconomic
status
stereotype
stereotypes
systemic
systemically
they/them
trans
transgender
transsexual
trauma
traumatic
tribal
unconscious bias
underappreciated
underprivileged
underrepresentation
underrepresented
underserved
undervalued
victim
victims
vulnerable populations
women
women and underrepresented


On Tue, Mar 11, 2025 at 6:59 PM Herbert J. Bernstein 
mailto:yaya...@gmail.com>> wrote:
Dear Colleagues,
  When I got home today, Frances presented me with an article from the
NY Times which contained the attached list of words and the explanation,
 "As President Trump seeks to purge the federal government of "woke" 
initiatives, agencies have flagged hundreds of words to limit or avoid,
according to a compilation of government documents."
  For this audience in particular, please note that "Mx", "polarization", 
"orientation", "status", "systemic". "discrimination", "equality", 
"expression", "barriers", and  "bias" are among the words to avoid.  Care 
should be
taken in writing proposals and reports since AIs may be used for screening
and they are' likely to miss explanatory context.
  Regard,
 Herbert




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



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-b

Re: [ccp4bb] Words to avoid

[Artem Evdokimov]

Hello friends,

For those of us who have lived in the USSR these developments should feel
quite familiar. I've often joked that the US is edging ever closer to how
the USSR used to be, but I think we've actually crossed this line now and
it's not funny anymore.

We can anticipate future developments like this: the emergence of Komissar
functions in institutions of higher learning (ideological purity review and
enforcement committees). These functions will emerge naturally (or
'organically' if you prefer) as institutions struggle with, and eventually
adapt to, the new language purity requirements. At first, Komissariat will
be viewed as helpful in making things easier for grant writers etc. but at
the end of the process the Komissars will hold equal or greater 'rank' to
that of the Dean or Provost, and will hold significant sway over the
decisions of a Chancellor or President (of a University or an equivalent
institution). Once these functions emerge and entrench within institutions
funded by the public, the 'need' for them will become clear to privately
funded organizations, companies, etc.

Again, this may sound funny, but I am not laughing.

https://en.wikipedia.org/wiki/Commissar

Artem

- Cosmic Cats approve of this message


On Tue, Mar 11, 2025 at 7:00 PM Herbert J. Bernstein 
wrote:

> Dear Colleagues,
>   When I got home today, Frances presented me with an article from the
> NY Times which contained the attached list of words and the explanation,
>  "As President Trump seeks to purge the federal government of "woke"
> initiatives, agencies have flagged hundreds of words to limit or avoid,
> according to a compilation of government documents."
>   For this audience in particular, please note that "Mx", "polarization",
> "orientation", "status", "systemic". "discrimination", "equality",
> "expression", "barriers", and  "bias" are among the words to avoid.  Care
> should be
> taken in writing proposals and reports since AIs may be used for screening
> and they are' likely to miss explanatory context.
>   Regard,
>  Herbert
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] 3 alternate position of metal ion

[Diana Tomchick]

There are plenty of Zinc hydrolase enzymes that adopt octahedral geometry 
around the metal ion when you include a water in the 6th coordination site.

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)



On Mar 12, 2025, at 6:14 AM, Roger Rowlett  wrote:

External Mail
This email originated from outside of UT Southwestern. Please be cautious.

Report Suspicious
It would be unusual for a coordinated metal ion to have multiple occupancies. 
Are you sure your metal is zinc? Zinc coordination sites are typically 
pseudotetrahedral (occasionally 5-coordinate) with waters filling out the 
coordination shell in a His-His-Asp/Glu ligand environment, with Zn-N(O) bond 
distances of 2.0A plus or minus. There are metalloenzymes with fairly plastic 
metal affinities (e.g. certain carbonic anhydrases) that can naturally 
accommodate Cd or Fe. The former has coordination geometries similar to Zn with 
longer bond lengths. The latter will typically be in an octahedral coordination 
environment.

Roger Rowlett
Gordon & Dorothy Kline Professor of Chemistry, Emeritus
Colgate University

On Wed, Mar 12, 2025, 5:45 AM Shikha Gupta 
mailto:shikha.gupta.01...@gmail.com>> wrote:
Dear all,

I have a complex structure where zinc

metal ion is present in the active site (evidence from several PDBs). However, 
despite multiple efforts, I am getting lot of positive densities close to the 
metal ion (please see image attached). I have also tried to place water or two 
zinc ions but that also doesn’t seem to work. The last and overall best 
solution I came up with was by positioning three zinc ions with combined 
occupancy of 1 (0.3+0.2+0.3). Although I still see positive densities around 
but this is best I have achieved.

This was a soaked crystals, any suggestions on this. Is this the right way to 
do this. The resolution of the structure is 1.7 angs.

Thanks,
Shikha



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The future of medicine, today.



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Re: [ccp4bb] Words to avoid

[Artem Evdokimov]

The first thing that happens as freedom of speech dies is that diligent
self censorship becomes the norm. People acquire a Komissar inside their
heads.

When I was a kid, my parents had to remind me daily not to share with
school kids the jokes told at home because 'mommy does not want to go to
Gulag'.

Word to the wise.

Artem

On Wed, Mar 12, 2025, 15:21 Katherine Sippel 
wrote:

> I love this conversation. It is an important one right now that addresses
> the intersection between the precise language needed to communicate science
> and the greater zeitgeist around politicization of vocabulary. It will be
> interesting to see how the etymology of scientific language migrates in
> response to this selective pressure.
>
> However, if you will allow me to put on my tinfoil hat for a moment, I
> feel compelled to remind the faculty from publicly funded universities in
> the US that your institutional emails may be subject to Freedom of
> Information Act requests. I was at the University of Florida when the
> Organic Consumers Association decided to go after Kevin Folta via US Right
> to Know, and it was nasty. I would not put it past the administration to
> weaponize FOIA requests in the future to root out dissent among US
> academics. Just something to consider when engaging in these types of
> conversations.
>
> Cheers,
> Kat Sippel, PhD, ELS
>
> On Wed, Mar 12, 2025 at 1:41 PM Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> "_golf_ of America” particularly apt with current POTUS…
>>
>> Harry
>>
>> > On 12 Mar 2025, at 17:49, Oganesyan, Vaheh <
>> vaheh.oganes...@astrazeneca.com> wrote:
>> >
>> > You never know what is on their minds (Musk&Don). Would you guess
>> anything related to Greenland before hearing it, or golf of America?
>> >
>> > Vaheh
>> >
>> > From: CCP4 bulletin board  On Behalf Of Harry
>> Powell
>> > Sent: Wednesday, March 12, 2025 1:30 PM
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: Re: [ccp4bb] Words to avoid
>> >
>> > I don’t thnk that’s why it’s been banned...
>> >
>> > > On 12 Mar 2025, at 17:09, Ian Tickle  wrote:
>> > >
>> > >
>> > > - Forwarded message -
>> > > From: Ian Tickle 
>> > > Date: Wed, 12 Mar 2025, 14:08
>> > > Subject: Re: [ccp4bb] Words to avoid
>> > > To: Herbert J. Bernstein 
>> > >
>> > > I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' =
>> 'Pole Star').
>> > >
>> > > Cheers
>> > >
>> > > -- Ian
>> > >
>> > >
>> > > On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein, 
>> wrote:
>> > > Dear Colleagues,
>> > > When I got home today, Frances presented me with an article from the
>> > > NY Times which contained the attached list of words and the
>> explanation,
>> > > "As President Trump seeks to purge the federal government of "woke"
>> initiatives, agencies have flagged hundreds of words to limit or avoid,
>> > > according to a compilation of government documents."
>> > > For this audience in particular, please note that "Mx",
>> "polarization", "orientation", "status", "systemic". "discrimination",
>> "equality", "expression", "barriers", and "bias" are among the words to
>> avoid. Care should be
>> > > taken in writing proposals and reports since AIs may be used for
>> screening
>> > > and they are' likely to miss explanatory context.
>> > > Regard,
>> > > Herbert
>> > >
>> > >
>> > > To unsubscribe from the CCP4BB list, click the following link:
>> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> > >
>> > >
>> > > To unsubscribe from the CCP4BB list, click the following link:
>> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> > >
>> >
>> > 
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> >
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>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
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>> in error, please notify us and remove it from your system and note that you
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>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
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>> mailing list hosted by

Re: [ccp4bb] Words to avoid

[Katherine Sippel]

I love this conversation. It is an important one right now that addresses
the intersection between the precise language needed to communicate science
and the greater zeitgeist around politicization of vocabulary. It will be
interesting to see how the etymology of scientific language migrates in
response to this selective pressure.

However, if you will allow me to put on my tinfoil hat for a moment, I feel
compelled to remind the faculty from publicly funded universities in the US
that your institutional emails may be subject to Freedom of Information Act
requests. I was at the University of Florida when the Organic Consumers
Association decided to go after Kevin Folta via US Right to Know, and it
was nasty. I would not put it past the administration to weaponize FOIA
requests in the future to root out dissent among US academics. Just
something to consider when engaging in these types of conversations.

Cheers,
Kat Sippel, PhD, ELS

On Wed, Mar 12, 2025 at 1:41 PM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> "_golf_ of America” particularly apt with current POTUS…
>
> Harry
>
> > On 12 Mar 2025, at 17:49, Oganesyan, Vaheh <
> vaheh.oganes...@astrazeneca.com> wrote:
> >
> > You never know what is on their minds (Musk&Don). Would you guess
> anything related to Greenland before hearing it, or golf of America?
> >
> > Vaheh
> >
> > From: CCP4 bulletin board  On Behalf Of Harry
> Powell
> > Sent: Wednesday, March 12, 2025 1:30 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Words to avoid
> >
> > I don’t thnk that’s why it’s been banned...
> >
> > > On 12 Mar 2025, at 17:09, Ian Tickle  wrote:
> > >
> > >
> > > - Forwarded message -
> > > From: Ian Tickle 
> > > Date: Wed, 12 Mar 2025, 14:08
> > > Subject: Re: [ccp4bb] Words to avoid
> > > To: Herbert J. Bernstein 
> > >
> > > I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' =
> 'Pole Star').
> > >
> > > Cheers
> > >
> > > -- Ian
> > >
> > >
> > > On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein, 
> wrote:
> > > Dear Colleagues,
> > > When I got home today, Frances presented me with an article from the
> > > NY Times which contained the attached list of words and the
> explanation,
> > > "As President Trump seeks to purge the federal government of "woke"
> initiatives, agencies have flagged hundreds of words to limit or avoid,
> > > according to a compilation of government documents."
> > > For this audience in particular, please note that "Mx",
> "polarization", "orientation", "status", "systemic". "discrimination",
> "equality", "expression", "barriers", and "bias" are among the words to
> avoid. Care should be
> > > taken in writing proposals and reports since AIs may be used for
> screening
> > > and they are' likely to miss explanatory context.
> > > Regard,
> > > Herbert
> > >
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > >
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
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> in error, please notify us and remove it from your system and note that you
> must not copy, distribute or take any action in reliance on it. Any
> unauthorized use or disclosure of the contents of this message is not
> permitted and may be unlawful.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
>
> 
>
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Re: [ccp4bb] Words to avoid

[Oganesyan, Vaheh]

This would be funny if it wouldn’t be so sad.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01DB9333.6B72EA70]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com



From: CCP4 bulletin board  On Behalf Of Herbert J. 
Bernstein
Sent: Tuesday, March 11, 2025 7:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Words to avoid

Sorry the prior message lost the attachment.  Here is a complete version:

Dear Colleagues,
  When I got home today, Frances presented me with an article from the
NY Times which contained the attached list of words and the explanation,
 "As President Trump seeks to purge the federal government of "woke"
initiatives, agencies have flagged hundreds of words to limit or avoid,
according to a compilation of government documents."
  For this audience in particular, please note that "Mx", "polarization",
"orientation", "status", "systemic". "discrimination", "equality", "expression",
"barriers", and  "bias" are among the words to avoid.  Care should be
taken in writing proposals and reports since AIs may be used for screening
and they are' likely to miss explanatory context.
  Regard,
 Herbert

From: f...@marbuta.pair.com 
mailto:f...@marbuta.pair.com>>
Sent: Tuesday, March 11, 2025 6:29:06 PM (UTC-05:00) Eastern Time (US & Canada)
To: Bernstein, Herbert
Subject: words not to use (NYT Imes)

accessible
activism
activists
advocacy
advocate
advocates
affirming care
all-inclusive
allyship
anti-racism
antiracist
assigned at birth
assigned female at birth
assigned male at birth
at risk
barrier
barriers
belong
bias
biased
biased toward
biases
biases towards
biologically female
biologically male
BIPOC
Black
breastfeed + people
breastfeed + person
chestfeed + people
chestfeed + person
clean energy
climate crisis
climate science
commercial sex worker
community diversity
community equity
confirmation bias
cultural competence
cultural differences
cultural heritage
cultural sensitivity
culturally appropriate
culturally responsive
DEI
DEIA
DEIAB
DEIJ
disabilities
disability
discriminated
discrimination
discriminatory
disparity
diverse
diverse backgrounds
diverse communities
diverse community
diverse group
diverse groups
diversified
diversify
diversifying
diversity
enhance the diversity
enhancing diversity
environmental quality
equal opportunity
equality
equitable
equitableness
equity
ethnicity
excluded
exclusion
expression
female
females
feminism
fostering inclusivity
GBV
gender
gender based
gender based violence
gender diversity
gender identity
gender ideology
gender-affirming care
genders
Gulf of Mexico
hate speech
health disparity
health equity
hispanic minority
historically
identity
immigrants
implicit bias
implicit biases
inclusion
inclusive
inclusive leadership
inclusiveness
inclusivity
increase diversity
increase the diversity
indigenous community
inequalities
inequality
inequitable
inequities
inequity
injustice
institutional
intersectional
intersectionality
key groups
key people
key populations
Latinx
LGBT
LGBTQ
marginalize
marginalized
men who have sex with men
mental health
minorities
minority
most risk
MSM
multicultural
Mx
Native American
non-binary
nonbinary
oppression
oppressive
orientation
people + uterus
people-centered care
person-centered
person-centered care
polarization
political
pollution
pregnant people
pregnant person
pregnant persons
prejudice
privilege
privileges
promote diversity
promoting diversity
pronoun
pronouns
prostitute
race
race and ethnicity
racial
racial diversity
racial identity
racial inequality
racial justice
racially
racism
segregation
sense of belonging
sex
sexual preferences
sexuality
social justice
sociocultural
socioeconomic
status
stereotype
stereotypes
systemic
systemically
they/them
trans
transgender
transsexual
trauma
traumatic
tribal
unconscious bias
underappreciated
underprivileged
underrepresentation
underrepresented
underserved
undervalued
victim
victims
vulnerable populations
women
women and underrepresented


On Tue, Mar 11, 2025 at 6:59 PM Herbert J. Bernstein 
mailto:yaya...@gmail.com>> wrote:
Dear Colleagues,
  When I got home today, Frances presented me with an article from the
NY Times which contained the attached list of words and the explanation,
 "As President Trump seeks to purge the federal government of "woke" 
initiatives, agencies have flagged hundreds of words to limit or avoid,
according to a compilation of government documents."
  For this audience in particular, please note that "Mx", "polarization", 
"orientation", "status", "systemic". "discrimination", "equality", 
"expression", "barriers", and  "bias" are among the words to avoid.  Care 
should be
taken in writing proposals and reports since AIs may be used for screening
and they are' likely to miss explanatory context.
  Regard,
 Herbert




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https://www

[ccp4bb] postdoc position in time-resolved serial crystallography (Melbourne, AU)

[Nadia Zatsepin]

We’re looking for a postdoc to work on developing time-resolved serial 
crystallography based at Swinburne University of Technology, Melbourne, 
Australia.



Position 
description
 and how to apply: 
https://swinjobs.nga.net.au/?jati=881A1479-9477-097E-6BA2-E3944FDB93F4

Applications close Friday 28th March11 pm (Melbourne time; AEDT)

3 years full time, level B  (+17 % super) 




The focus will be two-fold: developing serial crystallography at the Australia 
Synchrotron and developing time-resolved serial crystallography to capture the 
structural dynamics of disulfide bond-forming enzyme A (DsbA) during its 
enzymatic cycle. DsbA plays a crucial role in oxidative protein folding and is 
a potential drug target to combat antimicrobial resistance. The position offers 
a unique opportunity to contribute to both technical advancements in 
crystallographic methodology as well as deepening our understanding of the 
molecular mechanisms governing disulfide bond formation.

The ideal candidate will have experience in protein crystallization, X-ray 
crystallography experiments and data analysis, with a strong interest in serial 
and time-resolved crystallography. They should have excellent organisational, 
projectmanagement, and communication skills, as well as experience with student 
supervision and mentoring. Experience in setting up a crystallization 
laboratory would be highly valued.

Thanks,
Nadia



--
Nadia Zatsepin
ARC Future Fellow
Associate Professor, Department of Physics and Astronomy
Swinburne University of Technology
nzatse...@swin.edu.au
sites.google.com/view/zatsepinlab





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Re: [ccp4bb] naturally obsessed - the movie

[Harry Powell]

Hi

It’s subject to copyright, but the last time I looked, the copyright holders 
could not be traced - I wrote to several people named on the production but did 
not receive any replies.

Harry

> On 12 Mar 2025, at 02:39, SUBSCRIBE CCP4BB Anirban Banerjee 
>  wrote:
> 
> Following up on this. Anyone has a copy that can be shared ?
> 
> Best regards,
> 
> Anirban
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
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Re: [ccp4bb] Words to avoid

[Harry Powell]

I don’t thnk that’s why it’s been banned...

> On 12 Mar 2025, at 17:09, Ian Tickle  wrote:
> 
> 
> - Forwarded message -
> From: Ian Tickle 
> Date: Wed, 12 Mar 2025, 14:08
> Subject: Re: [ccp4bb] Words to avoid
> To: Herbert J. Bernstein 
> 
> I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' = 'Pole 
> Star').
> 
> Cheers
> 
> -- Ian
> 
> 
> On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein,  wrote:
> Dear Colleagues,
>   When I got home today, Frances presented me with an article from the 
> NY Times which contained the attached list of words and the explanation,
>  "As President Trump seeks to purge the federal government of "woke" 
> initiatives, agencies have flagged hundreds of words to limit or avoid, 
> according to a compilation of government documents."
>   For this audience in particular, please note that "Mx", "polarization", 
> "orientation", "status", "systemic". "discrimination", "equality", 
> "expression", "barriers", and  "bias" are among the words to avoid.  Care 
> should be 
> taken in writing proposals and reports since AIs may be used for screening 
> and they are' likely to miss explanatory context.
>   Regard,
>  Herbert
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 



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Re: [ccp4bb] Words to avoid

[Oganesyan, Vaheh]

You never know what is on their minds (Musk&Don). Would you guess anything 
related to Greenland before hearing it, or golf of America?

Vaheh

From: CCP4 bulletin board  On Behalf Of Harry Powell
Sent: Wednesday, March 12, 2025 1:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Words to avoid

I don’t thnk that’s why it’s been banned...

> On 12 Mar 2025, at 17:09, Ian Tickle 
> mailto:ianj...@gmail.com>> wrote:
>
>
> - Forwarded message -
> From: Ian Tickle mailto:ianj...@gmail.com>>
> Date: Wed, 12 Mar 2025, 14:08
> Subject: Re: [ccp4bb] Words to avoid
> To: Herbert J. Bernstein mailto:yaya...@gmail.com>>
>
> I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' = 'Pole 
> Star').
>
> Cheers
>
> -- Ian
>
>
> On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein, 
> mailto:yaya...@gmail.com>> wrote:
> Dear Colleagues,
> When I got home today, Frances presented me with an article from the
> NY Times which contained the attached list of words and the explanation,
> "As President Trump seeks to purge the federal government of "woke" 
> initiatives, agencies have flagged hundreds of words to limit or avoid,
> according to a compilation of government documents."
> For this audience in particular, please note that "Mx", "polarization", 
> "orientation", "status", "systemic". "discrimination", "equality", 
> "expression", "barriers", and "bias" are among the words to avoid. Care 
> should be
> taken in writing proposals and reports since AIs may be used for screening
> and they are' likely to miss explanatory context.
> Regard,
> Herbert
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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and proprietary information. If you have received this message in error, please 
notify us and remove it from your system and note that you must not copy, 
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[ccp4bb] Postdoctoral position, Krakow, Poland

[Tomasz Borowski]

Postdoctoral position at ICSC PAS, Kraków, Poland: Deadline March 27, 2025


Postdoctoral fellow in protein structural biology.


https://ikifp.edu.pl/en/news/asystent-post-doc-w-grupie-biokataliza-teoretyczna-i-eksperymentalna/


We seek a motivated and skilled post-doctoral research fellow in protein 
structural biology (XRD) to join a science project on iron-dependent enzymes. 
The project aims to unravel the enzymatic reaction mechanism and identify 
factors affecting reaction regiospecificity. The enzymes studied catalyze 
intriguing reactions leading to cyclic compounds of medicinal relevance. Within 
the project, we are combining XRD, spectroscopy, enzymatic kinetics 
measurements and computational methods. This position is supervised by Tomasz 
Borowski.


Na stronie internetowej Administratora https://ikifp.edu.pl/rodo/ znajduje się 
obowiązek informacyjny RODO, w którym wskazujemy w jaki sposób Państwa dane 
osobowe przetwarzane są przez Instytut Katalizy i Fizykochemii Powierzchni im. 
Jerzego Habera Polskiej Akademii Nauk.

The Administrator's website https://ikifp.edu.pl/rodo/ contains the GDPR 
information obligation, it indicates how your personal data is processed by the 
Jerzy Haber Institute of Catalysis and Surface Chemistry of the Polish Academy 
of Sciences.



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[ccp4bb] Words to avoid

[Ian Tickle]

- Forwarded message -
From: Ian Tickle 
Date: Wed, 12 Mar 2025, 14:08
Subject: Re: [ccp4bb] Words to avoid
To: Herbert J. Bernstein 

I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' = 'Pole
Star').

Cheers

-- Ian


On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein,  wrote:

> Dear Colleagues,
>   When I got home today, Frances presented me with an article from the
> NY Times which contained the attached list of words and the explanation,
>  "As President Trump seeks to purge the federal government of "woke"
> initiatives, agencies have flagged hundreds of words to limit or avoid,
> according to a compilation of government documents."
>   For this audience in particular, please note that "Mx", "polarization",
> "orientation", "status", "systemic". "discrimination", "equality",
> "expression", "barriers", and  "bias" are among the words to avoid.  Care
> should be
> taken in writing proposals and reports since AIs may be used for screening
> and they are' likely to miss explanatory context.
>   Regard,
>  Herbert
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] IDS in PDB

[James Holton]

In my experience the decision to model disordered atoms as missing or 
with high B factors has little to do with "correctness", but rather is 
most highly correlated with the user's favorite refinement program.  If 
you use phenix.refine it will, by default, tend to allow B factors to 
"blow up" and that tends to get rid of difference density. With refmac, 
however, the B factor restraints are implemented differently, using 
something called a K-L divergence, which I believe is based on PDB-wide 
statistics. This tends to restrain adjacent B factors in disordered side 
chains to be much more similar than you will get with phenix. You see a 
big red difference peak, and that inspires you to delete the offending 
atoms.


So, we get two classes of complaints:
1) This pdb has missing atoms, but when I add them back and refine with 
phenix I get better stats and there is no difference density. Silly 
depositors! They should have made their model more complete!
2) This pdb has atoms sticking out into nowhere, and when I refine in 
refmac I get big red blobs. When I delete them and re-refine I get 
better stats. Silly depositors! They should never have built those 
"non-existent" atoms!


This, in a nutshell, has been my experience.

At the risk of entering a semantics rant, I do feel I should point out 
that a B factor is nothing more than a width. It is not an "uncertainty" 
or an "error bar" any more than the ~25 nm width of the UV absorption 
peak of tryptophan at 280 nm is an "error bar" on how accurately you 
know to measure at 280 nm. The Trp absorption peak is broad, but that 
doesn't mean that sometimes the max is at 270 nm and sometimes its at 
290 nm. It is ALWAYS at 280, just weaker away from the middle of the 
peak.  If you fit a curve to a Trp absorption spectrum you might use a 
Gaussian for this peak. The resulting best-fit curve will have a width, 
and a height, but will also reproducibly arrive at ~280 nm as the 
centroid.  In the same way, when you fit a coordinate model to density 
data the "fit" (aka refinement) will arrive at a width, height and 
midpoint. These are analogous to B, occupancy*B^(3/2), and xyz 
coordinates.  (Yes, the B factor reduces modeled peak height by a a 
factor of B raised to the power of 1.5 because the B factor has 
dimensions of squared length and the number of electrons must be 
preserved in 3D space, but that's not important right now). The "tails" 
of neighboring features (analogous to the peptide bond absorption at < 
250 nm) are a source of error in determining the best parameters, but 
that is a systematic error, not a random one.  But, I digress.  
Practically speaking, for highly disordered regions it is usually only 
the B factor restraints imposed by the refinement program that limit how 
high the B factor can go.


The largest representable B factor in the PDB format is 999.99, and that 
corresponds to a peak with full-width-half-max (FWHM) of ~8.4 Angstom.  
That is to say: "this atom is wandering around here with average density 
of roughly Gaussian shape within a ~4 A radius, but centered >here<".  
For B=100, which many programs put as an upper limit, the diameter of 
the density peak is ~2.7A wide.  The formula is:fwhm = 
sqrt(B*log(2))/pi. That is if we disregard intrinsic atomic width, which 
is a good approximation for large B factors.  If we want to include 
intrinsic atomic width, you can usually just add ~14 to the B factor 
(corresponding to fwhm=1 A). Or, of course, just use the tabulated 
atomic form factors, (which is most accurate, but harder to wrap your 
head around).


This "width" is all that is really being "said" by current B-factor 
based disorder models.  Are there better models? Yes there are. There is 
an "order parameter" gaining in popularity out there.  But, ultimately, 
a multi-conformer model is called for (IMHO). A floppy Lys or Arg side 
chain can easily traverse 7-8 A depending on the rotamer, and the 
resulting electron density of the "bouquet" of alternate locations is 
far from Gaussian. So, a simple B factor cannot really capture it. The 
bulk solvent also "fills in" when the side chain is elsewhere, making 
things flatter, but still more complicated. If you are worried about 
observations/parameters, don't be. Polynomials can give you an 
artificial Rwork=0 when observations=parameters, but Gaussian-based 
models don't. If they did, it would be easy to get Rwork=0 at 6 A 
resolution, where observations << parameters. To my knowledge, nobody 
has ever gotten Rwork=0 for a crystal structure. Not with reasonable 
geometry.


Hope this helps! The models we use are actually rather simple. And maybe 
that is the problem?


-James Holton
MAD Scientist


On 3/8/2025 2:59 AM, Italo Carugo Oliviero wrote:


If I may, I would attempt a very brief summary of this brilliant 
discussion.


It seems there is a general agreement on indicating, with a single 
parameter similar to AlphaFold's pLDDT, the reliability of the 
position o

Re: [ccp4bb] problem with RELION particle picking

[Preeti]

Dear Takanori,

  Thank you for your help. The issue is now resolved. I regret not
recognizing the minor error earlier.
  I will be more careful about not sending screenshots of errors in the
future

Best regards,
Preeti

On Wed, Mar 12, 2025 at 6:56 AM Takanori Nakane <
tnakane.prot...@osaka-u.ac.jp> wrote:

> Hi,
>
> Your file name contains space: "E1 11-2-25 URAC.tif".
> This is not allowed. Please remove space from file names.
>
> Also please don't use screenshots to show textual error messages.
> Copy and paste them as texts next time.
>
> Best regards,
>
> Takanori Nakane
>
> On 2025/03/11 22:18, Preeti wrote:
> > Dear Takanori,
> >
> >Thank you for your help. I was doing exactly as you mentioned, but
> > with RELION 4.0.1. I will try it with RELION 5.0 instead
> >
> > On Tue, Mar 11, 2025 at 5:19 PM Takanori Nakane  > u.ac.jp > wrote:
> >
> > Hi,
> >
> > I cannot reproduce your problem.
> > I did (with RELION 5.0):
> >
> > 1. Import: make sure to set "Are these multi-frame movies:" No.
> > 2. Manual picking: select "Import/jobXXX/micrographs.star".
> >
> > Best regards,
> >
> > Takanori Nakane
> >
> > On 3/11/25 20:29, Preeti wrote:
> >  > Hello everyone,
> >  >
> >  > I am currently encountering an issue during the processing of
> > negative
> >  > stain EM micrographs. I collected the raw images in |.tif| format
> > during
> >  > negative stain EM imaging and intended to perform manual particle
> >  > picking using RELION. After successfully importing the
> > micrographs, I
> >  > proceeded directly to manual particle picking, skipping both
> motion
> >  > correction and CTF estimation steps. However, when attempting to
> run
> >  > manual particle picking using the imported micrographs as input,
> > RELION
> >  > returns an error stating that it 'cannot read the file or that
> > the file
> >  > does not exist' — even though the files are clearly present and
> >  > functional, as Gaussian auto-picking (RELION) works without issue
> > on the
> >  > same micrographs. I would appreciate any guidance or suggestions
> to
> >  > resolve this issue, or recommendations for alternative software
> >  > platforms where I can perform manual particle picking on negative
> > stain
> >  > micrographs
> >  >
> >  > Best regards,
> >  > Preeti
> >  >
> >  >
> >
>  
> >  >
> >  > To unsubscribe from the CCP4BB list, click the following link:
> >  > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > 
> >  >  > >
> >  >
> >
>
>



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Re: [ccp4bb] Words to avoid

[Katherine Sippel]

My response was more of a suggestion to make sure these types of
conversations are held via a personal email where "The Man" would require
sufficient probable cause for a judge to issue a warrant rather than an
institutional email that does not have such a barrier. That being said, I
have had more than one work email recently where I asked myself "would you
want to have to defend this in front of a McCarthy-esque congressional
inquest" and made a phone call instead. So, you're completely right. Thank
you for the gut check.

Cheers,
Kat

On Wed, Mar 12, 2025 at 2:31 PM Artem Evdokimov 
wrote:

> The first thing that happens as freedom of speech dies is that diligent
> self censorship becomes the norm. People acquire a Komissar inside their
> heads.
>
> When I was a kid, my parents had to remind me daily not to share with
> school kids the jokes told at home because 'mommy does not want to go to
> Gulag'.
>
> Word to the wise.
>
> Artem
>
> On Wed, Mar 12, 2025, 15:21 Katherine Sippel 
> wrote:
>
>> I love this conversation. It is an important one right now that addresses
>> the intersection between the precise language needed to communicate science
>> and the greater zeitgeist around politicization of vocabulary. It will be
>> interesting to see how the etymology of scientific language migrates in
>> response to this selective pressure.
>>
>> However, if you will allow me to put on my tinfoil hat for a moment, I
>> feel compelled to remind the faculty from publicly funded universities in
>> the US that your institutional emails may be subject to Freedom of
>> Information Act requests. I was at the University of Florida when the
>> Organic Consumers Association decided to go after Kevin Folta via US Right
>> to Know, and it was nasty. I would not put it past the administration to
>> weaponize FOIA requests in the future to root out dissent among US
>> academics. Just something to consider when engaging in these types of
>> conversations.
>>
>> Cheers,
>> Kat Sippel, PhD, ELS
>>
>> On Wed, Mar 12, 2025 at 1:41 PM Harry Powell <
>> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> "_golf_ of America” particularly apt with current POTUS…
>>>
>>> Harry
>>>
>>> > On 12 Mar 2025, at 17:49, Oganesyan, Vaheh <
>>> vaheh.oganes...@astrazeneca.com> wrote:
>>> >
>>> > You never know what is on their minds (Musk&Don). Would you guess
>>> anything related to Greenland before hearing it, or golf of America?
>>> >
>>> > Vaheh
>>> >
>>> > From: CCP4 bulletin board  On Behalf Of Harry
>>> Powell
>>> > Sent: Wednesday, March 12, 2025 1:30 PM
>>> > To: CCP4BB@JISCMAIL.AC.UK
>>> > Subject: Re: [ccp4bb] Words to avoid
>>> >
>>> > I don’t thnk that’s why it’s been banned...
>>> >
>>> > > On 12 Mar 2025, at 17:09, Ian Tickle  wrote:
>>> > >
>>> > >
>>> > > - Forwarded message -
>>> > > From: Ian Tickle 
>>> > > Date: Wed, 12 Mar 2025, 14:08
>>> > > Subject: Re: [ccp4bb] Words to avoid
>>> > > To: Herbert J. Bernstein 
>>> > >
>>> > > I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' =
>>> 'Pole Star').
>>> > >
>>> > > Cheers
>>> > >
>>> > > -- Ian
>>> > >
>>> > >
>>> > > On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein, 
>>> wrote:
>>> > > Dear Colleagues,
>>> > > When I got home today, Frances presented me with an article from the
>>> > > NY Times which contained the attached list of words and the
>>> explanation,
>>> > > "As President Trump seeks to purge the federal government of "woke"
>>> initiatives, agencies have flagged hundreds of words to limit or avoid,
>>> > > according to a compilation of government documents."
>>> > > For this audience in particular, please note that "Mx",
>>> "polarization", "orientation", "status", "systemic". "discrimination",
>>> "equality", "expression", "barriers", and "bias" are among the words to
>>> avoid. Care should be
>>> > > taken in writing proposals and reports since AIs may be used for
>>> screening
>>> > > and they are' likely to miss explanatory context.
>>> > > Regard,
>>> > > Herbert
>>> > >
>>> > >
>>> > > To unsubscribe from the CCP4BB list, click the following link:
>>> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>> > >
>>> > >
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>>> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>> > >
>>> >
>>> >
>>> 
>>> >
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Re: [ccp4bb] Words to avoid

[Bernhard Rupp]

Baja de gringo loco

On Wed, Mar 12, 2025, 19:41 Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> "_golf_ of America” particularly apt with current POTUS…
>
> Harry
>
> > On 12 Mar 2025, at 17:49, Oganesyan, Vaheh <
> vaheh.oganes...@astrazeneca.com> wrote:
> >
> > You never know what is on their minds (Musk&Don). Would you guess
> anything related to Greenland before hearing it, or golf of America?
> >
> > Vaheh
> >
> > From: CCP4 bulletin board  On Behalf Of Harry
> Powell
> > Sent: Wednesday, March 12, 2025 1:30 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Words to avoid
> >
> > I don’t thnk that’s why it’s been banned...
> >
> > > On 12 Mar 2025, at 17:09, Ian Tickle  wrote:
> > >
> > >
> > > - Forwarded message -
> > > From: Ian Tickle 
> > > Date: Wed, 12 Mar 2025, 14:08
> > > Subject: Re: [ccp4bb] Words to avoid
> > > To: Herbert J. Bernstein 
> > >
> > > I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' =
> 'Pole Star').
> > >
> > > Cheers
> > >
> > > -- Ian
> > >
> > >
> > > On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein, 
> wrote:
> > > Dear Colleagues,
> > > When I got home today, Frances presented me with an article from the
> > > NY Times which contained the attached list of words and the
> explanation,
> > > "As President Trump seeks to purge the federal government of "woke"
> initiatives, agencies have flagged hundreds of words to limit or avoid,
> > > according to a compilation of government documents."
> > > For this audience in particular, please note that "Mx",
> "polarization", "orientation", "status", "systemic". "discrimination",
> "equality", "expression", "barriers", and "bias" are among the words to
> avoid. Care should be
> > > taken in writing proposals and reports since AIs may be used for
> screening
> > > and they are' likely to miss explanatory context.
> > > Regard,
> > > Herbert
> > >
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > >
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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> >
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> >
> >
> >
> >
> >
> >
> >
> >
> >
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>
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Re: [ccp4bb] Words to avoid

[Oganesyan, Vaheh]

Pardon me, autocorrection made it golf instead of gulf.

Vaheh

From: CCP4 bulletin board  On Behalf Of Harry Powell
Sent: Wednesday, March 12, 2025 2:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Words to avoid

"_golf_ of America” particularly apt with current POTUS…

Harry

> On 12 Mar 2025, at 17:49, Oganesyan, Vaheh 
> mailto:vaheh.oganes...@astrazeneca.com>> 
> wrote:
>
> You never know what is on their minds (Musk&Don). Would you guess anything 
> related to Greenland before hearing it, or golf of America?
>
> Vaheh
>
> From: CCP4 bulletin board 
> mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Harry 
> Powell
> Sent: Wednesday, March 12, 2025 1:30 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Words to avoid
>
> I don’t thnk that’s why it’s been banned...
>
> > On 12 Mar 2025, at 17:09, Ian Tickle 
> > mailto:ianj...@gmail.com>> wrote:
> >
> >
> > - Forwarded message -
> > From: Ian Tickle mailto:ianj...@gmail.com>>
> > Date: Wed, 12 Mar 2025, 14:08
> > Subject: Re: [ccp4bb] Words to avoid
> > To: Herbert J. Bernstein mailto:yaya...@gmail.com>>
> >
> > I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' = 'Pole 
> > Star').
> >
> > Cheers
> >
> > -- Ian
> >
> >
> > On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein, 
> > mailto:yaya...@gmail.com>> wrote:
> > Dear Colleagues,
> > When I got home today, Frances presented me with an article from the
> > NY Times which contained the attached list of words and the explanation,
> > "As President Trump seeks to purge the federal government of "woke" 
> > initiatives, agencies have flagged hundreds of words to limit or avoid,
> > according to a compilation of government documents."
> > For this audience in particular, please note that "Mx", "polarization", 
> > "orientation", "status", "systemic". "discrimination", "equality", 
> > "expression", "barriers", and "bias" are among the words to avoid. Care 
> > should be
> > taken in writing proposals and reports since AIs may be used for screening
> > and they are' likely to miss explanatory context.
> > Regard,
> > Herbert
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
>
> 
>
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This message was issued to m

Re: [ccp4bb] Words to avoid

[Artem Evdokimov]

Given the unbridled affection (toadying is a good word, but i actually like
toads) showered on the regime by the techno-oligarchs, I would say that
there is no safety in any recordable communication. Any email can be asily
retrieved (perhaps with the exception of services designed with privacy in
mind like protonmail, those can be retrieved with some difficulty).

Anyways... stay frosty.

Artem

On Wed, Mar 12, 2025, 17:04 Katherine Sippel 
wrote:

> My response was more of a suggestion to make sure these types of
> conversations are held via a personal email where "The Man" would require
> sufficient probable cause for a judge to issue a warrant rather than an
> institutional email that does not have such a barrier. That being said, I
> have had more than one work email recently where I asked myself "would you
> want to have to defend this in front of a McCarthy-esque congressional
> inquest" and made a phone call instead. So, you're completely right. Thank
> you for the gut check.
>
> Cheers,
> Kat
>
> On Wed, Mar 12, 2025 at 2:31 PM Artem Evdokimov 
> wrote:
>
>> The first thing that happens as freedom of speech dies is that diligent
>> self censorship becomes the norm. People acquire a Komissar inside their
>> heads.
>>
>> When I was a kid, my parents had to remind me daily not to share with
>> school kids the jokes told at home because 'mommy does not want to go to
>> Gulag'.
>>
>> Word to the wise.
>>
>> Artem
>>
>> On Wed, Mar 12, 2025, 15:21 Katherine Sippel 
>> wrote:
>>
>>> I love this conversation. It is an important one right now that
>>> addresses the intersection between the precise language needed to
>>> communicate science and the greater zeitgeist around politicization of
>>> vocabulary. It will be interesting to see how the etymology of scientific
>>> language migrates in response to this selective pressure.
>>>
>>> However, if you will allow me to put on my tinfoil hat for a moment, I
>>> feel compelled to remind the faculty from publicly funded universities in
>>> the US that your institutional emails may be subject to Freedom of
>>> Information Act requests. I was at the University of Florida when the
>>> Organic Consumers Association decided to go after Kevin Folta via US Right
>>> to Know, and it was nasty. I would not put it past the administration to
>>> weaponize FOIA requests in the future to root out dissent among US
>>> academics. Just something to consider when engaging in these types of
>>> conversations.
>>>
>>> Cheers,
>>> Kat Sippel, PhD, ELS
>>>
>>> On Wed, Mar 12, 2025 at 1:41 PM Harry Powell <
>>> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
 "_golf_ of America” particularly apt with current POTUS…

 Harry

 > On 12 Mar 2025, at 17:49, Oganesyan, Vaheh <
 vaheh.oganes...@astrazeneca.com> wrote:
 >
 > You never know what is on their minds (Musk&Don). Would you guess
 anything related to Greenland before hearing it, or golf of America?
 >
 > Vaheh
 >
 > From: CCP4 bulletin board  On Behalf Of Harry
 Powell
 > Sent: Wednesday, March 12, 2025 1:30 PM
 > To: CCP4BB@JISCMAIL.AC.UK
 > Subject: Re: [ccp4bb] Words to avoid
 >
 > I don’t thnk that’s why it’s been banned...
 >
 > > On 12 Mar 2025, at 17:09, Ian Tickle  wrote:
 > >
 > >
 > > - Forwarded message -
 > > From: Ian Tickle 
 > > Date: Wed, 12 Mar 2025, 14:08
 > > Subject: Re: [ccp4bb] Words to avoid
 > > To: Herbert J. Bernstein 
 > >
 > > I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris'
 = 'Pole Star').
 > >
 > > Cheers
 > >
 > > -- Ian
 > >
 > >
 > > On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein, 
 wrote:
 > > Dear Colleagues,
 > > When I got home today, Frances presented me with an article from
 the
 > > NY Times which contained the attached list of words and the
 explanation,
 > > "As President Trump seeks to purge the federal government of "woke"
 initiatives, agencies have flagged hundreds of words to limit or avoid,
 > > according to a compilation of government documents."
 > > For this audience in particular, please note that "Mx",
 "polarization", "orientation", "status", "systemic". "discrimination",
 "equality", "expression", "barriers", and "bias" are among the words to
 avoid. Care should be
 > > taken in writing proposals and reports since AIs may be used for
 screening
 > > and they are' likely to miss explanatory context.
 > > Regard,
 > > Herbert
 > >
 > >
 > > To unsubscribe from the CCP4BB list, click the following link:
 > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
 > >
 > >
 > > To unsubscribe from the CCP4BB list, click the following link:
 > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
 > >
 >
 >
 

Re: [ccp4bb] Words to avoid

[Harry Powell]

"_golf_ of America” particularly apt with current POTUS…

Harry

> On 12 Mar 2025, at 17:49, Oganesyan, Vaheh  
> wrote:
> 
> You never know what is on their minds (Musk&Don). Would you guess anything 
> related to Greenland before hearing it, or golf of America?
>  
> Vaheh
>  
> From: CCP4 bulletin board  On Behalf Of Harry Powell
> Sent: Wednesday, March 12, 2025 1:30 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Words to avoid
>  
> I don’t thnk that’s why it’s been banned...
> 
> > On 12 Mar 2025, at 17:09, Ian Tickle  wrote:
> > 
> > 
> > - Forwarded message -
> > From: Ian Tickle 
> > Date: Wed, 12 Mar 2025, 14:08
> > Subject: Re: [ccp4bb] Words to avoid
> > To: Herbert J. Bernstein 
> > 
> > I spell it 'polarisation' anyway (from Late Latin 'Stella Polaris' = 'Pole 
> > Star').
> > 
> > Cheers
> > 
> > -- Ian
> > 
> > 
> > On Tue, 11 Mar 2025, 20:00 Herbert J. Bernstein,  wrote:
> > Dear Colleagues,
> > When I got home today, Frances presented me with an article from the 
> > NY Times which contained the attached list of words and the explanation,
> > "As President Trump seeks to purge the federal government of "woke" 
> > initiatives, agencies have flagged hundreds of words to limit or avoid, 
> > according to a compilation of government documents."
> > For this audience in particular, please note that "Mx", "polarization", 
> > "orientation", "status", "systemic". "discrimination", "equality", 
> > "expression", "barriers", and "bias" are among the words to avoid. Care 
> > should be 
> > taken in writing proposals and reports since AIs may be used for screening 
> > and they are' likely to miss explanatory context.
> > Regard,
> > Herbert
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > 
> 
> 
> 
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Re: [ccp4bb] Inappropriate

[Andrew Gnann]

. . . That one time people tested out turning the CCP4BB into an
electronic, dry speakeasy.

This thread confused me for some time, hah!

On Wed, Mar 12, 2025, 10:57 PM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> bingo.
>
> But now everone knows…
>
> Harry
>
> > On 11 Mar 2025, at 22:38, Gloria Borgstahl  wrote:
> >
> > Thanks for the help everyone,  I found them.  Harry my buddy Wolfie was
> at a pub in Darmstat if I remember right!
> >
> > On Tue, Mar 11, 2025, 8:02 PM Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> > Hmmm. I think if Gloria actually sent this, it might have come from her
> work address…
> >
> > If I’m wrong, the sender would be able to tell me where we met Wolfie…
> >
> > Harry
> >
> > > On 11 Mar 2025, at 07:42, Gloria Borgstahl 
> wrote:
> > >
> > > Trying to find Tom Peat and Janet
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> > >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
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