Re: [ccp4bb] Expi 293 (Met-) expression medium for selenomethionine labeling

[Weaver, Grant]

Hi Laura,

For what it’s worth, you’re not alone. I ordered two bottles back in January 
and have gotten availability dates ranging from March to May. However, it might 
be worth calling Thermo and checking with them on your specific order.

Last week I was told that they had a batch that was undergoing QC and I just 
got off the phone with someone who told me that my bottles were shipping today! 
Depending on where you are in the queue, you may have a shipment coming too.


Good luck!

Grant

- - - - - - - - - - - - -
Grant Weaver
PhD Candidate
Stern Lab
UMass Medical School


From: CCP4 bulletin board  On Behalf Of LAURA DEL AMO 
MAESTRO
Sent: Tuesday, March 10, 2020 1:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Expi 293 (Met-) expression medium for selenomethionine 
labeling

Dear ccp4 community,

I am in my last 3 months of my PhD, working at the Structural Biology Unit at 
IBMB-CSIC in Barcelona. As my experimental phasing trials using various heavy 
metals failed so far, we ordered two months ago Expi 293 (Met-) expression 
medium for selenomethionine labeling (see the reference: 
https://www.thermofisher.com/order/catalog/product/A4096701#/A4096701.
 But we got now the notice that it will not be delivered until end of April.

I had been working so hard on this project, and this medium is essential to 
finished with the experimental part of my thesis. Thus, I was wondering if 
someone in the community has a bottle (1L) of this expression medium without 
methionine that I could borrow, and which I would return immediately once our 
medium arrives.

Also in case you have recommendations or other sources of a defined Se-Met 
medium for Expi293 cells, please let me know. With kind regards from Barcelona, 
and hope someone can help,

Laura

---
Laura del Amo Maestro - Proteolysis Lab
SBU-Structural Biology Unit, IBMB CSIC
Barcelona, Spain, Europe



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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

[Gerard Bricogne]

Dear all,

 I don't quite know what to say about the direction in which the initial
topic is getting derailed ... .

 The substance of it is that an official (IUCr) online definition of a
statistic very much relied upon contained both a mathematical error and an
erroneous verbal description, and that this was promptly corrected through
an immediate mobilisation of good will (thank you Randy and Brian).

 Why not leave it at that?


 With best wishes,

  Gerard.

--
On Wed, Mar 11, 2020 at 04:53:25PM +, Eleanor Dodson wrote:
> Am I missing something? He? She? It? Are they now interchangeable?
> 
> On Wed, 11 Mar 2020 at 16:15, Tim Gruene  wrote:
> 
> > Dear Gerard,
> >
> > you are wrong. 'he'  in this context has as much information as 'someone'
> > and
> > 'person'. It does not refer to the sex of the person spoken about.
> >
> > Best regards,
> > Tim
> >
> > On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> > > >>>   Sorry to have taken this matter up in such a visible manner: I
> > > >>>   noticed
> > > >>>
> > > >>> this very wrong formula in someone's paper, and that person then
> > told me
> > > >>> where he had found it. Having landed on that page, I didn't know
> > where
> > > >>> to go
> > > For the students:
> > >
> > > "someone" = systematic absence of information = 0 bits
> > > "person" = systematic absence of information = 0 bits
> > > "he" = 1 bit of information!
> > >
> > > --The other Gerard (1 bit of information!)
> > >
> > > **
> > > Gerard J. Kleywegt
> > >
> > >http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> > > **
> > > The opinions in this message are fictional.  Any similarity
> > > to actual opinions, living or dead, is purely coincidental.
> > > **
> > > Little known gastromathematical curiosity: let "z" be the
> > > radius and "a" the thickness of a pizza. Then the volume
> > >  of that pizza is equal to pi*z*z*a !
> > > **
> > >
> > > 
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> > --
> > --
> > 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] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

[Rasmus Fogh]

Dear Eleanor,

In the English I (and Gerard) learned at school, 'he' was (also) the 
generic way to refer to an unknown person. In the English of the future, 
the use of 'he' may well be discouraged altogether. Meanwhile the top 
generic pronoun is currently 'they'.


So, who knows how you are supposed to interpret that word in a BB 
message in 2020??


;-)

Rasmus Fogh

On 11/03/2020 16:53, Eleanor Dodson wrote:

Am I missing something? He? She? It? Are they now interchangeable?

On Wed, 11 Mar 2020 at 16:15, Tim Gruene > wrote:


Dear Gerard,

you are wrong. 'he'  in this context has as much information as
'someone' and
'person'. It does not refer to the sex of the person spoken about.

Best regards,
Tim

On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
 > >>>       Sorry to have taken this matter up in such a visible
manner: I
 > >>>       noticed
 > >>>
 > >>> this very wrong formula in someone's paper, and that person
then told me
 > >>> where he had found it. Having landed on that page, I didn't
know where
 > >>> to go
 > For the students:
 >
 > "someone" = systematic absence of information = 0 bits
 > "person" = systematic absence of information = 0 bits
 > "he" = 1 bit of information!
 >
 > --The other Gerard (1 bit of information!)
 >
 > **
 >                             Gerard J. Kleywegt
 >
 > http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se

 > **
 >     The opinions in this message are fictional.  Any similarity
 >     to actual opinions, living or dead, is purely coincidental.
 > **
 >     Little known gastromathematical curiosity: let "z" be the
 >     radius and "a" the thickness of a pizza. Then the volume
 >              of that pizza is equal to pi*z*z*a !
 > **
 >
 >

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

-- 
--

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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--
Rasmus H. Fogh   Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom



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Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

[Eleanor Dodson]

Am I missing something? He? She? It? Are they now interchangeable?

On Wed, 11 Mar 2020 at 16:15, Tim Gruene  wrote:

> Dear Gerard,
>
> you are wrong. 'he'  in this context has as much information as 'someone'
> and
> 'person'. It does not refer to the sex of the person spoken about.
>
> Best regards,
> Tim
>
> On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> > >>>   Sorry to have taken this matter up in such a visible manner: I
> > >>>   noticed
> > >>>
> > >>> this very wrong formula in someone's paper, and that person then
> told me
> > >>> where he had found it. Having landed on that page, I didn't know
> where
> > >>> to go
> > For the students:
> >
> > "someone" = systematic absence of information = 0 bits
> > "person" = systematic absence of information = 0 bits
> > "he" = 1 bit of information!
> >
> > --The other Gerard (1 bit of information!)
> >
> > **
> > Gerard J. Kleywegt
> >
> >http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> > **
> > The opinions in this message are fictional.  Any similarity
> > to actual opinions, living or dead, is purely coincidental.
> > **
> > Little known gastromathematical curiosity: let "z" be the
> > radius and "a" the thickness of a pizza. Then the volume
> >  of that pizza is equal to pi*z*z*a !
> > **
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
> --
> 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] Expi 293 (Met-) expression medium for selenomethionine labeling

[Artem Evdokimov]

Hello

Bad news: Expi cells work poorly in non-Expi medium :(
Good news: you can add SelenoMet and make partially seleniated protein,
which is usually enough. Note that too much SeMet is pretty toxic, and that
the toxicity is associated with BOTH enantiomers of the amino acid, so if
you have the ability to use the L-SeMet pure as opposed to the more common
L,D-mix then you can put in more. Either way, it works.

Expect your yield to suffer.

Question: did you try iodine incorporation? You can do it on the level of
pure protein, or crystals...

Artem

- Cosmic Cats approve of this message


On Tue, Mar 10, 2020 at 1:51 PM LAURA DEL AMO MAESTRO 
wrote:

> Dear ccp4 community,
>
> I am in my last 3 months of my PhD, working at the Structural Biology Unit
> at IBMB-CSIC in Barcelona. As my experimental phasing trials using various
> heavy metals failed so far, we ordered two months ago Expi 293 (Met-)
> expression medium for selenomethionine labeling (see the reference:
> https://www.thermofisher.com/order/catalog/product/A4096701#/A4096701.
> But we got now the notice that it will not be delivered until end of April.
>
> I had been working so hard on this project, and this medium is essential
> to finished with the experimental part of my thesis. Thus, I was wondering
> if someone in the community has a bottle (1L) of this expression medium
> without methionine that I could borrow, and which I would return
> immediately once our medium arrives.
>
> Also in case you have recommendations or other sources of a defined Se-Met
> medium for Expi293 cells, please let me know. With kind regards from
> Barcelona, and hope someone can help,
>
>
> Laura
>
> ---
>
> Laura del Amo Maestro - Proteolysis Lab
> SBU-Structural Biology Unit, IBMB CSIC
> Barcelona, Spain, Europe
>
> --
>
> 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] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

[Tim Gruene]

Dear Gerard,

you are wrong. 'he'  in this context has as much information as 'someone' and 
'person'. It does not refer to the sex of the person spoken about. 

Best regards,
Tim

On Wednesday, March 11, 2020 4:44:47 PM CET Gerard DVD Kleywegt wrote:
> >>>   Sorry to have taken this matter up in such a visible manner: I
> >>>   noticed
> >>> 
> >>> this very wrong formula in someone's paper, and that person then told me
> >>> where he had found it. Having landed on that page, I didn't know where
> >>> to go
> For the students:
> 
> "someone" = systematic absence of information = 0 bits
> "person" = systematic absence of information = 0 bits
> "he" = 1 bit of information!
> 
> --The other Gerard (1 bit of information!)
> 
> **
> Gerard J. Kleywegt
> 
>http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
> **
> The opinions in this message are fictional.  Any similarity
> to actual opinions, living or dead, is purely coincidental.
> **
> Little known gastromathematical curiosity: let "z" be the
> radius and "a" the thickness of a pizza. Then the volume
>  of that pizza is equal to pi*z*z*a !
> **
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
--
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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Description: This is a digitally signed message part.

Re: [ccp4bb] [g...@globalphasing.com: [ccp4bb] An error in the IUCr Online Dictionary of Crystallography] (fwd)

[Gerard DVD Kleywegt]

  Sorry to have taken this matter up in such a visible manner: I noticed
this very wrong formula in someone's paper, and that person then told me
where he had found it. Having landed on that page, I didn't know where to go


For the students:

"someone" = systematic absence of information = 0 bits
"person" = systematic absence of information = 0 bits
"he" = 1 bit of information!

--The other Gerard (1 bit of information!)

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] [3dem] Which resolution?

[Gerard DVD Kleywegt]

If this is the case, why can't we use model B factors to validate our 
structure? I know some people are skeptical about this approach because B 
factors are refinable parameters.


Rangana


It is not clear to me exactly what you are asking.

B factors _should_ be validated, precisely because they are refined parameters
that are part of your model.   Where have you seen skepticism?


Rangana said that B-values should not be used *to validate structures*, NOT 
that B-values themselves shouldn't be validated themselves.


I suppose I am at least in part to blame for the former notion and the reason 
for this (at least circa 1995 when the Angry Young Men from Uppsala first 
starting harping on about this) was that B-values tend(ed) to be error sinks 
which could "absorb" all sorts of errors and phenomena in addition to 
modelling atomic displacement (e.g., unresolved disorder, unresolved NCS 
differences, incorrect restraints, incorrect atom types modelled, partial 
ocupancies, etc.).


--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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[ccp4bb] Problem opening Jligand

[Jennifer Miles]

Hi all,

I hope someone can help.

I want to use Jligand to generate a description of a link but am having 
problems getting the software to work. I use a mac and in the current version 
of ccp4 (7.0) I have, when I try to open it in coot it opens a tab on the top 
menu bar but nothing else happens.

I’ve tried to get it to work using jligand.jar as well but when I open this now 
I get an error message stating ‘Cannot parse the standard monomer library - 
please notify your system administrator’ and nothing works.

Any help with this would be much appreciated.

Best wishes,
Jennifer


--
Dr Jennifer Miles
Postdoctoral Research Fellow
School of Molecular and Cellular Biology
University of Leeds
j.mi...@leeds.ac.uk




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Re: [ccp4bb] Expi 293 (Met-) expression medium for selenomethionine labeling

[Roversi, Pietro (Dr.)]

Dear Laura,

a few years ago - when I realised that mamalian cell expression media *without 
Met* costed much more than *with Met* because it is classified as custom media 
- I tried to persuade the rep that there was a market for it - to no avail.

I did then plan an experiment in which I would deplete the media of Met using 
this enzyme :


https://en.wikipedia.org/wiki/Methionine_gamma-lyase

and then supplement the Met-depleted media with Se-Met.

At the time I discussed purchase of Met gamma-lyase from:

Alpha Laboratories

Web: www.alphalabs.co.uk

Before I could attempt the experiment - a Pt salt then came to my rescue and I 
was able to calculate initial phases by SAD with a diffraction experiment at a 
Pt-edge wavelength - so I cannot tell you if the idea of generating my own 
media would have worked.

Just in case it helps!

Ciao

Pietro


Pietro Roversi

Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/

LISCB Wellcome Trust ISSF Fellow

https://le.ac.uk/liscb/research-groups/pietro-roversi


Leicester Institute of Structural and Chemical Biology
Department of Molecular and Cell Biology, University of Leicester
Henry Wellcome Building
Lancaster Road, Leicester, LE1 7HB
England, United Kingdom

Skype: roversipietro
Mobile phone  +44 (0) 7927952047
Tel. +44 (0)116 2297237




From: CCP4 bulletin board  on behalf of LAURA DEL AMO 
MAESTRO 
Sent: 10 March 2020 17:40
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Expi 293 (Met-) expression medium for selenomethionine 
labeling


Dear ccp4 community,

I am in my last 3 months of my PhD, working at the Structural Biology Unit at 
IBMB-CSIC in Barcelona. As my experimental phasing trials using various heavy 
metals failed so far, we ordered two months ago Expi 293 (Met-) expression 
medium for selenomethionine labeling (see the reference: 
https://www.thermofisher.com/order/catalog/product/A4096701#/A4096701.
 But we got now the notice that it will not be delivered until end of April.

I had been working so hard on this project, and this medium is essential to 
finished with the experimental part of my thesis. Thus, I was wondering if 
someone in the community has a bottle (1L) of this expression medium without 
methionine that I could borrow, and which I would return immediately once our 
medium arrives.

Also in case you have recommendations or other sources of a defined Se-Met 
medium for Expi293 cells, please let me know. With kind regards from Barcelona, 
and hope someone can help,

Laura

---

Laura del Amo Maestro - Proteolysis Lab
SBU-Structural Biology Unit, IBMB CSIC
Barcelona, Spain, Europe



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[ccp4bb] Multiple Postdoctoral Fellowships available at the “Multiscale Research Institute for Complex Systems” at Fudan University of Shanghai

[lyguo]

The Multiscale Research Institute for Complex Systems (MRICS) at Fudan 
University is located at the Zhangjiang Campus of Fudan University and is 
supported by the Shanghai High-level Talents Program.  MRICS is strongly 
committed to the development of novel and effective multi-scale imaging 
technology that spans microscopic molecular structures all the way to 
macroscopic medical imaging, with the aim to provide unprecedented spatial and 
temporal insights into the structures and functions of living beings at all 
levels (molecules, cells, tissues, organs and even whole organisms).  
Specifically for structural biology, MRICS is equipped with a state-of-the-art 
cryo-EM facility that includes FEI Titan Krios with Volta phase plate, Glacios, 
Talos and Aquilos.  MRICS is also located next to Shanghai Synchrotron 
Radiation Facility for X-ray crystallography.
 
Our team includes Nobel laureate and international leading interdisciplinary 
experts.
 
We have new openings for multiple postdoctoral fellows in structural biology 
who will mainly study important biological systems by means of cryo-electron 
microscopy including single-particle and tomography. 
   
Requirements: 
 
The applicants should have a recent Ph.D. degree (within two years of 
graduation) or will have a Ph.D. degree within the next six months in biology 
or chemistry-related fields, be devoted to excellence in scientific research, 
have strong sense of responsibility, and be highly motivated and hardworking.  
For these positions, extensive experience in protein expression and 
purification is a must, while prior experience in X-ray crystallography or 
cryo-EM is a plus, but is not required.  
 
Compensation: 
 
1)We offer internationally competitive salary, fringe benefits and yearly 
bonus.  The level of salary will be determined according to the applicant's 
experience and qualification; 
2)Low-rent housing on campus is provided; 
3)There are ample opportunities to collaborate with world-renown 
laboratories;
4)We provide support for applying for funding opportunities whenever 
applicable.  
 
Shanghai is one of the most cosmopolitan cities in China with strong economy 
and vibrant scientific community. 
 
For interested applicants, please submit postdoctoral application packages (a 
combined pdf) including resumes, representative publications, phone numbers and 
email addresses of three academic referees to mrics...@fudan.edu.cn.
 
We look forward to your joining of our first-class team!



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