Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Problem with peakmax

[Edward A. Berry]

On 06/10/2021 11:19 AM, James Holton wrote:


I'm afraid the only bash command I know is: "tcsh"


I learned csh by studying "elves"



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

[ccp4bb] European Crystallography School ECS6

[John R Helliwell]

Dear Colleagues,
I commend to you the European Crystallography School ECS6. 
Full details are here:-
https://akcongress.com/ecs6/ 
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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

Re: [ccp4bb] Problem with peakmax

[Mohamed Ibrahim]

Many thanks, James, for the tips. This one worked also,

peakmax MAPIN "mymap.ccp4" XYZOUT "mypeaks_output.pdb" <<- EOF
EOF

Best regards,





On Thu, Jun 10, 2021 at 5:19 PM James Holton  wrote:

>
> I'm afraid the only bash command I know is: "tcsh"
>
> However, in addition to suggestions so far, I expect this will work:
>
> echo "" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>
> Your peakmax is waiting for options to come in on "standard input".  The
> vertical bar "|" is a "pipe" that takes the "standard output" of the first
> command (echo ""), and re-directs it to the standard input of the next
> command.  Pipes are a very powerful tool.  Save a lot of
> cutting-and-pasting.  Fortunately, both bash and tcsh recognize "|" in the
> same way. Unfortunately, they differ on how to re-direct output to a file.
>
> Oh, and that magic little "#!" that you put at the start of the first line
> of the script is called a "shebang".
>
> -James Holton
> MAD Scientist
>
> On 6/8/2021 11:06 AM, Mohamed Ibrahim wrote:
>
> Thanks Paul,
> Is it possible to add Ctrl-D to my bash script?
>
> Best regards,
>
> On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim <
> mohamed.ibra...@hu-berlin.de> wrote:
>
>> Thanks Paul,
>> Is it possible to add Ctrl-D to my bash script?
>>
>> Best regards,
>>
>> On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley 
>> wrote:
>>
>>> On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>>> >
>>> > I am trying to get the peak values from omit maps. The peakmax from
>>> the GUI works fine. However, I tried to run
>>> > peakmax from the terminal, and it stuck when returning P1. Same map
>>> file works fine, when I use the GUI. Any ideas,
>>> > how to solve this problem?
>>> >
>>> > command used
>>> > peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>>> >
>>>
>>> Ctrl-D
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
>>>
>>
>>
>> --
>> ​
>> * ​ --*
>> *Dr. Mohamed Ibrahim*
>> *Postdoctoral Researcher *
>>
>> *Humboldt University *
>> *Berlin, Germany*
>> *Tel: +49 30 209347931 *
>>
>
>
> --
> ​
> * ​ --*
> *Dr. Mohamed Ibrahim*
> *Postdoctoral Researcher *
>
> *Humboldt University *
> *Berlin, Germany*
>
> *Tel: +49 30 209347931  *
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>

-- 
​
*​--*
*Dr. Mohamed Ibrahim*
*Postdoctoral Researcher   *

*Humboldt University   *
*Berlin, Germany  *

*Tel: +49 30 209347931 *



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

Re: [ccp4bb] Problem with peakmax

[Clemens Vonrhein]

On Thu, Jun 10, 2021 at 08:19:01AM -0700, James Holton wrote:
> I'm afraid the only bash command I know is: "tcsh"

I'm using the exact opposite direction ;-)



  To everyone using "echo" (interactively and/or in scripts): be careful
  which command is picked up at any given point. There are shell
  built-in versions of "echo" and then there is /bin/echo. Some
  recognize "\n" and some don't. Some support "-e" flag and some
  don't. A better command might be

printf "THREshold RMS 5.0\n" | peakmax MAPIN "myfile.ccp4" XYZOUT 
"myfiles_omit_atom.pdb"

  or (if no cards are to be used)

peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" < /dev/null

  or

printf "\n" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"

  (not all CCP4 programs support the "END" card").

  If you want to write instantly portable scripts, it might be best to
  have "#!/bin/sh": not all systems will have /bin/bash, /bin/csh or
  /bin/tcsh installed. Of course, /bin/sh might point to /bin/bash, but
  it could also point to /bin/dash (another variant) ... or something
  else entirely (MacOS is known to replace "standard" Linux/UNIX
  commands from time to time, often going from GNU versions to BSD based
  ones - or something else again). With /bin/sh you /should/ be within a
  POSIX sh environment: maybe more limited to other shells, but
  standardized and therefore much more portable since every UNIX-like
  system so far will always have /bin/sh available.



Cheers

Clemens

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



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

[ccp4bb] Postdoc position: Cryo-EM of Chromatin Complexes, Halic Lab

[Bilokapic, Silvija]

Dear all

Halic lab is looking for highly motivated and enthusiastic postdoctoral 
candidate interested in cryo-EM of chromatin complexes. Strong background in 
molecular cloning, expression, and purification of protein complexes is 
essential. Experience in X-ray crystallography or single particle cryo-EM would 
be a plus but not required.
The successful applicant will join a vibrant community at Department of 
Structural Biology, St. Jude Children's Research Hospital, which provides 
access to state-of-the-art integrated structural approaches comprising 
cryo-electron microscopy and tomography (Titan Krios, Talos Arctica and Talos 
L120C ), X-ray crystallography and biomolecular NMR.

To apply, please send a brief letter of interest, a CV, and the names of three 
references to mario.ha...@stjude.org

@LabHalic



Silvija Bilokapic, PhD

Structural Biology

St. Jude Children’s Research Hospital

262 Danny Thomas Place

Memphis, TN 38105-3678




Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer



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

Re: [ccp4bb] Problem with peakmax

[James Holton]

I'm afraid the only bash command I know is: "tcsh"

However, in addition to suggestions so far, I expect this will work:

echo "" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"

Your peakmax is waiting for options to come in on "standard input". The 
vertical bar "|" is a "pipe" that takes the "standard output" of the 
first command (echo ""), and re-directs it to the standard input of the 
next command.  Pipes are a very powerful tool.  Save a lot of 
cutting-and-pasting.  Fortunately, both bash and tcsh recognize "|" in 
the same way. Unfortunately, they differ on how to re-direct output to a 
file.


Oh, and that magic little "#!" that you put at the start of the first 
line of the script is called a "shebang".


-James Holton
MAD Scientist

On 6/8/2021 11:06 AM, Mohamed Ibrahim wrote:

Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim 
mailto:mohamed.ibra...@hu-berlin.de>> 
wrote:


Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:

On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>
> I am trying to get the peak values from omit maps. The
peakmax from the GUI works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1.
Same map file works fine, when I use the GUI. Any ideas,
> how to solve this problem?
>
> command used
> peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>

Ctrl-D



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




-- 
​

/*
​
--*/
/*Dr. Mohamed Ibrahim */
/*Postdoctoral Researcher
*//**//*
*/
/*Humboldt University
*/
/*Berlin, Germany
*/
/*Tel: +49 30 209347931*/



--
​
/*
​
--*/
/*Dr. Mohamed Ibrahim */
/*Postdoctoral Researcher
*//**//*
*/
/*Humboldt University
*/
/*Berlin, Germany
*/
/*Tel: +49 30 209347931
*/



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








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

Re: [ccp4bb] Should Rmerge be reported?

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Tim,

can I explain? To be honest no! Other than old habits and all. Should converge 
to the same value in the end, so you have a valid point.

All the best Graeme



From: Tim Gruene
Sent: Thursday, June 10, 2021 14:02
To: Winter, Graeme (DLSLtd,RAL,LSCI)
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Should Rmerge be reported?

Hi Graeme,

could you explain why Rmeas does not serve the same purpose as Rmerge?
I guess Manfred (and others) have no objection to reporting Rmeas just
instead of Rmerge.

@ Christy: If one of my manuscript were rejected solely because Rmerge
was not mentioned, I would make a phone call to the boss if the editor.
Afterall, Rmerge can be recovered from the unmerged data, which ideally
you did deposit at the PDB.

Best,
Tim


On Thu, 10 Jun 2021 12:42:10 + "Winter, Graeme (DLSLtd,RAL,LSCI)"
 wrote:

> Once again I find myself jumping to the defence of this rather poor
> statistic!
>
> Yes, Rmerge is a very poor estimator of "data quality" and has many
> well published flaws related to multiplicity, but the low resolution
> Rmerge, if combined with a multiplicity > (say) 5, is a good
> indicator of whether the data set is "good" or there is something odd
> going on.
>
> For example, if you claim a 1.6A structure with an inner shell Rmerge
> of 0.11, 5-fold multiplicity and an overall I/sig(I) of 68 I would
> "smell a rat"
>
> To me it does have a value, as an unbiased estimator of your true
> unmerged I/sigma as it does not depend on any manipulation you have
> done to your sigmas. It is not a good estimator of where the
> resolution should be cut or any other decisions.
>
> The above situation could be an indicator that there was radiation
> damage, for example
>
> There are better ways of measuring damage - Rd, Rcp, ... but these
> are not commonplace graphs as I understand it. This little number in
> the middle of the table does give you that hint.
>
> So while I would say rejecting a paper because it was not included
> was very heavy handed, I would not like to see it erased from all
> papers either.
>
> All the best Graeme
> 
> From: CCP4 bulletin board  on behalf of
> Manfred S. Weiss  Sent: 10 June
> 2021 13:30 To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Should Rmerge be reported?
>
> Dear Cristy,
>
> this is really hilarious. And it just shows how attached
> some ppl are to outdated numbers. Against better
> knowledge.
>
> It has been shown many times that Rmerge is flawed
> at various levels.
>
> The only reason I can see to report it is to be backwards
> compatible. But of course, this is a really weak reason.
>
> I would love to see it disappear.
>
> All the best
> Manfred
>
> Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
> Dear Colleagues
> Hope to find you all well and healthy.
>
> I have a question regarding Rmerge. In recent years, we have
> published our crystallographic structures in highly respected
> journals using CC1/2, I/sigma(I), completeness and multiplicity as
> quality parameters for our diffraction data.
>
> Recently this year, We submitted a paper using the same strategy, but
> one of the reviewers asked us to provide the Rmerge, arguing that
> providing this data was compulsory and it was important to estimate
> radiation damage.
>
> We replied to the editor arguing that Rmerge should not be used as a
> quality parameter, as suggested by more recent literature, such as
> the article published by Karplus and Diederichs
> (10.1016/j.sbi.2015.07.003). We also argued that there are modern and
> efficient methods to estimate radiation damage (
> doi.org/10.1107/S1600576718005241;
> doi.org/10.1107/S0907444909040177).
> It is my opinion that an experienced crystallographer can even
> monitor radiation damage over the course of data processing.
>
> And our paper was rejected  due to the fact I did not
> provide Rmerge which I certainly could have done If I found necessary.
>
> Journals like Nature ((https://www.nature.com › documents ›
> nr-tables-xray)
> and even IUCr Journals
> (https://journals.iucr.org/f/services/structuralcommunications/)
> still list Rmerge as a data to be reported. I always took this as a
> suggestion since there are people still using Rmerge for data cutoff,
> but I never took this as if Rmerge was a compulsory data to be
> reported.
>
> I would like to hear the opinion of this community. Should we
> compulsorily report Rmerge?  If so, Why?
>
> Cheers,
>
> Cristy
> --
> Cristina Nonato
> Associate Professor
> Laboratório de Cristalografia de Proteínas
> Faculdade de Ciências Farmacêuticas de Ribeirão Preto
> University of São Paulo
>
>
>
> 
>
> 

[ccp4bb] PostdoctoralPosition@UCIrvine

[Celia Goulding]

A funded postdoctoral position in structural biology is available immediately 
in the laboratory of Professor Celia Goulding at the University of California, 
Irvine.  Our studies focus on the structural biology and biochemistry of 
Mycobacterium tuberculosis iron/heme uptake and bacterial contact-dependent 
growth inhibition.  Potential projects will utilize X-ray crystallography, 
electron microscopy and biochemical studies.  A Ph.D. in biochemistry or 
molecular biology with experience in protein crystallography is preferred.  
This position is an excellent opportunity to develop broad skills in structure 
determination, kinetics, spectroscopy, genetics, and molecular biology while 
working in an energetic, interdisciplinary environment 7 miles from the 
beautiful Southern California coast.

Please refer to http://faculty.sites.uci.edu/celiagoulding and apply to 
celia.gould...@uci.edu.

Celia Goulding.



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

Re: [ccp4bb] Should Rmerge be reported?

[Jon Cooper]

Correct me if I'm wrong, but the first papers to stop reporting R-anything were 
XFEL ones so I assumed it was a particularly bad estimator of data quality for 
those expt's ;-

With a more normal expt, again correct this if it's wrong, the problems with 
R-merge only throw it off by a few percent?

Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 10 Jun 2021, 14:07, Frank von Delft wrote:

> Or just boycott the journal...??
>
> On 10/06/2021 14:02, Tim Gruene wrote:
>> Hi Graeme,
>>
>> could you explain why Rmeas does not serve the same purpose as Rmerge?
>> I guess Manfred (and others) have no objection to reporting Rmeas just
>> instead of Rmerge.
>>
>> @ Christy: If one of my manuscript were rejected solely because Rmerge
>> was not mentioned, I would make a phone call to the boss if the editor.
>> Afterall, Rmerge can be recovered from the unmerged data, which ideally
>> you did deposit at the PDB.
>>
>> Best,
>> Tim
>>
>>
>> On Thu, 10 Jun 2021 12:42:10 + "Winter, Graeme (DLSLtd,RAL,LSCI)"
>>  wrote:
>>
>>> Once again I find myself jumping to the defence of this rather poor
>>> statistic!
>>>
>>> Yes, Rmerge is a very poor estimator of "data quality" and has many
>>> well published flaws related to multiplicity, but the low resolution
>>> Rmerge, if combined with a multiplicity > (say) 5, is a good
>>> indicator of whether the data set is "good" or there is something odd
>>> going on.
>>>
>>> For example, if you claim a 1.6A structure with an inner shell Rmerge
>>> of 0.11, 5-fold multiplicity and an overall I/sig(I) of 68 I would
>>> "smell a rat"
>>>
>>> To me it does have a value, as an unbiased estimator of your true
>>> unmerged I/sigma as it does not depend on any manipulation you have
>>> done to your sigmas. It is not a good estimator of where the
>>> resolution should be cut or any other decisions.
>>>
>>> The above situation could be an indicator that there was radiation
>>> damage, for example
>>>
>>> There are better ways of measuring damage - Rd, Rcp, ... but these
>>> are not commonplace graphs as I understand it. This little number in
>>> the middle of the table does give you that hint.
>>>
>>> So while I would say rejecting a paper because it was not included
>>> was very heavy handed, I would not like to see it erased from all
>>> papers either.
>>>
>>> All the best Graeme
>>> 
>>> From: CCP4 bulletin board  on behalf of
>>> Manfred S. Weiss  Sent: 10 June
>>> 2021 13:30 To: CCP4BB@JISCMAIL.AC.UK 
>>> Subject: Re: [ccp4bb] Should Rmerge be reported?
>>>
>>> Dear Cristy,
>>>
>>> this is really hilarious. And it just shows how attached
>>> some ppl are to outdated numbers. Against better
>>> knowledge.
>>>
>>> It has been shown many times that Rmerge is flawed
>>> at various levels.
>>>
>>> The only reason I can see to report it is to be backwards
>>> compatible. But of course, this is a really weak reason.
>>>
>>> I would love to see it disappear.
>>>
>>> All the best
>>> Manfred
>>>
>>> Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
>>> Dear Colleagues
>>> Hope to find you all well and healthy.
>>>
>>> I have a question regarding Rmerge. In recent years, we have
>>> published our crystallographic structures in highly respected
>>> journals using CC1/2, I/sigma(I), completeness and multiplicity as
>>> quality parameters for our diffraction data.
>>>
>>> Recently this year, We submitted a paper using the same strategy, but
>>> one of the reviewers asked us to provide the Rmerge, arguing that
>>> providing this data was compulsory and it was important to estimate
>>> radiation damage.
>>>
>>> We replied to the editor arguing that Rmerge should not be used as a
>>> quality parameter, as suggested by more recent literature, such as
>>> the article published by Karplus and Diederichs
>>> (10.1016/j.sbi.2015.07.003). We also argued that there are modern and
>>> efficient methods to estimate radiation damage (
>>> doi.org/10.1107/S1600576718005241;
>>> doi.org/10.1107/S0907444909040177).
>>> It is my opinion that an experienced crystallographer can even
>>> monitor radiation damage over the course of data processing.
>>>
>>> And our paper was rejected  due to the fact I did not
>>> provide Rmerge which I certainly could have done If I found necessary.
>>>
>>> Journals like Nature ((https://www.nature.com › documents ›
>>> nr-tables-xray)
>>> and even IUCr Journals
>>> (https://journals.iucr.org/f/services/structuralcommunications/)
>>> still list Rmerge as a data to be reported. I always took this as a
>>> suggestion since there are people still using Rmerge for data cutoff,
>>> but I never took this as if Rmerge was a compulsory data to be

Re: [ccp4bb] Should Rmerge be reported?

[Frank von Delft]

Or just boycott the journal...??


On 10/06/2021 14:02, Tim Gruene wrote:

Hi Graeme,

could you explain why Rmeas does not serve the same purpose as Rmerge?
I guess Manfred (and others) have no objection to reporting Rmeas just
instead of Rmerge.

@ Christy: If one of my manuscript were rejected solely because Rmerge
was not mentioned, I would make a phone call to the boss if the editor.
Afterall, Rmerge can be recovered from the unmerged data, which ideally
you did deposit at the PDB.

Best,
Tim


On Thu, 10 Jun 2021 12:42:10 + "Winter, Graeme (DLSLtd,RAL,LSCI)"
 wrote:


Once again I find myself jumping to the defence of this rather poor
statistic!

Yes, Rmerge is a very poor estimator of "data quality" and has many
well published flaws related to multiplicity, but the low resolution
Rmerge, if combined with a multiplicity > (say) 5, is a good
indicator of whether the data set is "good" or there is something odd
going on.

For example, if you claim a 1.6A structure with an inner shell Rmerge
of 0.11, 5-fold multiplicity and an overall I/sig(I) of 68 I would
"smell a rat"

To me it does have a value, as an unbiased estimator of your true
unmerged I/sigma as it does not depend on any manipulation you have
done to your sigmas. It is not a good estimator of where the
resolution should be cut or any other decisions.

The above situation could be an indicator that there was radiation
damage, for example

There are better ways of measuring damage - Rd, Rcp, ... but these
are not commonplace graphs as I understand it. This little number in
the middle of the table does give you that hint.

So while I would say rejecting a paper because it was not included
was very heavy handed, I would not like to see it erased from all
papers either.

All the best Graeme

From: CCP4 bulletin board  on behalf of
Manfred S. Weiss  Sent: 10 June
2021 13:30 To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Should Rmerge be reported?

Dear Cristy,

this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.

It has been shown many times that Rmerge is flawed
at various levels.

The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.

I would love to see it disappear.

All the best
Manfred

Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have
published our crystallographic structures in highly respected
journals using CC1/2, I/sigma(I), completeness and multiplicity as
quality parameters for our diffraction data.

Recently this year, We submitted a paper using the same strategy, but
one of the reviewers asked us to provide the Rmerge, arguing that
providing this data was compulsory and it was important to estimate
radiation damage.

We replied to the editor arguing that Rmerge should not be used as a
quality parameter, as suggested by more recent literature, such as
the article published by Karplus and Diederichs
(10.1016/j.sbi.2015.07.003). We also argued that there are modern and
efficient methods to estimate radiation damage (
doi.org/10.1107/S1600576718005241;
doi.org/10.1107/S0907444909040177).
It is my opinion that an experienced crystallographer can even
monitor radiation damage over the course of data processing.

And our paper was rejected  due to the fact I did not
provide Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents ›
nr-tables-xray)
and even IUCr Journals
(https://journals.iucr.org/f/services/structuralcommunications/)
still list Rmerge as a data to be reported. I always took this as a
suggestion since there are people still using Rmerge for data cutoff,
but I never took this as if Rmerge was a compulsory data to be
reported.

I would like to hear the opinion of this community. Should we
compulsorily report Rmerge?  If so, Why?

Cheers,

Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo





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


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, 

Re: [ccp4bb] Should Rmerge be reported?

[Tim Gruene]

Hi Graeme,

could you explain why Rmeas does not serve the same purpose as Rmerge?
I guess Manfred (and others) have no objection to reporting Rmeas just
instead of Rmerge.

@ Christy: If one of my manuscript were rejected solely because Rmerge
was not mentioned, I would make a phone call to the boss if the editor.
Afterall, Rmerge can be recovered from the unmerged data, which ideally
you did deposit at the PDB.

Best,
Tim


On Thu, 10 Jun 2021 12:42:10 + "Winter, Graeme (DLSLtd,RAL,LSCI)"
 wrote:

> Once again I find myself jumping to the defence of this rather poor
> statistic!
> 
> Yes, Rmerge is a very poor estimator of "data quality" and has many
> well published flaws related to multiplicity, but the low resolution
> Rmerge, if combined with a multiplicity > (say) 5, is a good
> indicator of whether the data set is "good" or there is something odd
> going on.
> 
> For example, if you claim a 1.6A structure with an inner shell Rmerge
> of 0.11, 5-fold multiplicity and an overall I/sig(I) of 68 I would
> "smell a rat"
> 
> To me it does have a value, as an unbiased estimator of your true
> unmerged I/sigma as it does not depend on any manipulation you have
> done to your sigmas. It is not a good estimator of where the
> resolution should be cut or any other decisions.
> 
> The above situation could be an indicator that there was radiation
> damage, for example
> 
> There are better ways of measuring damage - Rd, Rcp, ... but these
> are not commonplace graphs as I understand it. This little number in
> the middle of the table does give you that hint.
> 
> So while I would say rejecting a paper because it was not included
> was very heavy handed, I would not like to see it erased from all
> papers either.
> 
> All the best Graeme
> 
> From: CCP4 bulletin board  on behalf of
> Manfred S. Weiss  Sent: 10 June
> 2021 13:30 To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Should Rmerge be reported?
> 
> Dear Cristy,
> 
> this is really hilarious. And it just shows how attached
> some ppl are to outdated numbers. Against better
> knowledge.
> 
> It has been shown many times that Rmerge is flawed
> at various levels.
> 
> The only reason I can see to report it is to be backwards
> compatible. But of course, this is a really weak reason.
> 
> I would love to see it disappear.
> 
> All the best
> Manfred
> 
> Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
> Dear Colleagues
> Hope to find you all well and healthy.
> 
> I have a question regarding Rmerge. In recent years, we have
> published our crystallographic structures in highly respected
> journals using CC1/2, I/sigma(I), completeness and multiplicity as
> quality parameters for our diffraction data.
> 
> Recently this year, We submitted a paper using the same strategy, but
> one of the reviewers asked us to provide the Rmerge, arguing that
> providing this data was compulsory and it was important to estimate
> radiation damage.
> 
> We replied to the editor arguing that Rmerge should not be used as a
> quality parameter, as suggested by more recent literature, such as
> the article published by Karplus and Diederichs
> (10.1016/j.sbi.2015.07.003). We also argued that there are modern and
> efficient methods to estimate radiation damage (
> doi.org/10.1107/S1600576718005241;
> doi.org/10.1107/S0907444909040177).
> It is my opinion that an experienced crystallographer can even
> monitor radiation damage over the course of data processing.
> 
> And our paper was rejected  due to the fact I did not
> provide Rmerge which I certainly could have done If I found necessary.
> 
> Journals like Nature ((https://www.nature.com › documents ›
> nr-tables-xray)
> and even IUCr Journals
> (https://journals.iucr.org/f/services/structuralcommunications/)
> still list Rmerge as a data to be reported. I always took this as a
> suggestion since there are people still using Rmerge for data cutoff,
> but I never took this as if Rmerge was a compulsory data to be
> reported.
> 
> I would like to hear the opinion of this community. Should we
> compulsorily report Rmerge?  If so, Why?
> 
> Cheers,
> 
> Cristy
> --
> Cristina Nonato
> Associate Professor
> Laboratório de Cristalografia de Proteínas
> Faculdade de Ciências Farmacêuticas de Ribeirão Preto
> University of São Paulo
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
> --
> Dr. Manfred S. Weiss
> Macromolecular Crystallography
> Helmholtz-Zentrum Berlin
> Albert-Einstein-Str. 15
> D-12489 Berlin
> Germany
> 
> 
> 
> Helmholtz-Zentrum 

Re: [ccp4bb] Should Rmerge be reported?

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear Manfred,

I completely agree. However this is not routinely reported.

The discussion is of removing one indicator of this signal, rather than 
replacing it with a superior measure - the latter is something I would more 
actively support however would involve adding new stuff which is an uphill 
battle.

All the best Graeme

From: Manfred S. Weiss 
Sent: 10 June 2021 13:43
To: Winter, Graeme (DLSLtd,RAL,LSCI) ; 
CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Should Rmerge be reported?

Dear Graeme,

a better number to look at is Isa. Instead of low resolution Rmerge.
Seriously. We monitor that to assess beamline performance.

Cheers, Manfred

Am 10.06.2021 um 14:42 schrieb Winter, Graeme (DLSLtd,RAL,LSCI):
Once again I find myself jumping to the defence of this rather poor statistic!

Yes, Rmerge is a very poor estimator of "data quality" and has many well 
published flaws related to multiplicity, but the low resolution Rmerge, if 
combined with a multiplicity > (say) 5, is a good indicator of whether the data 
set is "good" or there is something odd going on.

For example, if you claim a 1.6A structure with an inner shell Rmerge of 0.11, 
5-fold multiplicity and an overall I/sig(I) of 68 I would "smell a rat"

To me it does have a value, as an unbiased estimator of your true unmerged 
I/sigma as it does not depend on any manipulation you have done to your sigmas. 
It is not a good estimator of where the resolution should be cut or any other 
decisions.

The above situation could be an indicator that there was radiation damage, for 
example

There are better ways of measuring damage - Rd, Rcp, ... but these are not 
commonplace graphs as I understand it. This little number in the middle of the 
table does give you that hint.

So while I would say rejecting a paper because it was not included was very 
heavy handed, I would not like to see it erased from all papers either.

All the best Graeme

From: CCP4 bulletin board  
on behalf of Manfred S. Weiss 

Sent: 10 June 2021 13:30
To: CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Should Rmerge be reported?

Dear Cristy,

this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.

It has been shown many times that Rmerge is flawed
at various levels.

The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.

I would love to see it disappear.

All the best
Manfred

Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our 
crystallographic structures in highly respected journals using CC1/2, 
I/sigma(I), completeness and multiplicity as quality parameters for our 
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one of 
the reviewers asked us to provide the Rmerge, arguing that providing this data 
was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a quality 
parameter, as suggested by more recent literature, such as the article 
published by Karplus and Diederichs (10.1016/j.sbi.2015.07.003). We also argued 
that there are modern and efficient methods to estimate radiation damage ( 
doi.org/10.1107/S1600576718005241; 
doi.org/10.1107/S0907444909040177). 
It is my opinion that an experienced crystallographer can even  monitor 
radiation damage over the course of data processing.

And our paper was rejected  due to the fact I did not provide 
Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › 
nr-tables-xray)
 and even IUCr Journals 
(https://journals.iucr.org/f/services/structuralcommunications/) still list 
Rmerge as a data to be reported. I always took this as a suggestion since there 
are people still using Rmerge for data cutoff, but I never took this as if 
Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily 
report Rmerge?  If so, Why?

Cheers,

Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo





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


--
Dr. Manfred S. 

Re: [ccp4bb] Should Rmerge be reported?

[Manfred S. Weiss]

Dear Graeme,

a better number to look at is Isa. Instead of low resolution Rmerge.
Seriously. We monitor that to assess beamline performance.

Cheers, Manfred

Am 10.06.2021 um 14:42 schrieb Winter, Graeme (DLSLtd,RAL,LSCI):
Once again I find myself jumping to the defence of this rather poor statistic!

Yes, Rmerge is a very poor estimator of "data quality" and has many well published flaws 
related to multiplicity, but the low resolution Rmerge, if combined with a multiplicity > (say) 5, 
is a good indicator of whether the data set is "good" or there is something odd going on.

For example, if you claim a 1.6A structure with an inner shell Rmerge of 0.11, 5-fold 
multiplicity and an overall I/sig(I) of 68 I would "smell a rat"

To me it does have a value, as an unbiased estimator of your true unmerged 
I/sigma as it does not depend on any manipulation you have done to your sigmas. 
It is not a good estimator of where the resolution should be cut or any other 
decisions.

The above situation could be an indicator that there was radiation damage, for 
example

There are better ways of measuring damage - Rd, Rcp, ... but these are not 
commonplace graphs as I understand it. This little number in the middle of the 
table does give you that hint.

So while I would say rejecting a paper because it was not included was very 
heavy handed, I would not like to see it erased from all papers either.

All the best Graeme

From: CCP4 bulletin board  on behalf 
of Manfred S. Weiss 

Sent: 10 June 2021 13:30
To: CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Should Rmerge be reported?

Dear Cristy,

this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.

It has been shown many times that Rmerge is flawed
at various levels.

The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.

I would love to see it disappear.

All the best
Manfred

Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our 
crystallographic structures in highly respected journals using CC1/2, 
I/sigma(I), completeness and multiplicity as quality parameters for our 
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one of 
the reviewers asked us to provide the Rmerge, arguing that providing this data 
was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a quality parameter, as 
suggested by more recent literature, such as the article published by Karplus and 
Diederichs (10.1016/j.sbi.2015.07.003). We also argued that there are modern and efficient 
methods to estimate radiation damage ( 
doi.org/10.1107/S1600576718005241; 
doi.org/10.1107/S0907444909040177). It is 
my opinion that an experienced crystallographer can even  monitor radiation damage over the 
course of data processing.

And our paper was rejected  due to the fact I did not provide 
Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › 
nr-tables-xray)
 and even IUCr Journals (https://journals.iucr.org/f/services/structuralcommunications/) still list Rmerge as a data 
to be reported. I always took this as a suggestion since there are people still using Rmerge for data cutoff, but I 
never took this as if Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily 
report Rmerge?  If so, Why?

Cheers,

Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo





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


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:

Re: [ccp4bb] Should Rmerge be reported?

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Once again I find myself jumping to the defence of this rather poor statistic!

Yes, Rmerge is a very poor estimator of "data quality" and has many well 
published flaws related to multiplicity, but the low resolution Rmerge, if 
combined with a multiplicity > (say) 5, is a good indicator of whether the data 
set is "good" or there is something odd going on.

For example, if you claim a 1.6A structure with an inner shell Rmerge of 0.11, 
5-fold multiplicity and an overall I/sig(I) of 68 I would "smell a rat"

To me it does have a value, as an unbiased estimator of your true unmerged 
I/sigma as it does not depend on any manipulation you have done to your sigmas. 
It is not a good estimator of where the resolution should be cut or any other 
decisions.

The above situation could be an indicator that there was radiation damage, for 
example

There are better ways of measuring damage - Rd, Rcp, ... but these are not 
commonplace graphs as I understand it. This little number in the middle of the 
table does give you that hint.

So while I would say rejecting a paper because it was not included was very 
heavy handed, I would not like to see it erased from all papers either.

All the best Graeme

From: CCP4 bulletin board  on behalf of Manfred S. Weiss 

Sent: 10 June 2021 13:30
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Should Rmerge be reported?

Dear Cristy,

this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.

It has been shown many times that Rmerge is flawed
at various levels.

The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.

I would love to see it disappear.

All the best
Manfred

Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our 
crystallographic structures in highly respected journals using CC1/2, 
I/sigma(I), completeness and multiplicity as quality parameters for our 
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one of 
the reviewers asked us to provide the Rmerge, arguing that providing this data 
was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a quality 
parameter, as suggested by more recent literature, such as the article 
published by Karplus and Diederichs (10.1016/j.sbi.2015.07.003). We also argued 
that there are modern and efficient methods to estimate radiation damage ( 
doi.org/10.1107/S1600576718005241; 
doi.org/10.1107/S0907444909040177). 
It is my opinion that an experienced crystallographer can even  monitor 
radiation damage over the course of data processing.

And our paper was rejected  due to the fact I did not provide 
Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › 
nr-tables-xray)
 and even IUCr Journals 
(https://journals.iucr.org/f/services/structuralcommunications/) still list 
Rmerge as a data to be reported. I always took this as a suggestion since there 
are people still using Rmerge for data cutoff, but I never took this as if 
Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily 
report Rmerge?  If so, Why?

Cheers,

Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo





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


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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

-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee 

[ccp4bb] Structural Biology Postdoc at Princeton

[Philip D. Jeffrey]

An NIH-funded postdoctoral research position is available immediately in the 
Hughson lab at Princeton University. Our group’s research focuses on the 
remarkable protein machinery that generates the interior architecture of 
eukaryotic cells by orchestrating the formation and fusion of cargo-carrying 
transport vesicles. Our recent discoveries lay the foundation for exciting new 
projects studying how membrane tethering proteins work together with membrane 
fusion proteins to ensure accurate and efficient cargo delivery. This work will 
combine structural techniques (cryoEM, crystallography) with mechanism-directed 
functional studies. If this sounds interesting, please apply to join our team 
by sending your CV, a cover letter describing your research interests, and 
contact information for three references to  
hugh...@princeton.edu .



Princeton University is renowned for its scientific excellence and collegial, 
interactive environment. Located in Princeton, New Jersey, a vibrant community 
of about 30,000 people, it is just a quick train ride away from New York City 
and Philadelphia. Princeton University is an equal opportunity employer, and 
all qualified applicants will receive consideration for employment without 
regard to race, color, religion, sex, sexual orientation, gender identity, 
national origin, disability status, protected veteran status, or any other 
characteristic protected by law.



Fred Hughson

Professor of Molecular Biology

Princeton University

Princeton, NJ 08544




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

Re: [ccp4bb] Should Rmerge be reported?

[Manfred S. Weiss]

Dear Cristy,

this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.

It has been shown many times that Rmerge is flawed
at various levels.

The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.

I would love to see it disappear.

All the best
Manfred

Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our 
crystallographic structures in highly respected journals using CC1/2, 
I/sigma(I), completeness and multiplicity as quality parameters for our 
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one of 
the reviewers asked us to provide the Rmerge, arguing that providing this data 
was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a quality parameter, as 
suggested by more recent literature, such as the article published by Karplus and 
Diederichs (10.1016/j.sbi.2015.07.003). We also argued that there are modern and efficient 
methods to estimate radiation damage ( 
doi.org/10.1107/S1600576718005241; 
doi.org/10.1107/S0907444909040177). It is 
my opinion that an experienced crystallographer can even  monitor radiation damage over the 
course of data processing.

And our paper was rejected  due to the fact I did not provide 
Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › 
nr-tables-xray)
 and even IUCr Journals (https://journals.iucr.org/f/services/structuralcommunications/) still list Rmerge as a data 
to be reported. I always took this as a suggestion since there are people still using Rmerge for data cutoff, but I 
never took this as if Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily 
report Rmerge?  If so, Why?

Cheers,

Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo





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


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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

[ccp4bb] Principal Beamline Scientist Position at Diamond Light Source

[Hall, Dave (DLSLtd,RAL,LSCI)]

Dear all

We have an opportunity for a scientist with a keen interest in beamline 
development, automation and/or structural biology to join the macromolecular 
crystallography leadership team at Diamond to guide and develop the I03 
beamline. I03 is at the forefront of cryogenic automated data collection 
developments at Diamond as well as being uniquely equipped for experiments at 
biological containment level III.

For more information on the position and to apply follow the link below:

https://vacancies.diamond.ac.uk/vacancy/principal-beamline-scientist-i03-445608.html

The closing date is Sunday 11th July.

If you are interested in applying and have questions about the role please 
contact me directly.

Best wishes

Dave Hall
--
MX Group Leader
Diamond Light Source
dls.mx


-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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

[ccp4bb] Should Rmerge be reported?

[Maria Cristina Nonato]

Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our
crystallographic structures in highly respected journals using CC1/2,
I/sigma(I), completeness and multiplicity as quality parameters for our
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one
of the reviewers asked us to provide the Rmerge, arguing that providing
this data was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a
quality parameter, as suggested by more recent literature, such as the
article published by Karplus and Diederichs (10.1016/j.sbi.2015.07.003). We
also argued that there are modern and efficient methods to estimate
radiation damage ( doi.org/10.1107/S1600576718005241;
doi.org/10.1107/S0907444909040177). It is my opinion that an experienced
crystallographer can even  monitor radiation damage over the course of data
processing.

And our paper was rejected  due to the fact I did not
provide Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › nr-tables-xray

) and even IUCr Journals (
https://journals.iucr.org/f/services/structuralcommunications/) still list
Rmerge as a data to be reported. I always took this as a suggestion since
there are people still using Rmerge for data cutoff, but I never took this
as if Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily
report Rmerge?  If so, Why?

Cheers,

Cristy
-- 

*Cristina Nonato*
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo



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

Re: [ccp4bb] Topology diagrams software

[Mark J. van Raaij]

some info here:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Topology_plots
(haven’t done it myself for a while, so not sure which programs are still being 
maintained)

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 10 Jun 2021, at 13:14, Gambelli, Lavinia  wrote:
> 
> Hello, 
> 
> I'm looking for a software to make topology diagrams of proteins. Ideally, 
> I'd like to submit a pdb file and obtain the topology model. Do you know what 
> alternatives are out there? So far I'm only aware of PDBsum that can do this, 
> but I was wondering if there is something else available. 
> 
> Kind regards,
> Lavinia
> 
> Dr. Lavinia Gambelli
> Postdoctoral Researcher
> Office number: 01392 727468
>  
> http://emps.exeter.ac.uk/physics-astronomy/staff/lg496
>  
> - - - - - - - - - - - - - - - - - - 
> University of Exeter 
> Living Systems Institute 
> Stocker Road, Exeter, Devon, EX4 4QD, UK
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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

Re: [ccp4bb] Topology diagrams software

[Paul Emsley]

On 10/06/2021 12:14, Gambelli, Lavinia wrote:


I'm looking for a software to make topology diagrams of proteins. Ideally, I'd like to submit a pdb file and 
obtain the topology model. Do you know what alternatives are out there? So far I'm only aware of PDBsum that 
can do this, but I was wondering if there is something else available.




TopDraw?



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

[ccp4bb] Topology diagrams software

[Gambelli, Lavinia]

Hello,

I'm looking for a software to make topology diagrams of proteins. Ideally, I'd 
like to submit a pdb file and obtain the topology model. Do you know what 
alternatives are out there? So far I'm only aware of PDBsum that can do this, 
but I was wondering if there is something else available.

Kind regards,
Lavinia


Dr. Lavinia Gambelli

Postdoctoral Researcher

Office number: 01392 727468
http://emps.exeter.ac.uk/physics-astronomy/staff/lg496

- - - - - - - - - - - - - - - - - -

University of Exeter
Living Systems Institute
Stocker Road, Exeter, Devon, EX4 4QD, UK




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

[ccp4bb] CryoEM Field Applications Scientist - USA

[Michele Darrow]

I'd like to draw your attention to an opening at SPT Labtech for a US-based 
Field Applications Scientist position in CryoEM. Please find a description 
below.

For more info and to apply, please visit: 
https://apply.workable.com/spt-labtech/j/20D368B245/?utm_medium=social_share_link

Applications will be assessed on a rolling basis until the position is filled. 
Feel free to get in touch with any questions!

Best,
Michele

Description
SPT Labtech has an exciting opportunity for a Field Applications Scientist, 
specializing in CryoEM, to help deliver and support new sample preparation 
technologies that will enable emerging methods of determining biomolecular 
structures. This is a fantastic opportunity to work on cutting-edge sample 
preparation technology and aid in its introduction to the market.
You will be part of our global FAS team that serves as the key interface 
between the Sales team, Marketing, and end-users. You will help shape the 
development and delivery of the chameleon as a key member of our structural 
biology team. We are looking for a personable scientist who has specialized in 
cryoEM.
This role requires excellent relationship-building skills with both our 
internal commercial team and our US customer base. As such, you will be 
required to travel extensively across North America and occasionally to our UK 
headquarters, and so this position must be based near a convenient travel hub. 
Being that we are a global company, you will be working with colleagues from 
across multiple time zones and territories, requiring some flexibility in 
meeting schedules. As our FAS team are home-based, you will have flexibility in 
your scheduled appointments with customers and colleagues, allowing you to 
balance your work and personal responsibilities.
SPT Labtech is a global supplier of innovative products for advancing life 
sciences and accelerating science, and for the past twenty years have brought a 
combination of the best science and first-rate engineering to the structural 
biology community. Our company culture supports diversity and is inclusive of 
all regardless of race, ethnicity, gender, gender identity, sexual orientation, 
physical ability, or family status, and we endeavour to support our employees' 
needs to the best of our ability.
Responsibilities include, but are not limited to:

  *   Supporting the development and roll-out of our chameleon cryoEM sample 
preparation instrument
  *   Engaging with customers to provide best practices in the use of the 
chameleon within the cryoEM workflow (sample prep, microscopy, data collection, 
image processing)
  *   Leadership of diverse cross functional research teams through the 
introductory stages of cryoEM methods
  *   Engaging in remote and on-site training
  *   Supporting the sales team with product demonstrations
  *   Understanding product requirements through collaboration with customers
  *   Liaising between customers and development teams to identify and enable 
product improvements
  *   Managing placements with customer development partners, including 
training, analysis, and interpretation of customer data, and providing feedback 
on the customer experience
  *   Advising on the possible direction of further development as a product 
expert
  *   Preparing and presenting material for scientific publications and 
meetings as well as marketing purposes, such as posters and application notes.
|  Michele Darrow  |  development scientist  |  SPT Labtech Ltd.  |  +44 1223 
627555  |  +44 01223 627320  (direct dial)
designed for discovery - working together to accelerate life science research
sptlabtech.com  |  
LinkedIn  |  
YouTube  | 
Twitter



The information contained in this e-mail and any attachments is intended for 
the named recipient(s) only. It may also be privileged and confidential. If you 
are not an intended recipient, you must not copy, distribute or take any action 
in reliance upon it. Please notify the sender immediately by e-mail if you 
believe you have received this e-mail by mistake and delete this e-mail from 
your system. No warranties or assurances are made in relation to safety, 
content and/or any attachments. No liability is accepted for any consequences 
arising from it. No warranties are given by SPT Labtech Ltd, and no liability 
is accepted by SPT Labtech Ltd, in relation to any loss arising from reliance 
placed on the information supplied in this email and attachments, other than 
those warranties expressly stated in SPT Labtech Ltd's Standard Terms and 
Conditions of Sale. SPT Labtech Ltd's Standard Terms and Conditions of Sale 
apply at all times. SPT Labtech Ltd Plc, registered in England no. 3300999,
  Melbourn Science Park, Cambridge Road, Melbourn, SG8 6HB Tel +44(0)1223 
627555, This email has been scanned for viruses and malware by ProofPoint

Re: [ccp4bb] Coot shortcut key for Mutate

[Firdous Tarique]

Dear Paul

Thank you. I installed it through curlew. Now it works fine. It is Shift +
c for the dialogue box to appear then type the amino acid code you want to
mutate the residue with and boom..new amino acid appears at its original
position.

Thanks

Firdous

On Thu, Jun 10, 2021 at 1:14 AM Paul Emsley 
wrote:

> On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote:
> > Hello everyone
> >
> > Can anybody tell me the Coot shortcut key for mutate or mutate and
> refine. Is there any way to turn it on or to assign
> > a particular key if it is disabled ?
> >
>
> "Keyboard mutate" Curlew. You will have to remember your single-letter
> codes. It comprehends lowercase to save you a
> keystroke. "C" to active it.
>
> "H" will do a bonded-neighbs refine with auto-accept.
>
> Paul.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
>



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