Re: [ccp4bb] request for applications

[Bernhard Rupp]

> what would YOU do if you had $1e12 USD for your science? 

(a) Embezzle most of and (b) do sociologically relevant research with the rest, 
like
https://www.ruppweb.org/Garland/PICD.html

Best, BR
-----
Bernhard Rupp 
k.k. Hofkristallamt
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.hofkristallamt.org/ 
-
Hope is not a strategy - hope is a mistake.
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Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Bernhard Rupp]

Thanks, Jon. Finding the peaks is not the problem; the *.ha file contains 
those, as do the pdf. map sections.

It is that I don’t know how to properly fix that Interface Configuration file 
to have the PS distiller and mapslicer display the output.

 

This problem occurs on 2 independent CCP4i installations on different Windows 
10/11 computers

 

Thx, BR

From: CCP4 bulletin board  On Behalf Of Jon Cooper
Sent: Sunday, February 18, 2024 09:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Interface Configuration and Mapslicer Question

 

You could search for peaks of decreasing height by stepping back through 
through alphabet with your text searches. Of course, peakmax will do a good job 
of finding them anyway. 


Best wishes, Jon Cooper. jon.b.coo...@protonmail.com 
<mailto:jon.b.coo...@protonmail.com> 

Sent from Proton Mail mobile



 Original Message 
On 18 Feb 2024, 17:35, Jon Cooper < 
488a26d62010-dmarc-requ...@jiscmail.ac.uk 
<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk> > wrote:


I think we used to use mapsig for printing map sections with single characters 
to show peak height. You could set it so that low or no density was just a dot 
and higher values were 0...9 ... A... Z ... * #, etc. up to the maximum or 
maybe it was another one of Ian's programs. It made peak searching with a text 
editor pretty easy just by searching for the characters corressponding to the 
high values. I don't know if that's any use. 


Best wishes, Jon Cooper. jon.b.coo...@protonmail.com 
<mailto:jon.b.coo...@protonmail.com> 

Sent from Proton Mail mobile



 Original Message 
On 18 Feb 2024, 03:29, Bernhard Rupp < hofkristall...@gmail.com 
<mailto:hofkristall...@gmail.com> > wrote:

 

Der CCP4 Experts & Developers,

 

I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native Patterson 
maps for NCS analysis, using ‘patterson’ of FFT which produces the *.map (dump) 
file and 3 Harker *.plt files.

 

Unfortunately, epic fail on the display of the results. 

The ghostview (cf. image) I cannot install (some dll error) and it also seems 
deprecated.

As a workaround I use pltdev to generate a *.ps file and distil it into a pdf 
and then display. Works, but ghostly 20th century

...or I display the map directly in Coot and eyeball the peakssurprisingly 
neat and educational.

 

Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt files?

 

I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
blanks).

But the entry in the Interface Configuration (config.def) seems sensibly quoted:

PS_PREVIEW_NAME,4 _text acrodist.exe

PS_PREVIEW_COM,4  _text "C:\Program Files 
(x86)\Adobe\Acrobat DC\Acrobat\acrodist.exe"

 

Q2: how do I properly enter the path to the distiller in the interface 
configuration? 

 

Mapslicer is also uncooperative (cf. img). 

The Interface Configuration entry informs me that “ccp4mapwish [file join 
[GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.

 

Q3: How should I fix this (I swear I did not wish with the installation)?  

 

In search of a more modern approach to this map analysis I also tried CCP4i2 
and Phenix, but there was no task like 

“Make a native Patterson and show me the *&%# map” to be found.

 

Q4: would this be a useful task to provide?

 

(a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing works 
just fine).

 

Cheers, BR 

 

--

Bernhard Rupp, Psilosopher

 <https://psilosophy.org/> https://psilosophy.org/

 <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

All models are wrong but some are useful.

--

 

 


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This message was issued to me

[ccp4bb] Interface Configuration and Mapslicer Question

[Bernhard Rupp]

Der CCP4 Experts & Developers,

 

I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native
Patterson maps for NCS analysis, using 'patterson' of FFT which produces the
*.map (dump) file and 3 Harker *.plt files.

 

Unfortunately, epic fail on the display of the results. 

The ghostview (cf. image) I cannot install (some dll error) and it also
seems deprecated.

As a workaround I use pltdev to generate a *.ps file and distil it into a
pdf and then display. Works, but ghostly 20th century

...or I display the map directly in Coot and eyeball the
peakssurprisingly neat and educational.

 

Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt
files?

I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat
DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the
blanks).

But the entry in the Interface Configuration (config.def) seems sensibly
quoted:

PS_PREVIEW_NAME,4 _text acrodist.exe

PS_PREVIEW_COM,4  _text "C:\Program Files
(x86)\Adobe\Acrobat DC\Acrobat\acrodist.exe"

 

Q2: how do I properly enter the path to the distiller in the interface
configuration? 

 

Mapslicer is also uncooperative (cf. img). 

The Interface Configuration entry informs me that "ccp4mapwish [file join
[GetEnvPath CCP4I_TOP] bin mapslicer.tcl]".

 

Q3: How should I fix this (I swear I did not wish with the installation)?  

 

In search of a more modern approach to this map analysis I also tried CCP4i2
and Phenix, but there was no task like 

"Make a native Patterson and show me the *&%# map" to be found.

 

Q4: would this be a useful task to provide?

 

(a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing
works just fine).

 

Cheers, BR 

 

--

Bernhard Rupp, Psilosopher

 <https://psilosophy.org/> https://psilosophy.org/

 <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

All models are wrong but some are useful.

--

 




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Re: [ccp4bb] How to make GDP.BeF3 solution ?

[Bernhard Rupp]

Some blast from the past: Facility management came in full hazmat suits to 
decommission the old multiwire detectors with the large Be windows.

https://www.ruppweb.org/Garland/gallery/Ch8/pages/Biomolecular_Crystallography_Fig_8-07.htm

 

Anyhow, got one on the DOE Beryllium worker’s list. Free lung X-rays

 

--

Bernhard Rupp, Psilosopher

 <https://psilosophy.org/> https://psilosophy.org/

 <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Don’t lick it and don’t breathe it. 

--

 

From: CCP4 bulletin board  On Behalf Of Diana Tomchick
Sent: Friday, January 5, 2024 13:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

 

Be aware that beryllium is also quite toxic.

 

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

 

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 <mailto:diana.tomch...@utsouthwestern.edu> 
(214) 645-6383 (phone)
(214) 645-6353 (fax)

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Dr. Kevin M Jude mailto:kj...@stanford.edu> 
>
Sent: Friday, January 5, 2024 1:51 PM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>  
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ? 

 

EXTERNAL MAIL

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, 
you will want to prepare that stock in a fume hood.

 

Best wishes

Kevin

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Matthew BOWLER mailto:mbow...@embl.fr> >
Date: Thursday, January 4, 2024 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>  
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
advantage of metal fluoride transition state analogue and ground state analogue 
complexes is the fact that all components are present in solution and readily 
self-assemble in the active site forming stable enzyme complexes that are 
relevant to the catalytic cycle. The inorganic metal fluoride salts (AlF3, and 
MgF2) are too insoluble to use; therefore, the fluoride anion and metal cation 
components must be added from separate stock solutions. Both ammonium fluoride 
and sodium fluoride are suitable as the source of fluoride and are readily 
soluble in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the critical 
aspects in preparing metal fluoride enzyme complexes is the pH of the resulting 
solution. In particular, solutions of AlCl3 and BeCl2 are highly acidic (pH 2) 
samples should be prepared in 100 mM unbuffered Tris base. The optimized 
sequence of component addition is to add fluoride to the prepared buffer first, 
then the metal chloride stock.

Hope this helps, Matt

 

 

 

 

 

On 02/01/2024 18:53, Firdous Tarique wrote:

Hi 

 

I would appreciate it if someone could share with me a step by step protocol 
for making a stable GDP.BeF3 solution which is often used as a transition state 
analogue for structural studies of a protein complex ? 

 

Or a vendor from where it can be purchased directly.

 

Regards

 

Firdous

 


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European Molecular Biology Laboratory
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CS 90181 F-38042 Grenoble
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.20.71.99
 
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Re: [ccp4bb] what is isomorphous?

[Bernhard Rupp]

The Drenth rule of thumb makes sense. Whether 2 in the macromolecular sense 
isomorphous structures are isomorphous, is a matter or resolution, and it has 
to do with the reciprocal space overlap function aka G-function. So up to a 
certain resolution, 2 data sets may be isomorphous, but at high resolution, not 
anymore. 

 

In practical words, think of it in real space instead of FT reciprocal terms: 
to the myopic low-resolution eye, everything looks like a sphere and thus 
isomorphous. Just as in NCS, when you put on your high-resolution goggles, 
differences in real space (atom positions) become visible and the FT then 
becomes also non-isomorphous. In ML phasing, the non-isomorphism in essence 
pancakes your phasing probabilities due to increased variance.

 

Result: The subtle art of data cut-off when exploiting isomorphism and 
shell-wise phase extension etc. 

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Marius Schmidt
Sent: Wednesday, December 20, 2023 14:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] what is isomorphous?

 

According to Jon, Isomorphous Replacement ALWAYS works,

because it is only supposed to be isomorphous.

Isomorphous difference maps can ALWAYS be calculated

with sensible results, because the unit cells of the reference and the

time-resolved data are only supposed to be isomorphous.

Something is not right here...

What is a "same unit cell?": unit cell params exact to the 6th digit,

or maybe only to a fraction of the highest resolution, what fraction?

Drenth says unit cells that differ by 0.25 x highest resolution can be 
considered

isomorphous (0.5 A for 2 A data). What if 0.4 x highest resolution.

 

Best

Marius

 

 

Marius Schmidt, Dr. rer. Nat. (habil.)
Professor
University of Wisconsin-Milwaukee
Kenwood Interdisciplinary Research Complex
Physics Department, Room 3087
3135 North Maryland Avenue
Milwaukee, Wi 53211
phone (office): 1-414-229-4338
phone (lab): 414-229-3946
email: smar...@uwm.edu  
https://uwm.edu/physics/people/schmidt-marius/
https://sites.uwm.edu/smarius/
  https://www.bioxfel.org/

Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk 
 >
Sent: Wednesday, December 20, 2023 4:21 PM
To: CCP4BB@JISCMAIL.AC.UK   
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] what is isomorphous? 

 

Unless you have a degree in maths, the IUCr's "Little Dictionary of 
Crystallography" by A. Authier and G. Chapuis (2014) defies comprehension on 
this matter (it's all to do with set / group theory, I think, and there are 
many more morphisms covered in about 6 pages: homo, epi, mono, endo, auto). 

Having discussed this with Ian Tickle, about 10 or 12 years ago, the formal (?) 
definition of isomorphous simply means that the unit cells of two or more 
crystals are the same, but the structure/molecule/compound/mineral, etc, does 
not even have to be the same. A sensible definition for dumb biologists might 
be to say that A and B are isomorphous, but C isn't. 


Best wishes, Jon Cooper. jon.b.coo...@protonmail.com 
 

Sent from Proton Mail mobile



 Original Message 
On 20 Dec 2023, 20:15, Hekstra, Doeke Romke < doeke_heks...@harvard.edu 
 > wrote: 

 

Dear colleagues,

 

Something to muse over during the holidays:

 

Let’s say we have three crystal forms of the same protein, for example 
crystallized with different ligands. Crystal forms A and B have the same 
crystal packing, except that one unit cell dimension differs by, for example, 
3%. Crystal form C has a different crystal packing arrangement altogether. What 
is the right nomenclature to describe the relationship between these crystal 
forms? 

 

If A and B are sufficiently different that their phases are essentially 
uncorrelated, what do we call them? Near-isomorphous? Non-isomorphous? 

Do we need a different term to distinguish them from C or do we call all three 
datasets non-isomorphous?

 

Thanks for helping us resolve our semantic tangle.

 

Happy holidays!

Doeke

 

=  

 

Doeke Hekstra

Assistant Professor of Molecular & Cellular Biology, and of Applied Physics 
(SEAS),

Director of Undergraduate Studies, Chemical and Physical Biology

Center for Systems Biology, Harvard University

52 Oxford Street, NW311

Cambridge, MA 02138

Office:617-496-4740

Admin:   617-495-5651 (Lin Song)

 

 

 

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[ccp4bb] Goniometer heads

[Bernhard Rupp]

Hi Fellows,

 

For those who concern themselves with fossilist activities, I am cleaning
out remnants of X-ray lab debris from my garage and found 6 serviceable
goniometer heads looking for a home. One has the infamous YLID standard
crystal still mounted...

 

https://www.ebay.com/itm/256336772397

 

Collecting home data - priceless. For everything else, there are beamlines. 

 

Cheers, BR 

 

--

Bernhard Rupp

 <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

-

Doors and corners - that's where they get you

-

 

 




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[ccp4bb] Laser pointers for diffraction grating experiments

[Bernhard Rupp]

Dear (US) Teaching Fellows,

 

I found a box of 15 class IIIa laser pointers I used to employ for
diffraction experiments in class.

If a diffractionist wins, I throw in a handful of the diffraction slides cf.


https://www.ruppweb.org/Garland/gallery/Ch6/pages/Biomolecular_Crystallograp
hy_Fig_6-23.htm 

 

Understanding diffraction: Priceless. For anything else, there is PayPal.
Bargain for $10.50 so far.

 

https://www.ebay.com/itm/256191715837

 

Cheers, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

-

Doors and corners - that's where they get you

-

 

 




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Re: [ccp4bb] [ccpem] CCPEM Refmac servalcat error

[Bernhard Rupp]

> ADP values are constrained to be positive, because negative values do not 
> have physical meaning.

Negative B-factors have physical meaning. 
It means Hell has frozen over.

Regards, BR

--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
+1 925 209 7429
+43 676 571 0536
-
Doors and corners – that’s where they get you
-


On Wed, 23 Aug 2023 at 16:04, Adwaith Bini Bose Uday 
 wrote:
>
> Hi Keitaro,
>
> Thank you for the answer. I will try that.
>
> Also, does using unsharpened half maps apply to PHENIX real space refine as 
> well? What is the advantage of using that instead of sharpened maps?
>
> Thank you
> Adwaith
>
> --
> -
> Adwaith B Uday
> Ph.D student
> Zeytuni lab, Department of Anatomy and Cell Biology McGill University, 
> Canada 
> From: Keitaro Yamashita 
> Sent: Friday, August 18, 2023 11:43 AM
> To: Adwaith Bini Bose Uday 
> Cc: cc...@jiscmail.ac.uk 
> Subject: Re: [ccpem] CCPEM Refmac servalcat error
>
> [You don't often get email from kyamash...@mrc-lmb.cam.ac.uk. Learn 
> why this is important at https://aka.ms/LearnAboutSenderIdentification 
> ]
>
> Dear Adwaith,
>
> This is a bug of the old version (up to 0.6.0 I think) of the gemmi 
> library that Servalcat heavily uses. It happens while reading the CCP4 
> monomer library, and "." value in new_period causes the problem. We 
> just recently also fixed the monomer library for an old gemmi user
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgith
> ub.com%2FMonomerLibrary%2Fmonomers%2Fpull%2F29=05%7C01%7Cadwaith.biniboseuday%40mail.mcgill.ca%7Ced8073dc380044322d2008dba0023c2d%7Ccd31967152e74a68afa9fcf8f89f09ea%7C0%7C0%7C638279703797578781%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=sUaid30ECNCDPBgVdhwBCEaqResSfzmUkCmijvu9r0A%3D=0
>  but it has not yet been distributed by CCP4.
>
> So the problem can be solved either by using a newer gemmi or the 
> latest monomer library. The latter should be easier.
>
> To the CCP-EM people: does Refmac/Servalcat job in the CCP-EM use the 
> monomer library in the CCP-EM package or from external? Would it work 
> if one downloads the new library and sets CLIBD_MON?
>
> By the way, please always use unsharpened half maps as an input!
>
> Best regards,
> Keitaro
>
> On Fri, 18 Aug 2023 at 16:20, Adwaith B Uday 
>  wrote:
> >
> > Hi,
> >
> > I am trying to use a sharpened map from cryosparc and a model in CCPEM 
> > Refmac. However, the job fails just after starting with the following error.
> >
> > Traceback (most recent call last):
> >   File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 174, in 
> > _run_module_as_main
> > "__main__", fname, loader, pkg_name)
> >   File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 72, in _run_code
> > exec code in run_globals
> >   File 
> > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/command_line.py",
> >  line 126, in 
> > main()
> >   File 
> > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/command_line.py",
> >  line 116, in main
> > modules[args.command].main(args)
> >   File 
> > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/spa/run_refmac.py",
> >  line 245, in main
> > stop_for_unknowns=True, check_hydrogen=(args.hydrogen=="yes"))
> >   File 
> > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/utils/restraints.py",
> >  line 95, in load_monomer_library
> > monlib = gemmi.read_monomer_lib(monomer_dir, resnames, 
> > ignore_missing=True)
> > ValueError: not an integer: .
> >
> > Error in sys.excepthook:
> > Traceback (most recent call last):
> >   File 
> > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/utils/logger.py",
> >  line 78, in handle_exception
> > atexit.unregister(exit_success)
> > AttributeError: 'module' object has no attribute 'unregister'
> >
> > Original exception was:
> > Traceback (most recent call last):
> >   File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 174, in 
> > _run_module_as_main
> > "__main__", fname, loader, pkg_name)
> >   File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 72, in _run_code
> >  

Re: [ccp4bb] About the A in AI

[Bernhard Rupp]

My bad. Both ChatGPT, here is bing:

https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0

 

 

From: Ian Tickle  
Sent: Friday, May 12, 2023 17:33
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] About the A in AI

 

 

Hi Bernhard

 

Methinks there's some cribbing going on between Bing and ChatGPT - not only 
deja-vu but the reviews are identical word for word!  How is that possible?

 

Cheers

 

-- Ian

 

 

On Fri, 12 May 2023 at 16:15, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

For those who concern themselves with such matters, here the responses from 
Bing and ChatGPT to the prompt:

 

“Please write a critical review report rejecting a scientific paper reporting 
that the 1.0 angstrom crystal structure shows that psiX is a trimethylating 
enzyme”

 

Enjoy the frightening reading and then we can chat (LOL) about the creepy 
feeling of déjà-vu you might experience….

 

https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0

https://www.dropbox.com/s/9gr34grpcrf7yk7/ChatGPT.docx?dl=0

 

Cheers, BR

 

-
Bernhard Rupp 

k.k. Hofkristallamt

001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org <mailto:b...@ruppweb.org> 
hofkristall...@gmail.com <mailto:hofkristall...@gmail.com> 
http://www.hofkristallamt.org/ 
-
Hope is not a strategy - hope is a mistake.

-

 

 

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[ccp4bb] About the A in AI

[Bernhard Rupp]

For those who concern themselves with such matters, here the responses from
Bing and ChatGPT to the prompt:

 

“Please write a critical review report rejecting a scientific paper
reporting that the 1.0 angstrom crystal structure shows that psiX is a
trimethylating enzyme”

 

Enjoy the frightening reading and then we can chat (LOL) about the creepy
feeling of déjà-vu you might experience….

 

https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0

https://www.dropbox.com/s/9gr34grpcrf7yk7/ChatGPT.docx?dl=0

 

Cheers, BR

 

-
Bernhard Rupp 

k.k. Hofkristallamt

001 (925) 209-7429
+43 (676) 571-0536
 <mailto:b...@ruppweb.org> b...@ruppweb.org
 <mailto:hofkristall...@gmail.com> hofkristall...@gmail.com
 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

-
Hope is not a strategy - hope is a mistake.

-

 




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Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

[Bernhard Rupp]

TCEP is known to form transition metal complexes. With the molecule alone 
already about 10A across, a ~11x11x46 cell is not unreasonable, and there might 
be alternatives to P3 (can’t tell from the single image). Would be interesting 
to collect and, as mentioned, toss into Direct methods assisted by anomalous P 
(or Zn?) signal... 

 

Have fun, BR

 

From: CCP4 bulletin board  On Behalf Of Mark J. van Raaij
Sent: Saturday, February 4, 2023 14:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

 

PS it’s probably not a salt crystal…TCEP is not a salt, your ligand I presume 
is also not a salt, a small cleaved peptide neither. As to why previously in a 
very similar condition you did get your desired protein plus (other) ligand 
crystal, it just means the molecule (TCEP') crystallises in a similar condition 
to your protein - I don’t think you can conclude much more than that (unless 
there is some other difference like the TCEP being older this time and more 
oxidised, for example).

 

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain

tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/

 

On 4 Feb 2023, at 15:48, kavyashreem mailto:kavyashr...@instem.res.in> > wrote:

 

Dear all, 

Sorry for the confusion created, I did not mean that a protein would have fit 
in the small unit cell. My question was -

1. Why are there closely spaced spots arising in salt crystal?

2. If TCEP could crystallize in the condition, I have got a protein (same as 
this)+ligand (different ligand) complex in very close condition. (ligand size 
is within 500Da).

Thank you

Kavya

 

On 2023-02-03 14:35, a.perra...@nki.nl   wrote:

Hi Kavya, 

 

Try https://csb.wfu.edu/tools/vmcalc/vm.html 

 

This tells you that a 30kD protein simply does not fit the cell.

 

I am pretty sure you crystallised the ligand, or TCEP actually.

 

Also, if you look at the diffractions pattern, its clear the crystal diffracts 
beyond 1.0A, diffraction spots are really very very very strong at 2.0A.

 

 

 

On 3 Feb 2023, at 09:22, kavyashreem mailto:kavyashr...@instem.res.in> > wrote:

Dear all,

We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
condition 10%PEG3350, 50mM Zinc acetate. 

Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8. 

Crystal: Crystal:   crystal 
under UV m

<8ef9453e.png>

When we collected the data at an in-house facility, it looked something like 
this:



The minimum resolution spot is around 9Ang and maximum ~2.2Ang. 

I have not come across a protein diffraction like this, nor of a salt. When I 
ran the gel for the incubated protein (protein+ligand), there was no 
degradation. 

Although, I was sure there is some problem with this image I tried processing, 
which could not be, But indexing showed a unit cell  of 11Ang, 11Ang, 46Ang in 
P3. which was quite expected for two of the axes but not the third.

Can anyone please shed some light on this diffraction image?

How can it happen?

 

Thank you 

Regards

Kavya

 

 


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[ccp4bb] PhD/Postdoc positions in Structural Biology (cryo-EM) aiming at structural investigations of protein complexes involved in cell signaling

[Bernhard Rupp]

Hi Fellows,

 

my former fellow Andreas Naschberger who advanced to a faculty position at
KAUST has attractive and well-supported positions available. 

Please contact Andreas for details and inquiries. 

 

Best regards, BR 

 

From: Collaborative Computational Project in Electron cryo-Microscopy
 On Behalf Of Andreas Naschberger
Sent: Friday, January 27, 2023 04:58
To: cc...@jiscmail.ac.uk
Subject: [ccpem] PhD/Postdoc positions in Structural Biology (cryo-EM)
aiming at structural investigations of protein complexes involved in cell
signaling

 

Dear Colleagues,

 

Two research positions (one Postdoc and one PhD student) are now available
in the lab of Andreas Naschberger at King Abdullah University of Science and
Technology (KAUST) to investigate the molecular basis of protein complexes
involved in cell signaling. These positions suit recent PhD or Master
graduates, with a career interest in structural studies using cryo-EM and
other biochemical/biophysical methods to characterize disease-related
protein assemblies. The postdoc position is fully funded for 2 years and can
be extended. The PhD position is funded for 4 years. The positions include
competitive salaries/fellowships and generous funding for research projects.


 

We ask fundamental questions about how signaling protein complexes function
within their regulatory networks. The project aims to investigate the
function and structural dynamics of these signaling networks.  

The lab is embedded in the BESE division ( 
https://bese.kaust.edu.sa), which provides and supports a multi-disciplinary
work environment. The KAUST core labs ( 
https://corelabs.kaust.edu.sa) are equipped with a state-of-the-art
transmission electron microscope (TEM) Titan Krios G4 with cold-FEG,
Selectris X energy filter, and a Falcon IV detector. The facility is
supervised by an experienced facility manager to ensure high-quality data
collection and effective training for users. A dedicated GPU cluster is
available for data processing. The ideal candidate combines an interest in
structural biology with experience in cryo-EM, cell culture, biochemical
method/protocol development, and protein purification from insect and
mammalian cell cultures. 

 

Needed qualifications 

*   A recent doctorate (Postdoc) or Master's degree (PhD student) in a
relevant discipline, such as Molecular Biology, Biotechnology, Biochemistry,
Structural Biology, Bioengineering, or a related discipline  
*   Experience in protein purification from E. coli, insect, and/or
mammalian cell culture 
*   Experience in single-particle cryo-EM (sample preparation, data
collection, data processing, and model building) 
*   A record of publications in quality, peer-reviewed journals (for
Postdoc only) 
*   Creative and self-motivated personality with an interest in
fundamental and applied science 

 

Application should include 







*   CV 
*   Statement of interest  
*   List of publications (Postdoc only) 
*   Names, and E-mail addresses, of two independent references familiar
with your work. 

 

Please send the application to Andreas Naschberger
(andreas.naschber...@kaust.edu.sa 
)  

 

King Abdullah University of Science and Technology (
 KAUST) is being established in Saudi Arabia, on
the Red Sea coastal area of Thuwal, as an international graduate-level
research university dedicated to inspiring a new age of scientific
achievement that will benefit the region and the world. As an independent
and merit-based institution and one of the best-endowed universities in the
world, KAUST intends to become a major new contributor to the global network
of collaborative research. It will enable researchers from around the globe
to work together to solve challenging scientific and technological problems.
The admission of students, the appointment, promotion and retention of
faculty and staff and all the educational, administrative and other
activities of the University shall be conducted on the basis of equality,
without regard to race, color, religion or gender. Further information can
be found at   www.kaust.edu.sa. 

 

Best wishes,

Andreas

 




Andreas Naschberger, PhD

Assistant Professor

Biological and Environmental Science and Engineering (BESE) Division  

King Abdullah University of Science and Technology (KAUST)

Thuwal 23955

Saudi Arabia  


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Re: [ccp4bb] binding pockets...

[Bernhard Rupp]

There is also a service from our Polish friends:
called Spaceball (jokes aside) that calculates the volume of protein cavities 
(http://www.ifpan.edu.pl/~chwastyk/spaceball/).
and the services in Hamburg are useful for visualization of binding pockets and 
channels
https://proteins.plus/

Best, BR


On 1/3/2023 7:14 AM, Harry Powell wrote:
> Hi folks
>
> I was wondering what people’s favourite program is to find binding pockets in 
> proteins. I’ve had a look at a couple but each has its own idiosyncrasies.
>
> HNY
>
> Harry



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[ccp4bb] windows 8.0.005 questions

[Bernhard Rupp]

Hi Fellows/Windows dev experts,

 

two minor issues on windows install of ccp4i 8.0.005 :

 

A.  the qtRview logs have no tables or graphs, but they offer (slightly
cryptic but plentiful) messages

 

'Inconsistent number of data records and plain table contents in XRT schema'

 

How can I fix this resp where should I look for the problem?

 

B.  When I start wincoot from that same log with the coot button, 

 

Wincoot 9.8.1 does not read my config file despite it being in
ccp4-8/wincoot/.coot-preferences.

Same preferences are loaded fine in the separate wincoot 9.8.1 install.

 

Which batch/config file should I fix to read my coot preferences files when
called from ccp4 qtRview logs? I tried several .bat and setup suspects in
ccp4-8/ to no avail.

Or, alternatively, how can I redirect the call from qtRview logs for coot in
ccp4-8/wincoot to the separate, preference reading, install in c:/wincoot?

 

Thanks, BR

 

-
Bernhard Rupp 

k.k. Hofkristallamt

001 (925) 209-7429
+43 (676) 571-0536
 <mailto:b...@ruppweb.org> b...@ruppweb.org
 <mailto:hofkristall...@gmail.com> hofkristall...@gmail.com
 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

-
Hope is not a strategy - hope is a mistake.

-

 

 




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[ccp4bb] bond angle deviation listing in refmac log

[Bernhard Rupp]

Hi Fellows/Garib,

 

I notice unexplained discrepancies between the PDB validation report and the
Refmac log file:

a.  If I set in  'Monitoring and Output Options' the angle sigma for the
log output reporting option to the PDB 5 sigma cutoff, 

I get zero angle deviations (i.e., no angle deviation printout at all in the
log), even at improbably low sigma levels such as 2.0 or 1.0

 

monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0

 

b.  PDB informs me that there are up to 10 sigma outliers on multiple
(and almost exclusively) ARG N-C-N angles (how to fix this we address
later).

 

Garib, I can send you a link to the complete log, below the header for
versions (windows) :

#CCP4I VERSION CCP4Interface 8.0.005

#CCP4I SCRIPT LOG refmac5

#CCP4I DATE 20 Oct 2022  13:17:07

#CCP4I USER 'UNKNOWN'

#CCP4I PROJECT data_mono

#CCP4I JOB_ID 13

#CCP4I SCRATCH C:/Users/br/AppData/Local/Temp

#CCP4I HOSTNAME BR-WORK

#CCP4I PID 10064

 









 

 ###

###

###

### CCP4 8.0.005: Refmac  version 5.8.0352 : 05/31/22##

###

 

Thx, BR

-
Bernhard Rupp 

k.k. Hofkristallamt

001 (925) 209-7429
+43 (676) 571-0536
 <mailto:b...@ruppweb.org> b...@ruppweb.org
 <mailto:hofkristall...@gmail.com> hofkristall...@gmail.com
 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

-
Doors and corners - that's where they get you

-

 

 

 




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Re: [ccp4bb] ligand binds to one molecule

[Bernhard Rupp]

As you stated, you have multiple protomers in the asymmetric unit, where they 
are free from 
crystallographic symmetry constraints. Generally that means different local 
environment for
each protomer. Inspecting the sites in the different protomers (frequently 
related by various 
non-crystallographic symmetry operations) often can reveal plausible reasons 
for different occupancies. One hydrogen bond more or less for example can mean 
a 
difference of 4 orders of magnitude in Kd.

Best, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of 
Sent: Saturday, March 5, 2022 12:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ligand binds to one molecule

Hello all,

In homo-dimeric or homo-oligomeric protein crystal structures, what would be 
the reason for having a ligand (chemical compound or fragment) binds to one 
molecule and not all molecules in the asymmetric unit?

I have soaked a fragment that has an affinity of 200 uM to a viral protein but 
I can only see it binds to one molecule (we have eight molecules in the AU). 
This is was also notable as well in some published PDB (dimeric protein).

Any suggestions?

Best wishes,
Shymaa



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[ccp4bb] Affordable open access publishing is finally here!

[Bernhard Rupp]

Glad to bring this opportunity to your attention….

 

From: Dr. Adil Laskar  
Sent: Monday, February 21, 2022 01:14
Subject: Need To Response

 

Respected Researcher,

 

With our fastest growing Himalayan Journals platform, we have constructed a 
management team of highly Interested Scientists & Research officials who are 
deeply concerned about your creativity and exploration.

Also, we would like to inform you that the creative Articles might get a 
special response from the research management team.

So we would like to invite you to publish your precious creativity and research 
articles on our Himalayan Journals.

 

Our Journals are as follows-

Himalayan Journal of Agriculture 

Website - https://himjournals.com/journal/hja 

  

Paper Submission-

* Online submission - https://himjournals.com/submit-manuscript 

 

* Email submission -   
himjourn...@gmail.com

*WhatsApp submission - +91 9678978384

Publication Fee- USD 25 (Foreign)/ Rs.1500 (India) <--<--<--<--<--

Indexing and Abstracting

Google Scholar, Index Copernicus, Research Bible, World Cat, Eurasian 
Scientific Journal Index (ESJI) Citefactor, SHERPA/RoMEO, Scientific Indexing 
Services (SIS), Road- Directory of Open Access Scholarly Resources, Directory 
of Research Journals Indexing (DRJI) and others in Progress.






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Re: [ccp4bb] Negative density

[Bernhard Rupp]

Hmm…compliment, pretty darn good density map for 1.7 A….maybe look at the 
resolution cut-off. 

If it is at a significant level, it could be truncation ripples?

Otherwise I second the noise opinion if it is already a well completed model.

 

Cheers, BR

 

 

From: CCP4 bulletin board  On Behalf Of S
Sent: Monday, February 21, 2022 21:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Negative density

 

Hi All,

 

I am getting this negative density in the centre of the ring. Could you please 
help me with this?

 

 

Resolution: 1.7A

2FoFc - 1.5

FoFc - 3.0

 

Thanks in advance.

Regards,

Renu

 

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[ccp4bb] PostDoc and PhD cryoEM positions SciLife lab Stockholm

[Bernhard Rupp]

Hi Fellows, 

 

please let me bring to your attention a PostDoc and PhD candidate position
at Marta Carroni’s cryoEM facility at the Scilife lab in Stockholm:

 

I am excited to announce that I am looking for a highly self-motivated
postdoctoral scientist and an enthusiastic PhD candidate to join my
newly-born research group at SciLifeLab in the Department of Biochemistry
and Biophysics (DBB) at Stockholm University (Sweden). The positions will be
funded by the Knut and Alice Wallenberg Foundation and DBB-Stockholm
University for a period of 5 years for the postdoctoral position and 4 years
for the PhD position. The team will together investigate the regulation of
AAA+ chaperones both in bacteria and in humans primarily using cryo-EM as a
tool, complemented with biochemistry and fluorescence imaging. 

The postdoctoral candidate should ideally come equipped with sound
experience in protein purification and protein structure determination using
single particle cryo-EM. Additional experience in cryo-electron tomography
and sub-tomogram averaging or knowledge in x-ray crystallography, NMR
spectroscopy and model building or prediction is a plus. 

The PhD student should have a background in Biology, Biochemistry,
Biophysics or similar, and be curious and interested to learn! Do you have a
background in another STEM field but are motivated to learn to use cryo-EM
as a tool to explore protein complexes? Still get in touch with me.

The team will work closely with members of the Cryo-EM Facility at
SciLifeLab ( <https://www.scilifelab.se/units/cryo-em/>
https://www.scilifelab.se/units/cryo-em/, Stockholm, Sweden) and will have
access to two Titan Krios (equipped with Gatan Bioquantum-K3 cameras and
CetaD for electron diffraction), one Talos Arctica (Falcon 3 and K2) and a
powerful GPU computer cluster. 

SciLifeLab offers access to a number of other facilities such as
super-resolution fluorescence microscopy, compound screening, NMR and
structural mass spectrometry offering numerous possibilities to learn,
explore cutting edge techniques, and to collaborate with different experts.

If you are interested in joining this young team and for any informal
enquiry, please contact me at  <mailto:marta.carr...@scilifelab.se>
marta.carr...@scilifelab.se by March 15, 2022.  

Cheers, Marta


Marta Carroni,





Cell and Molecular Imaging Platform Director, SciLifeLab

Head of Unit, SciLifeLab CryoEM Facility
Dept. Biochemistry & Biophysics, Stockholm University
Tomtebodavägen 23 A, gamma2 
17165, Solna
Sweden
Tel +468161013
Tel +46720181462

 

--

Bernhard Rupp

k.k. Hofkristallamt

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

--

Institute of Genetic Epidemiology

Medical University Innsbruck

Schöpfstr. 41

A 6020 Innsbruck

 <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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[ccp4bb] Sir David Cox

[Bernhard Rupp]

https://www.wsj.com/articles/british-statistician-won-global-acclaim-for-his
-methods-11643382040

 

The quote below is probably from him

 

Regards, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

All models are wrong

but some are useful.

--

 




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Re: [ccp4bb] Off-topic: happy 2022

[Bernhard Rupp]

For those who want to riddle it out (and as structural biologists hopefully

don’t come across mirror and glide planes) a ppt where you can

take the International Tables and superimpose the tetragonal PG diagrams on

the Kaleidoscope. Find the unit cell first, and then ferret out the rest.

 

https://www.dropbox.com/s/kpss03zueie2sbk/p4_plane_groups.pptx?dl=0

 

Cheers, BR




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[ccp4bb] The Magic of Mushrooms

[Bernhard Rupp]

Hi Fellows,

 

for an international project (lead in Innsbruck, and partner in Jena) I am
searching for 

a reasonably experienced PostDoc with an interest in exploring the Magic of
Mushrooms.

 

Details https://www.psilosophy.org/

 

Cheers, BR

--

Bernhard Rupp

Institute of Genetic Epidemiology

Medical University Innsbruck

Schöpfstr. 41

A 6020 Innsbruck

 <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at

+43 676 571 0536

--

k.k. Hofkristallamt

San Diego, CA 92084

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

--

Mit Psilo in der Rübe

ist deine Forschung niemals trübe

--

 




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Re: [ccp4bb] off-topic: structural motif / domain comparison

[Bernhard Rupp]

A lesser known service with very powerful search across domains and chains is 

TopSearch by Manfred Sippl & Cie.:

https://topsearch.services.came.sbg.ac.at/

 

Its training set includes PDB entries up to 2018.

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Sam Tang
Sent: Thursday, August 5, 2021 23:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off-topic: structural motif / domain comparison

 

Dear all

 

Sorry for an off-topic question here. I wonder if anyone may be aware of any 
search program which allows one to 'blast' a protein domain just like we 
'blast' a protein sequence? For example I have an epitope in hand and would 
like to find out whether this also exists in other proteins. Most programs I 
accessed are based on sequence similarity but is there any program which 
searches a structure against a database of structures?

 

BRs

 

Sam

 

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Re: [ccp4bb] AI papers in experimental macromolecular structure determination

[Bernhard Rupp]

Maybe we should get to the root of this - what qualifies as machine learning 
and what not?

Do nonparametric predictors such as KDE qualify?

https://www.ruppweb.org/mattprob/default.html

Happy toa dd to the confusion.

-Original Message-
From: CCP4 bulletin board  On Behalf Of Tim Gruene
Sent: Tuesday, August 3, 2021 11:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure 
determination

Hello Andrea,

profile fitting, like it is done in mosflm
(https://doi.org/10.1107/S090744499900846X) or evalccd, or ... probably also 
qualify as AI/machine learning.

Best wishes,
Tim

On Tue, 3 Aug 2021 11:43:06 +
"Thorn, Dr. Andrea"  wrote:

> Dear colleagues,
> I have compiled a list of papers that cover the application of 
> AI/machine learning methods in single-crystal structure determination 
> (mostly macromolecular crystallography) and single-particle Cryo-EM.
> The draft list is attached below.
> 
> If I missed any papers, please let me know. I will send the final list 
> back here, for the benefit of all who are interested in the topic.
> 
> Best wishes,
> 
> 
> Andrea.
> 
> 
> __
> General:
> - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. & 
> Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716.
> - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143.
> 
> Micrograph preparation:
> - (2020). Journal of Structural Biology. 210, 107498.
> 
> Particle Picking:
> - Sanchez-Garcia, R., Segura, J., Maluenda, D., Carazo, J. M. & 
> Sorzano, C. O. S. (2018). IUCrJ. 5, 854–865.
> - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC 
> Bioinformatics. 20, 1–26.
> - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R., 
> Paul, G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1–12.
> - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58, 
> 381–391.
> - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A.
> (2021). BMC Bioinformatics. 22, 1–28.
> - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. & 
> Zeng, J. (2016). Journal of Structural Biology. 195, 325–336.
> - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004).
> Journal of Structural Biology. 145, 157–167.
> 
> Motion description in Cryo-EM:
> - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. & 
> Okuno, Y. (2021). Nat Mach Intell. 3, 153–160.
> - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat 
> Methods. 18, 176–185.
> 
> Local resolution:
> - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S., 
> Vargas, J. & Si, D. (2019). Molecules. 24, 1181.
> - Ramírez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano, 
> C. O. S. (2019). IUCrJ. 6, 1054–1063.
> - (2021). QAEmap: A Novel Local Quality Assessment Method for Protein 
> Crystal Structures Using Machine Learning.
> 
> Map post-processing:
> - Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J. M., 
> Sorzano, C. O. S. & Vargas, J. (2020). BioRxiv. 2020.06.12.148296.
> 
> Secondary structure assignment in map:
> - Subramaniya, S. R. M. V., Terashi, G. & Kihara, D. (2019). Nat 
> Methods. 16, 911–917.
> - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE 
> International Conference on Bioinformatics and Biomedicine (BIBM), 
> Vol. pp. 41–46.
> - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97, 
> 698–708.
> - He, J. & Huang, S.-Y. Brief Bioinform.
> - Lyu, Z., Wang, Z., Luo, F., Shuai, J. & Huang, Y. (2021). Frontiers 
> in Bioengineering and Biotechnology. 9,.
> - Mostosi, P., Schindelin, H., Kollmannsberger, P. & Thorn, A.
> (2020). Angewandte Chemie International Edition.
> 
> Automatic structure building:
> - Alnabati, E. & Kihara, D. (2020). Molecules. 25, 82.
> - Si, D., Moritz, S. A., Pfab, J., Hou, J., Cao, R., Wang, L., Wu, T.
> & Cheng, J. (2020). Sci Rep. 10, 1–22.
> - Moritz, S. A., Pfab, J., Wu, T., Hou, J., Cheng, J., Cao, R., Wang, 
> L. & Si, D. (2019).
> - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D.
> 75, 753–763.
> 
> Crystallization:
> - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, 
> 1187–1195.
> - (2004). Methods. 34, 390–407.
> - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R., 
> Vanhoucke, V., Watkins, C. J., Williams, S. & Wilson, J. (2018). PLOS 
> ONE. 13, e0198883.
> 
> Crystal centering:
> - Ito, S., Ueno, G. & Yamamoto, M. (2019). J Synchrotron Rad. 26, 
> 1361–1366.
> - Crystal centering using deep learning in X-ray crystallography.
> - Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P. R., Mall, 
> R. & Bensmail, H. (2019). Bioinformatics. 35, 2216–2225.
> 
> Diffraction image analysis:
> - Czyzewski, A., Krawiec, F., Brzezinski, D., Porebski, P. J. & Minor, 
> W. (2021). Expert Systems with Applications. 174, 114740.
> 
> Peak search in serial crystallography:
> Ke, T.-W., Brewster, A. S., Yu, S. X., Ushizima, D., Yang, C. & 
> Sauter, N. K. (2018). J Synchrotron Rad. 25, 

Re: [ccp4bb] Analysis of NMR ensembles

[Bernhard Rupp]

https://pubmed.ncbi.nlm.nih.gov/8744573/

Old but worked...

Best br

On Wed, May 26, 2021, 19:43 Tristan Croll  wrote:

> (sending properly this time, rather than just to Rasmus)
>
> I don't believe a "color by RMS" option is in ChimeraX right now (I'll
> suggest it to the developers), but this will align all models then set
> B-factors for each residue to the RMS CA deviation from the mean position.
> Could be extended fairly trivially to do all-atom RMS if you wanted to.
> Change the extension for the attached text file to .py, open your NMR
> ensemble in ChimeraX, select all the models (typically just "sel #1" should
> do the trick), then use File/Open and choose color_by_rms.py (or just "open
> color_by_rms.py" on the command line if it's in your working directory). As
> long as all models have the same set of residues, it should do the trick.
> Example image for 2kv5 attached.
>
> Have fun!
>
> -- Tristan
> --
> *From:* CCP4 bulletin board  on behalf of Harry
> Powell - CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* 26 May 2021 16:04
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] Analysis of NMR ensembles
>
> Hi
>
> Given that there are plenty of people on this BB who are structural
> biologists rather than “just” crystallographers, I thought someone here
> might be able to help.
>
> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of
> structures that fit the NOEs, is there a tool available that will give me
> some idea about the bits of the structure that do not vary much (“rigid”)
> and the bits that are all over the place (“flexible”)?
>
> Would superpose or gesamt be a good tool for this? Ideally I’d like
> something that could add a figure to the B columns in a PDB file so I could
> see something in QTMG (or PyMol if forced…) or do other useful things with
> the information.
>
> Harry
> 
>
> 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
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>
> --
>
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Re: [ccp4bb] Omit maps in phenix and ccp4

[Bernhard Rupp]

> setting occupancies of omitted atoms to zero has the danger of leaving a hole 

 

Not quite. We probably need Garib to confirm this, but I tried this many times, 
and if in refmac the occupancy is really zero (0.00), then this does not 
happen, and the ligand is treated as not present. An occupancy of 0.02 however, 
already suffices to have the solvent excluded and the fo component from the 
solvent shows up nicely. 

 

The effect is indeed dramatic, cf. Figure 2 (and F1 for more fun with the same 
ligand)

https://febs.onlinelibrary.wiley.com/doi/epdf/10./febs.14320

 

Best, BR

From: CCP4 bulletin board  On Behalf Of Dirk Kostrewa
Sent: Wednesday, April 7, 2021 03:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Omit maps in phenix and ccp4

 

Dear Eleanor,

setting occupancies of omitted atoms to zero has the danger of leaving a hole 
with the shape of these atoms in the bulk solvent mask, leading to positive 
difference density just because of the missing bulk solvent density. Since the 
days of X-PLOR, I always removed the omitted atoms. I never tried this with 
REFMAC5, though.

Cheers,

Dirk.

On 07.04.21 11:46, Eleanor Dodson wrote:

Well - I use COOT for this sort of task, and dont trust the automated tools. 

my procedure is

load COOT - probably after a refinement cycle

set occupancy of ligand(s) to 0.00 ( Measures - residue information - change 
occupancy) 

Look at the environment critically . eg if an ARG or other bulky side chain 
nearby , or waters etc selectively set occupancies to 0.00

 

Doo some more cycles of refinement with this coordinate set to remove any 
memory of the ligand.

 

Look at the map - if the ligand and other zero occ atoms is still in the right 
place reinstate them, or try to reinterpret density..

Eleanor

 

 

 

On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund mailto:bjarte.l...@uit.no> > wrote:

Dear Hari,

 

With regards to 1) Is 15 the number of atoms in your molecule? Or is it the 
number of hydrogens? The CIF file may have the wrong residue name or lack the 
hydrogens depending on how you built the ligand-protein complex. 

There is also a phenixbb for phenix questions, 
http://www.phenix-online.org/mailman/listinfo/phenixbb

 

 

Kind regards,

 

Bjarte Aarmo Lund

Postdoc

UiT The Arctic University of Norway

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Hari shankar
Sent: Wednesday, April 7, 2021 08:47
To: CCP4BB@JISCMAIL.AC.UK  
Subject: [ccp4bb] Omit maps in phenix and ccp4

 


Dear All,

 

I have a ligand-protein complex and I wish to calculate different kinds of omit 
maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc 
maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have 
tried phenix for this purpose but get this error message consistently. 

 

"Fatal problems interpreting model file: no of atoms with unknown nonbonded 
energy type symbols: 15 Please edit the model file to resolve the problems 
and/of supply a CIF file with matching restraint definitions, along with 
apply_cif_modification and apply_cif_link parameter definitions if necessary."

 

This error occurs despite supplying the CIF file for the ligand. I have tried 
to remake the CIF/PDB files from SMILES strings, by drawing the molecule in 
both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). Nothing seems to 
work. 

 

1. Is there something I have missed out that can solve this issue?

2. Is there a program in CCP4i that can be used to generate the required omit 
maps? 

3. In general, how do I omit 3.5 ang of the space around the ligand during this 
map calculations?


Thank you so much for your time. 
Hari

 

 

 

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-- 
 
***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de  
kostr...@genzentrum.lmu.de  
WWW:www.genzentrum.lmu.de  
***

 

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[ccp4bb] New validation metric

[Bernhard Rupp]

Hi Fellows,

 

here is a link to my latest paper on ligand validation. Due to embargo
reasons I can

display only the first and last page but the links in it are all active for
those who are interested.

 

http://www.ruppweb.org/Rupp_2021_Phys_Rev_Letters_126(13)_LDC.pdf

 

Best, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

-

Doors and corners - that's where they get you

-

 

 




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Re: [ccp4bb] ideal ligands

[Bernhard Rupp]

True. Sameer seems to be on it. In the meantime, I simly adjust my
expectations of 'ideal' :-)

Cheers br

On Sat, Feb 6, 2021, 06:40 Tristan Croll  wrote:

> I know . Just suggesting the most likely cause of the problem.
>
> -- T
> --
> *From:* Bernhard Rupp 
> *Sent:* 06 February 2021 14:38
> *To:* Tristan Croll 
> *Cc:* CCP4BB@jiscmail.ac.uk 
> *Subject:* Re: [ccp4bb] ideal ligands
>
> That is what 'uranium atom solution' implies:
> All atoms collapsing into one :-)
>
> Cheers br
>
> On Sat, Feb 6, 2021, 06:34 Tristan Croll  wrote:
>
> The ideal coordinates in the CCD entries for BCR and LUT are null - my
> guess is that in these cases all the coordinates just default to (0,0,0) in
> the PDBeChem script.
> ------
> *From:* CCP4 bulletin board  on behalf of Bernhard
> Rupp 
> *Sent:* 05 February 2021 20:51
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] ideal ligands
>
>
> Hi Fellows,
>
>
>
> PDBeChem under ‘ideal’ coordinates returns a small molecule uranium atom
> solution for BCR, LUT, and possibly other xanthophylls, eg.
>
> ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/B/BCR/BCR_ideal.pdb
>
> while the representative files are ok.
>
>
>
> Is this intended?
>
>
>
> Thx, BR
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> 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
>
>



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Re: [ccp4bb] ideal ligands

[Bernhard Rupp]

That is what 'uranium atom solution' implies:
All atoms collapsing into one :-)

Cheers br

On Sat, Feb 6, 2021, 06:34 Tristan Croll  wrote:

> The ideal coordinates in the CCD entries for BCR and LUT are null - my
> guess is that in these cases all the coordinates just default to (0,0,0) in
> the PDBeChem script.
> --
> *From:* CCP4 bulletin board  on behalf of Bernhard
> Rupp 
> *Sent:* 05 February 2021 20:51
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] ideal ligands
>
>
> Hi Fellows,
>
>
>
> PDBeChem under ‘ideal’ coordinates returns a small molecule uranium atom
> solution for BCR, LUT, and possibly other xanthophylls, eg.
>
> ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/B/BCR/BCR_ideal.pdb
>
> while the representative files are ok.
>
>
>
> Is this intended?
>
>
>
> Thx, BR
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> 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
>



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[ccp4bb] ideal ligands

[Bernhard Rupp]

Hi Fellows,

 

PDBeChem under 'ideal' coordinates returns a small molecule uranium atom
solution for BCR, LUT, and possibly other xanthophylls, eg.

ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/B/BCR/BCR_ideal.pdb

while the representative files are ok.

 

Is this intended?

 

Thx, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

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at the presence of thought

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[ccp4bb] PDBe cif directories

[Bernhard Rupp]

Hi Fellows,

 

do I see this correctly that on the main PDB page for a HET entry, such as

https://www.ebi.ac.uk/pdbe/entry/pdb/4inx/bound/1EX

the link in pulldown downloads/CIF dictionary

ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/1EX.cif

dead ends in the old HET cif directory while from the PDBeChem

https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/1EX

the links goes to the new monomer library?

ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/1/1EX/1EX.cif

 

Is the old pdbechem database now deprecated and only V2 current?

 

Thx, BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

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at the presence of thought

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Re: [ccp4bb] Characterising potential drug-binding pockets

[Bernhard Rupp]

ICM PocketFinder might fit the bill (not free but academic license)

eg in

https://pubmed.ncbi.nlm.nih.gov/20977231/

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Sergei
Strelkov
Sent: Monday, January 25, 2021 11:02
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Characterising potential drug-binding pockets

 

Dear everyone,

 

In a drug discovery project where our aim is to interfere with some PPIs, we
could obtain binding of drug-like fragments in several potentially
interesting pockets on our target. We would like to make a projection on how
promising these individual pockets are. One way of doing this is through the
Sitemap program (Halgren, T. A. Identifying and characterizing binding sites
and assessing druggability. J. Chem. Inf. Model 49, 377-389 (2009)). Are
there other tools around to do this? In particular, we would like to have
accurate numbers for the pocket volume, surface, no. of H-bond donors and
acceptors, average hydrophobicity, etc etc. 

 

Thank you,

Sergei

 

 

 

Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49
bus 822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41
32 Lab pages:  
http://pharm.kuleuven.be/Biocrystallography

 

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Re: [ccp4bb] The weekly nonsense

[Bernhard Rupp]

I am not sure how the relevance of the subject obviates the need to read 

at least the abstract of your references.

 

I actually stumbled upon this because I am receiving more and more citation
alerts from 

papers in those odd journals in the 'pay to play' category which have little
connection 

to what they cite. 'Cite by Google'  is almost certainly on the rise..and
that it happens to

AI researchers I find particularly ironic.

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Frank Von
Delft
Sent: Friday, January 22, 2021 23:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The weekly nonsense

 

It's certainly a real problem they're writing about. Or at least, one that
some people say we should be worrying about.

 

Sent from tiny silly touch screen

  _  

From: Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk
<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk> >
Sent: Saturday, 23 January 2021 02:40
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] The weekly nonsense

 

Take care ;-

https://www.wicys.org/

Seems genuine enough group & everything to me. The referees should have
spotted that one ;-0

Sent from ProtonMail mobile



 Original Message 
On 22 Jan 2021, 23:03, Bernhard Rupp < hofkristall...@gmail.com
<mailto:hofkristall...@gmail.com> > wrote: 

 

Dear CCP4 Fellows, 

 

for the subscribers of my immensely popular show "The weekly nonsense" I
recommend

https://arxiv.org/pdf/2101.06308.pdf

particularly reference [27] and its contextual environs.

 

Am I alone suspecting that this is some AI generated auto-paper-mill
product?

 

Cheers, BR

 

--

Bernhard Rupp

The Amt

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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[ccp4bb] The weekly nonsense

[Bernhard Rupp]

Dear CCP4 Fellows, 

 

for the subscribers of my immensely popular show "The weekly nonsense" I
recommend

https://arxiv.org/pdf/2101.06308.pdf

particularly reference [27] and its contextual environs.

 

Am I alone suspecting that this is some AI generated auto-paper-mill
product?

 

Cheers, BR

 

--

Bernhard Rupp

The Amt

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

[Bernhard Rupp]

Btw, my numbers are calculated by the updated FPRIME code (permission of Don 
Cormer) including
the latest  Kissel & Pratt, Acta Cryst. A46, 170-175(1990) mods to the total 
energy (eterm)

Cheers, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Marcin Wojdyr
Sent: Friday, January 22, 2021 13:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

One can also use:

$ gemmi fprime Sr --wavelength=1.2782
Element E[eV]Wavelength[A]   f' f"
Sr9699.91 1.2782 -0.637561.3067

or

$ $CCP4/lib/py2/cctbx/bin/cctbx.eltbx.show_fp_fdp --wavelength=1.2782 
--elements=Sr
Wavelength: 1.2782 Angstrom

Element: Sr
  Henke et al.  : f'=-0.665752, f''=1.332521
  Sasaki et al. : f'=-0.75942 , f''=1.306888
  diff f''=-0.97 %

As you see, all these commands give slightly different values. I was told that 
nowadays XrayDB (not in CCP4) provides the most accurate
values:

$ python3 -c "import xraydb; print(xraydb.f1_chantler('Sr', 9699.91))"
-0.657390314908364

Crossec is the original code from Don Cromer. Gemmi, one of the cctbx tables, 
and I think Ethan's server also use code that stems from it, but with 
corrections added later when this code was circulating, such as Kissel & Pratt, 
Acta Cryst. A46, 170 (1990).

Marcin

On Fri, 22 Jan 2021 at 21:40, Mitchell D. Miller  
wrote:
>
> You can also use the ccp4 legacy program crossec --- 
> http://legacy.ccp4.ac.uk/html/crossec.html
>
> for your case --
>
> echo -e "NWAV 1 1.2782\nATOM Sr\nEND\n" | crossec | grep SR
>
>Atom symbol and number SR   38
>   $TABLE:Wave length v F' and F"-  SR   :
>   $GRAPHS:Lambda v F' and F" SR   :A:2,3,4: $$
> SR  1.2782-0.7663 1.3068
>
>
> I often ran it from a script to lookup the f'/f" for various elements 
> via a script crossec.sh which takes arguments of wavelength followed 
> by a list of elements
>
> #!/bin/bash
> #egrep '^ATOM|^HETATM' | cut -c77-78 file.pdb | sort -u`
>
> for atom in "$@"
>do
> if [ "$atom" != "$1" ]
>   then
> echo -e "NWAV 1 $1\nATOM $atom\nEND\n" | crossec | awk '/^ 
> Lambda  F/ {getline ; getline ; print $0}'
>   else
>echo "Atom_type   Lambda F"\'" F"\"
> fi
> done
>
>
>
> Quoting Bernhard Rupp :
>
> > ...or you can use the old anoweb app
> >
> > http://www.ruppweb.org/new_comp/anomalous_scattering.htm
> >
> >
> >
> > http://www.ruppweb.org/cgi-bin/anoweb_linux?Element=Sr
> > <http://www.ruppweb.org/cgi-bin/anoweb_linux?Element=Sr=1
> > =100=K=Cu=1000=2=1=700=Submit>
> > =1=100=K=Cu=1000=2=1=700=Subm
> > it
> >
> >
> >
> > HTH, BR
> >
> > From: CCP4 bulletin board  On Behalf Of rohit 
> > kumar
> > Sent: Friday, January 22, 2021 11:36
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom
> >
> >
> >
> > Hello All,
> >
> >
> >
> > I have data collected at Wavelength: 1.2782 (For Sr Heavy atom) with 
> > a resolution of 1.6 A. I was trying to run Crank in ccp4 for SAD 
> > phasing and It  asks me to fill the values of (scattering factors) f 
> > and f" for the heavy atom.
> >
> > Can anyone please help with this, how to calculate or where to find 
> > these f and f" values for Sr heavy atoms?
> >
> >
> >
> > Please let me If you need any information from my side.
> >
> >
> >
> > Thank you in advance
> >
> >
> >
> >
> >
> >
> > --
> >
> > Regards
> > Dr. Rohit Kumar Singh
> >
> > Postdoctoral fellow
> >
> >
> >
> >
> >
> >
> >
> >   _
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB
> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>
> > =1
> >
> >
> > 
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
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> > available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> ###

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

[Bernhard Rupp]

...or you can use the old anoweb app

http://www.ruppweb.org/new_comp/anomalous_scattering.htm

 

http://www.ruppweb.org/cgi-bin/anoweb_linux?Element=Sr 

 =1=100=K=Cu=1000=2=1=700=Submit

 

HTH, BR

From: CCP4 bulletin board  On Behalf Of rohit kumar
Sent: Friday, January 22, 2021 11:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

 

Hello All,

 

I have data collected at Wavelength: 1.2782 (For Sr Heavy atom) with a 
resolution of 1.6 A. I was trying to run Crank in ccp4 for SAD phasing and It  
asks me to fill the values of (scattering factors) f and f" for the heavy atom. 

Can anyone please help with this, how to calculate or where to find these f and 
f" values for Sr heavy atoms?

 

Please let me If you need any information from my side.

 

Thank you in advance




 

-- 

Regards
Dr. Rohit Kumar Singh

Postdoctoral fellow

 

 

 

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Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Bernhard Rupp]

Thanks Fellows,

 

> I agree with Marcin that his GEMMI program is the way to go.  It does 
> everything you need and Marcin is very quick to respond to any issues.

 

Yes, found it also in the windows distribution will try

 

> From your description the axes in the SG symbol have been permuted but the 
> cell axes remain in the original order?  If so that's plainly a bug which 
> should be fixed (or CIF2MTZ put in retirement).

 

Bug. No swap of indices -> chaos if you run Refmac thereafter. Will retire 
cif2mtz in my hacks. 

 

Robbie suggested eliminating the SG number in the CIF as a workaround.

 

Many thx, BR

 

 

On Wed, 6 Jan 2021 at 19:38, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Dear Developers,

 

running cif2mtz in ccp4i (or from the console) in the case of non-standard 
settings of space group 18 (which should be discouraged, to phrase it mildly) 

on the mmcif from the PDB

_symmetry.space_group_name_H-M   "P 21 2 21" <--

_symmetry.Int_Tables_number  18 

#

 

leads to a problem because the resulting mtz file has the standard 18 symbol

 

Type  Merged MTZ

Space group   P 21 21 2 <-- 

Space group confidenceX  (confidence flag is not set)

Cell 88.578  44.416  71.56490  90  90  

 

Not sure if this is a loss of information when generating the mmcif upon 
submission,

or the SG is retrieved solely by SG number not symbol (the latter can give rise 
to a few more such situations).

 

Best, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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[ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Bernhard Rupp]

Dear Developers,

 

running cif2mtz in ccp4i (or from the console) in the case of non-standard
settings of space group 18 (which should be discouraged, to phrase it
mildly) 

on the mmcif from the PDB

_symmetry.space_group_name_H-M   "P 21 2 21" <--

_symmetry.Int_Tables_number  18 

#

 

leads to a problem because the resulting mtz file has the standard 18 symbol

 

Type  Merged MTZ

Space group   P 21 21 2 <-- 

Space group confidenceX  (confidence flag is not set)

Cell 88.578  44.416  71.56490  90  90  

 

Not sure if this is a loss of information when generating the mmcif upon
submission,

or the SG is retrieved solely by SG number not symbol (the latter can give
rise to a few more such situations).

 

Best, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

[Bernhard Rupp]

In addition to the Debye-Waller correction, you have additional attenuation 
from the Lorenz and Geometry factor (specific for your powder diffraction 
geometry) that convolutes with the DB apodization.

 

Meaning: the 400 will be more attenuated relative to 200 if you correct only 
for DBW.

 

A peak shift is not explained this way, because larger B and LPG only affect 
intensity. A cell change should affect both reflections similarly (Bragg). The 
whole intensity thing falls apart if you have in addition preferred orientation 
effects, but I do not know enough about your sort of experiment to say whether 
this is possible. Can monolayers warp or something like anisotropically expand?

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Kamil Krawczyk
Sent: Thursday, December 24, 2020 15:22
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Relationship of crystallographic planes and reflections, 
e.g. (200) and (400)

 

Hi all,

Thanks for the insight so far! To give better information re: the system, I am 
studying quantum dot monolayers. Yes, these diffractograms are powder 
diffraction images that have been condensed into 1D diffractograms. This is 
under the condition of laser photoexcitation, and while some signal is thermal 
(e.g. typical Debye-Waller type decrease of intensity which can be well 
characterized), I am just trying to better understand the anomalous effects and 
get a better picture of how the (400) and (200) reflections, and they're 
relevant atomic coordinates, are related. I can't imagine it being due to 
dynamic scattering effects as this is a monolayer and my coherence length of my 
electrons is great!

Thanks again!

 

On Wed, Dec 23, 2020 at 7:12 AM Jon Cooper mailto:jon.b.coo...@protonmail.com> > wrote:

Hello, when you say the (4, 0, 0) intensity goes down, I was wondering what is 
actually changing? Likewise for the shift in (2, 0, 0). If every atom lay in a 
particular diffraction plane, they would all scatter in phase and the 
diffraction from that plane would be nice and strong! The relative phase of 
each atom's scattering is dictated by the distance from the plane, right ;-? 
Diffractogram sounds like proper physics. Best wishes, Jon. C.


Sent from ProtonMail mobile



 Original Message 
On 22 Dec 2020, 22:26, Kamil Krawczyk < kamil.krawczyk7...@gmail.com 
 > wrote:

 

Hi all,

As an experimental physicist slowly becoming more acquainted with 
crystallography, I have a bit of clerical issue visualizing this particular 
problem in my head:

For example, the 400 and 200 reflections in a diffractogram are related to the 
100 family of crystallographic planes; I'd imagine, that in real space, the 
higher order plane (e.g. the 400) corresponds to atoms 'closer' to the center 
of the crystal/unit cell.

I have an interesting observation where I am seeing the 400 peak intensity go 
down (likely due to increased RMS motion), whereas the 200 reflection does not 
really change in its intensity. Furthermore, I see a shift in the 200 peak, 
implying an expansion (a shift to lower q), but no abnormal change in the 400 
peak position.

What I am having a really hard time wrapping my head around is how these two 
events can be occurring simultaneously; I would naively say that since the 400 
reflection is showing an increased RMS, the 400 peak should likely shift - not 
the 200. Does anybody have an easy way to visualize this? I am trying to look 
at crystallographic vectors in VESTA on a model system, but sadly have not been 
able to see the light just yet.

Thank you! And sorry for dropping all the parentheses on reflection names, it 
saved me some typing :p



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Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

[Bernhard Rupp]

A situation like you are describing can happen in small molecule and power 
diffraction. If you explain what you are actually doing, it might be possible 
to speculate...

Best, BR 

-Original Message-
From: CCP4 bulletin board  On Behalf Of Kamil Krawczyk
Sent: Tuesday, December 22, 2020 14:27
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. 
(200) and (400)

Hi all,

As an experimental physicist slowly becoming more acquainted with 
crystallography, I have a bit of clerical issue visualizing this particular 
problem in my head:

For example, the 400 and 200 reflections in a diffractogram are related to the 
100 family of crystallographic planes; I'd imagine, that in real space, the 
higher order plane (e.g. the 400) corresponds to atoms 'closer' to the center 
of the crystal/unit cell.

I have an interesting observation where I am seeing the 400 peak intensity go 
down (likely due to increased RMS motion), whereas the 200 reflection does not 
really change in its intensity. Furthermore, I see a shift in the 200 peak, 
implying an expansion (a shift to lower q), but no abnormal change in the 400 
peak position.

What I am having a really hard time wrapping my head around is how these two 
events can be occurring simultaneously; I would naively say that since the 400 
reflection is showing an increased RMS, the 400 peak should likely shift - not 
the 200. Does anybody have an easy way to visualize this? I am trying to look 
at crystallographic vectors in VESTA on a model system, but sadly have not been 
able to see the light just yet.

Thank you! And sorry for dropping all the parentheses on reflection names, it 
saved me some typing :p



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Re: [ccp4bb] Anomalous signal to noise details

[Bernhard Rupp]

> I don't know the justification; maybe just experience? Surely the higher the 
> better.  I've seen George Sheldrick deriving the value of ~0.8 when there is 
> _no_ anom signal but I forgot the details, sorry ...

It is derived from the mean absolute error (cf. p414 in Chapter 8 of BMC, with 
help of Ian Tickle), and holds for unmerged data. A reasonable good indication 
where to set the cutoff in practice is to look at the site vs occupancy plot. A 
distinct drop after a few good sites is usually a good sign, and that tends to 
cluster around the ~1.3 ratio.

http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-30_PART2.htm

The noise level is actually observable in data without anomalous signal

http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-29.htm

Best BR





best wishes,

Kay

>
>Thanks!
>-- David
>
>###
>#
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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Bernhard Rupp]

In reasonably compact format, the discussion topic is summarized in this
CCP4 weekend introduction

https://journals.iucr.org/d/issues/2013/02/00/wd5191/index.html

 

As far as the solvent exclusion self-deception via low occupancy goes, fig 2
here:

https://febs.onlinelibrary.wiley.com/doi/epdf/10./febs.14320

 

Good luck, BR

 

From: CCP4 bulletin board  On Behalf Of Nika Žibrat
Sent: Tuesday, November 24, 2020 03:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phenix.refine with ligand with ambiguous electron density

 

Hello, 

 

I have a question about protein-ligand, of which ligand displays an
ambiguous electron density. I am solving a structure of protein with ligand
which was obtained via soaking. Structural characteristics indicate the
ligand is present however the electron density is quite vague and too small
for the size of the whole ligand. I did a Polder map which showed much
larger area of green density. After insertion of my ligand into the green
density in Polder I ran phenix.refine and there is a lot of red on the spot
where the ligand is which was to be expected. This leaves me wondering how,
if even do I incorporate the polder map data into my refine input.

 

My question is, how do I continue refining and validating the structure in
this case? 

 

Thank you,

 

Nika Žibrat

 

 

  _  

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[ccp4bb] [RESOLVED]partially restrained mode?

[Bernhard Rupp]

Resolved:

Boaz kindly pointed me to the Refmac instructions on Garib's site 

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywor
ds.html#id.r2gu4ckb7nka

which show the proper command line (an example below):

restraint exclude residue 403 A *

Works.

 

Many thx, BR

 

Btw: None of the links from ccp4i 'classic' that I found actually point to
this full document.



Hi Fellows,

 

is there a way (keyword based) to refine in Refmac - given near atomic
resolution - a part of the model (protein chain) restrained, 

and another part (to check for ligand explosivity, for example)
unrestrained? 

 

Best, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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[ccp4bb] partially restrained mode?

[Bernhard Rupp]

Hi Fellows,

 

is there a way (keyword based) to refine in Refmac - given near atomic
resolution - a part of the model (protein chain) restrained, 

and another part (to check for ligand explosivity, for example)
unrestrained? 

 

Best, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Depositing structures of proteins of unknown sequence

[Bernhard Rupp]

At 25A the only discerning feature between Fabs is probably the elbow angle
and a rigid body fit might be enough to discriminate between those.

http://www.ruppweb.org/cvs/br/Stanfield_2006_JMB_antibody_elbow_angle.pdf

Best br

On Mon, Jul 27, 2020, 21:10 Roversi, Pietro (Dr.) 
wrote:

> Dear all,
>
> I am fitting a 25 Å negative stain EM map of a protein in complex with its
> FAb. I have restraints on the protein region the FAb recognises (from
> ELISAs on truncated versions of the protein) but I do not have the sequence
> of the FAb.
>
> I have a model for the protein and I picked a FAb from the PDB to be a
> representative FAb model which I believe is good enough to fit a 25 Å
> negative stain EM map. By "good enough" I mean: this model would answer the
> question: " Can I fit this map with the protein and a FAb model and would
> the relative FAb:protein arrangement satisfy the known restraints on the
> FAb epitope?"
>
> A PDB search with "unknown sequence" returns 17 entries:
>
> 1IVI,1TNV,1HR3,1QTJ,4CAT,2PGK,1PYK,1KGA,4GL8,1HKG,2YHX,1GRH,3LDH,4I79,1SNB,6IJ1,3CKM
>
> What is your experience with depositing into the PDB structures of
> proteins of unknown sequence?
>
> And as a user, would you accept an entry with a FAb as poly-Ala or Calphas
> only and poly-UNK?
>
> Thank you for any feedback you'll be able to let me have,
>
> with best wishes,
>
> 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
>
>
>
> --
>
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[ccp4bb] [refmac developers] unrestrained anisotropic

[Bernhard Rupp]

Hi Fellows,

 

Q for the Refmac cognosci:

 

Just curious: If I run unrestrained anisotropic refi on 1 A data, some
barely supported ligands display insane and physically impossible ADPs,

worthy of the ORTEP of the century. As cigars penetrate discs, it seems that
Hirschfeld criteria on

aniso ADPs are violated. 

 

Are they also turned off when I select unrestrained - they should remain in
effect regardless of

how bad or unsupported my atoms are? Do I need to change/adjust/optimize the
RBON/RIGU keywrd?

 

Best, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Quote source inquiry

[Bernhard Rupp]

Close enough verbatim and dead on in spirit.
Many thanks, BR

-Original Message-
From: Gerard DVD Kleywegt  
Sent: Wednesday, July 15, 2020 08:49
To: b...@hofkristallamt.org
Cc: CCP4 Bulletin Board 
Subject: Re: [ccp4bb] Quote source inquiry

Well, I've had this in my CSHL X-ray Course talk for many years.

In the attached 2007 Acta D paper it says (p 95): "Macromolecular X-ray
crystallography is a notoriously poor method for determining the structure
of small molecules that are bound to macromolecules [...]" and then goes on
to explain why this is the case.

In the attached 2003 paper (pooling the wisdom of several of the usual
suspects, including Eleanor) it says something similar (p 1057):

"Coordinates of molecules that have been determined in complex with
macromolecules previously can of course also be retrieved from the PDB
(Bernstein et al., 1977; Berman et al., 2000), HIC-Up (Kleywegt and Jones,
1998), or CHEMPDB (Boutselakis et al., 2003). However, one should keep in
mind that these coordinates are the result of refinement against
comparatively
low-resolu- tion data where the small molecule constituted only a minute
fraction of the total scattering matter. This makes these coordinates
inherently much less accurate than those obtained from the CSD. In addition,
the coordi- nates may contain errors due to the use of incorrect restraints.

Hence, such coordinate sets should only be used as a last resort, and only
after verification that they are reliable. The latter can be facilitated by
inspection of the electron density for the compound in question, for
instance at the Uppsala Electron-Density Server (http://
fsrv1.bmc.uu.se/eds) (G.J.K. 
et al., submitted)."

Happy to be confused with George though!

--Gerard (no, the other one)



On Tue, 14 Jul 2020, Bernhard Rupp wrote:

> Hi Fellows,
>
>
>
> afaicrimps (as far as I can recall in my progressing senility)  
> someone once wrote/stated/cursed somewhere that "Macromolecular 
> refinement is not a small molecule structure determination method".
>
>
>
> Any citable source - George Sheldrick might be a suspect.
>
>
>
> Thanks & best regards, BR
>
>
>
> --
>
> Bernhard Rupp
>
> <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/
>
> <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
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>


Best wishes,

--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] Quote source inquiry

[Bernhard Rupp]

Hi Fellows,

 

afaicrimps (as far as I can recall in my progressing senility)  someone once
wrote/stated/cursed somewhere that "Macromolecular refinement is not a small
molecule structure determination method".  

 

Any citable source - George Sheldrick might be a suspect.

 

Thanks & best regards, BR

 

------

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

languages does not mean we should abandon it.  Are we going to stop 
> eating "chips" just because we are not sure if our fried potato will come as 
> sliced wedges or thin crispy wafers? If you are unhappy with your meal, is it 
> the fault of the culture you are visiting? or the customer for forgetting 
> where they are? Context is everything. 
> 
> So, for those unfamiliar with one or more of the major English-speaking 
> cultures, here are a few other important differences to be aware of: 
> "Football" may not be the game you think it is. 
> If you are offered a "biscuit" in the US, do not expect it to be sweet. 
> If you want to leave a building you should take the "lift" to the "ground 
> floor", but if you take an "elevator" get off on the "1st floor". 
> A "dummy" is a pacifier for a baby in the UK/Australia, but in the US it only 
> means an unintelligent person, or a plastic replica of one. 
> "please" and "thank you" are considered baseline politeness in some English 
> cultures, but their excessive use in others, such as the US, can be seen as 
> rude.
> A "tap" in the US dispenses beer, water comes out of a "faucet".
> A "flat" in the US is not a place to live, but rather where we test rocket 
> cars. 
> "Gas" can be a liquid in the US.  
> "Rubber" is a substance in both languages, but in the US a lump of it meant 
> for erasing pencil marks is an "eraser". Do not ask for a "rubber" at the 
> shop unless you are sure which country you are in. 
> A "holiday" in the US is a special day on the calendar when everyone gets off 
> work, not just when an individual takes a "vacation". 
> If you go walking down the "pavement" you are risking getting hit by a car in 
> the US, because that is what we call the road bed, not the "sidewalk".  
> A "torch", is a handheld electric light in the UK, but in the US it is a 
> flaming stick of wood. 
> A "queue" is a line of people in the UK, but in the US it is known only to 
> computer scientists submitting jobs on a cluster. 
> 
> Then there are words like "capillary", which means the same thing in both 
> languages but the alternate pronunciations never fail to enrage someone. It 
> is perhaps odd that since US English and UK English are spoken with many 
> different accents we pronounce essentially every word at least slightly 
> differently, but for some reason "capillary" makes people angry.  Same with 
> "schedule". Equally emotional responses arise from how you pronounce the 
> letter "z".  Go figure.
> 
> Similar ire is risen for spelling. My favourite/favorite is 
> aluminum/aluminium, but equally divisive are colour/color, tire/tyre, 
> cheque/check, gray/grey, theatre/theater, pyjamas/pajamas, and many others. 
> 
> It is at this stage when you will find people of another culture trying to 
> "correct" you on how to speak or write your own language. This can be 
> confusing because you will probably not be corrected for calling a 
> "courgette" a "zucchini", especially if you are Italian. However, a native 
> Hindi speaker might feel compelled to correct your pronunciation of 
> "shampoo".  I am not singling out any one culture here, we have all given in 
> to the temptation to "correct" someone, perhaps even while visiting their 
> home.  Ahh, the errors of my youth.
> 
> All that said, I don't think this forum is the place to discuss cultural 
> differences.  This is especially true once we start using words like 
> "correct"/"incorrect" and "right"/"wrong", as these tend to generate far more 
> heat than light.  However, I do think it important to identify and describe 
> cultural differences when they start to impede scientific discussion.  It is 
> OK to disagree.  But let it be over interpretation of complete information 
> that both parties possess, not preconceived notions nor ignorance of the 
> complete picture. If we understand WHY another person thinks in a way we find 
> disagreeable, then perhaps we have a better chance of moving forward and 
> enjoying the upcoming celebrations of 
> Independence/GoodRiddanceUngratefulColonials Day.
> 
> Whatever you call it, an eggplant or an an aubergine, its odour/odor and 
> flavour/flavor are the same.  I apologize/apologise to my 
> neighbours/neighbors across the Lake/Pond for my behaviour/behavior if you 
> are not enamoured/enamored with my endeavour/endeavor at humor/humour.  It is 
> not my specialty/speciality.  fullstop/period

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

.…but there is a difference whether I measure the same identical hkl over again 
or ‘preferably in more than one symmetry-equivalent position’, to quote the

IUCr. So do we have a MPSR for the same reflection and a MPRR for the related 
reflections?

 

Cacophonically yours,

 

BR

 

From: CCP4 bulletin board  On Behalf Of John R Helliwell
Sent: Tuesday, June 30, 2020 08:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?

 

Dear Herman,

I think that MPR is a very neat and tidy, excellent, proposal.

Moreover it uses the word “measurements”, and we are an experimental based 
science.

I support it.

Great.

Greetings,

John 

Emeritus Professor John R Helliwell DSc

 

 

 

 

On 30 Jun 2020, at 15:10, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com> > wrote:

 

Dear BB,

 

Since there does not seem a generally accepted term for the subject of this 
discussions, and since even the IUCR scriptures do not give any guidance, I 
would propose to introduce a completely new term:

 

Measurements per reflection or MPR

 

This term is politically neutral, should adequately describe this particular 
statistic and is not associated with entrenched traditions at either side of 
the Atlantic.

 

What do you think?

Herman

 

 

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> Im Auftrag von John R Helliwell
Gesendet: Dienstag, 30. Juni 2020 14:34
An: CCP4BB@JISCMAIL.AC.UK  
Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

 

EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
  

 

Dear Colleagues,

In an effort to break this naming deadlock, and with Massimo and Ian not 
showing up as yet, I checked the IUCr Dictionary.

“Redundancy“ and “Multiplicity“ are not listed.

The more generic term “Statistical Descriptors“ is though and even offers 
Recommendations:-

http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html 

 

Point 1, first sentence, fits the various wishes of this thread succinctly, if 
not in a single word, and even not readily allowing an easy acronym. 

Greetings,

John 

 

Emeritus Professor John R Helliwell DSc

 

 





On 30 Jun 2020, at 13:11, Phil Jeffrey mailto:pjeff...@princeton.edu> > wrote:

The people that already use multiplicity are going to find reasons why it's 
the superior naming scheme - although the underlying reason has a lot to do 
with negative associations with 'redundant', perhaps hightened in the current 
environment.  And conversely redundant works for many others - Graeme's 
pragmatic defense of multiplicity actually works both ways - any person who 
takes the trouble to read the stats table, now exiled to Supplementary Data, 
knows what it means.  Surely, then, the only way forward on this almost totally 
irrelevant discussion is to come up with a universally-loathed nomenclature 
that pleases nobody, preferably an acronym whose origins will be lost to 
history and the dusty CCP4 archives (which contain threads similar to this 
one).  I humbly submit:

NFDOF: Nearly Futile Data Overcollection Factor ?
[*]

Or, even better, could we not move on to equally pointless discussions of the 
inappropriateness of "R-factor" ?  I have a long history of rearguard action 
trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
from me on this for years.

(Personally I'm pining for Gerard Kleywegt to resume his quest for overextended 
naming rationales, of which ValLigURL is a personal 'favo[u]rite'.  But I'm 
just old-fashioned.)

Ironically,
Phil Jeffrey
Princeton

[* I too have collected 540 degrees in P1 to solve a SAD structure, just 
because I could, hence "nearly"]
[** The actual answer to this thread is: history is written by the authors of 
scaling programs - and I think the Americans are currently losing at this game, 
thus perilously close to making themselves redundant.]

On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:



Or, we could accept the fact that crystallographers are kinda used to 
multiplicity of an individual Miller index being different to multiplicity of 
observations, and in Table 1 know which one you mean?  Given that they add new 
information (at the very least to the scaling model) they are strictly not 
“redundant”.

The amount that anyone outside of methods development cares about the “epsilon” 
multiplicity of reflections is … negligible?

Sorry for chucking pragmatism into a dogmatic debate 

Cheerio Graeme




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Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

Ah…the rise of the replicants …

 

https://www.youtube.com/watch?v=yWPyRSURYFQ

 

…and don’t forget the and the Voight-Kampff Test results in Table 1.

 

Best, BR

 

From: Pierre Rizkallah  
Sent: Monday, June 29, 2020 15:46
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] number of frames to get a full dataset?

 

You’re missing out on a grand opportunity for iconoclasm here. Try out ‘Degree 
of Replication’ or ‘Average Replication’ or ‘Replicate Frequency’. Any other 
offerings!

 

P.

***

Dr Pierre Rizkallah, Senior Lecturer Structural Biology 

Institute of Infection & Immunology, Sir Geraint Evans Building, 

School of Medicine, Heath Campus, Cardiff, CF14 4XN

email: rizkall...@cardiff.ac.uk <mailto:rizkall...@cardiff.ac.uk> 
phone: +44 29 2074 2248

http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Bernhard Rupp
Sent: 29 June 2020 23:36
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I think it is time to escalate that discussion to crystallographic definition 
purists like Massimo or to a logical consistency proponent like Ian who abhors 
definitional vacuum   

 

Cheers, BR

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Andreas Förster
Sent: Monday, June 29, 2020 15:24
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I like to think that the reflections I carefully measured at high multiplicity 
are not redundant, which the dictionary on my computer defines as "not or no 
longer needed or useful; superfluous" and the American Heritage Dictionary as 
"exceeding what is necessary or natural; superfluous" and "needlessly 
repetitive; verbose".

 

Please don't use the term Needless repetitivity in your Table 1.  It sends the 
wrong message.  Multiplicity is good.

 

All best.

 

 

Andreas

 

 

 

On Tue, Jun 30, 2020 at 12:03 AM James Holton mailto:jmhol...@lbl.gov> > wrote:

I have found that the use of "redundancy" vs "multiplicity" correlates very 
well with the speaker's favorite processing software.  The Denzo/HKL program 
scalepack outputs "redundancy", whereas scala/aimless and other more 
Europe-centric programs output "multiplicity".

At least it is not as bad as "intensity", which is so ambiguous as to be almost 
useless as a word on its own.

-James Holton
MAD Scientist

On 6/24/2020 10:27 AM, Bernhard Rupp wrote:

> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not 
uniquely defined. It can refer to 

a.  the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
b.  the multiplicity of the reflection, which means the superposition of 
reflections with the same d  (mostly powder diffraction) 
c.  the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental number.

How from (a) real space symmetry follows (b) in reciprocal space (including the 
epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscripts.iucr.org%2Fcgi-bin%2Fpaper%3Fa14080=02%7C01%7Crizkallahp%40CARDIFF.AC.UK%7C9d4374a0f1514697edbf08d81c7cdfe1%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637290669953538712=nROKLFzfjRttVaIi8qOBIbY5bB3IGusRudGkb6MX9t0%3D=0>
  

and also on page 306 in BMC.

Too much multiplicity might create duplicity…   

Cheers, BR

 

Jon Cooper

 

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au> > wrote:

I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences. 

I'm not a minimalist when it comes to data- redundancy is a good thing to have. 

cheers, tom 

 

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au <mailto:tom.p...@csiro.au>  

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of 0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<mailto:0c2488af9525-dmarc-requ...@jiscmail.ac.uk>  
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<mailto:0c2488af9525-dmarc-requ...@jiscmail.ac.uk> >
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>  
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] 

Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

I think it is time to escalate that discussion to crystallographic definition 
purists like Massimo or to a logical consistency proponent like Ian who abhors 
definitional vacuum   

 

Cheers, BR

 

From: CCP4 bulletin board  On Behalf Of Andreas Förster
Sent: Monday, June 29, 2020 15:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I like to think that the reflections I carefully measured at high multiplicity 
are not redundant, which the dictionary on my computer defines as "not or no 
longer needed or useful; superfluous" and the American Heritage Dictionary as 
"exceeding what is necessary or natural; superfluous" and "needlessly 
repetitive; verbose".

 

Please don't use the term Needless repetitivity in your Table 1.  It sends the 
wrong message.  Multiplicity is good.

 

All best.

 

 

Andreas

 

 

 

On Tue, Jun 30, 2020 at 12:03 AM James Holton mailto:jmhol...@lbl.gov> > wrote:

I have found that the use of "redundancy" vs "multiplicity" correlates very 
well with the speaker's favorite processing software.  The Denzo/HKL program 
scalepack outputs "redundancy", whereas scala/aimless and other more 
Europe-centric programs output "multiplicity".

At least it is not as bad as "intensity", which is so ambiguous as to be almost 
useless as a word on its own.

-James Holton
MAD Scientist

On 6/24/2020 10:27 AM, Bernhard Rupp wrote:

> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not 
uniquely defined. It can refer to 

a.  the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
b.  the multiplicity of the reflection, which means the superposition of 
reflections with the same d  (mostly powder diffraction) 
c.  the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental number.

How from (a) real space symmetry follows (b) in reciprocal space (including the 
epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 

and also on page 306 in BMC.

Too much multiplicity might create duplicity…   

Cheers, BR

 

Jon Cooper

 

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au> > wrote:

I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences. 

I'm not a minimalist when it comes to data- redundancy is a good thing to have. 

cheers, tom 

 

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au <mailto:tom.p...@csiro.au>  

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of 0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<mailto:0c2488af9525-dmarc-requ...@jiscmail.ac.uk>  
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
<mailto:0c2488af9525-dmarc-requ...@jiscmail.ac.uk> >
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>  
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] number of frames to get a full dataset? 

 

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit. 

Jon Cooper

 

On 23 Jun 2020 07:29, Andreas Förster mailto:andreas.foers...@dectris.com> > wrote:

Hi Murpholino,

 

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.

https://doi.org/10.1107/S2059798319003528


All best.

 

 

Andreas

 

 

(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.

 

 

 

On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro mailto:murpholi...@gmail.com> > wrote:

Hi. 
Quick question...

I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':

at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 

 

...also...

wh

Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

> Oh, and some of us prefer the word 'multiplicity' ;-0

Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not 
uniquely defined. It can refer to 

a.  the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
b.  the multiplicity of the reflection, which means the superposition of 
reflections with the same d  (mostly powder diffraction) 
c.  the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental number.

How from (a) real space symmetry follows (b) in reciprocal space (including the 
epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 

and also on page 306 in BMC.

Too much multiplicity might create duplicity…   

Cheers, BR

 

Jon Cooper

 

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au> > wrote:

I would just like to point out that for those of us who have worked too many 
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous 
differences. 

I'm not a minimalist when it comes to data- redundancy is a good thing to have. 

cheers, tom 

 

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au   

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of 0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
  
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
 >
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK   
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] number of frames to get a full dataset? 

 

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit. 

Jon Cooper

 

On 23 Jun 2020 07:29, Andreas Förster mailto:andreas.foers...@dectris.com> > wrote:

Hi Murpholino,

 

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.

https://doi.org/10.1107/S2059798319003528


All best.

 

 

Andreas

 

 

(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.

 

 

 

On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro mailto:murpholi...@gmail.com> > wrote:

Hi. 
Quick question...

I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':

at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 

 

...also...

what other factors can change n... besides symmetry and radiation damage?

 

Thanks

 

  _  

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



-- 

Andreas Förster, Ph.D.

Application Scientist Crystallography, Area Sales Manager Asia & Pacific

Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: 
andreas.foers...@dectris.com  

DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | 
www.dectris.com  

 

 

   


  

   
 

 

Confidentiality Note: This message is intended only for the use of the named 
recipient(s)

and may contain confidential and/or privileged information. If you are not the 
intended

recipient, please contact the sender and delete the message. Any unauthorized 
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the information contained in this message is prohibited.

 

 

 

  _  

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Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

Tom makes a good point. The minimum RS coverage necessary to obtain a unique
data set is just a simple calculation

that involves no experimental reality. 

 

To judge the expected usefulness of the data, you need to have some idea
about the possible errors, random and systematic.  

Random is easy. Just collect longer (Poisson) and the counting error
(precision) improves (sqrt(n)). Easy, would not

radiation damage throw a wrench in into this concept, cf. all the threads by
Holton, Elsbeth et al.

 

Systematic, error, in absence of knowing the true value, becomes more
interesting. One can average out some 

systematic errors by averaging multiple independent reflections (redundancy
is rarely a bad thing, except for additional systematic

error by overdoing exposure (as in hunt for highest resolution…) , but at
least the mean will become more precise (not

always, but often, more accurate too).

 

Without advertisement for Dectris, collecting as much as you can
(anomalously) as fast (lowest dose) as you can

and sort out the stats later is a reasonable default in absence of other
prior information. 

 

In his context, I’d like to make a push for routine anomalous data, I was
often surprised about the interpretative confirmation

you can gain from a few clear anomalous peaks (or their absence).   

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Peat, Tom
(Manufacturing, Parkville)
Sent: Tuesday, June 23, 2020 14:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

I would just like to point out that for those of us who have worked too many
times with P1 or P21 that even 360 degrees will not give you 'super'
anomalous differences. 

I'm not a minimalist when it comes to data- redundancy is a good thing to
have. 

cheers, tom 

 

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au   

 

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > on behalf of
0c2488af9525-dmarc-requ...@jiscmail.ac.uk

<0c2488af9525-dmarc-requ...@jiscmail.ac.uk
 >
Sent: Wednesday, June 24, 2020 1:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] number of frames to get a full dataset? 

 

Someone told me there is a cubic space group where you can get away with
something like 11 degrees of data. It would be interesting if that's
correct. These minimum ranges for data collection rely on the crystal being
pre-oriented, which is unheard-of these days, although they can help if
someone is nagging you to get off the beam line or if your diffraction fades
quickly. Going for 180 degrees always makes sense for a well-behaved
crystal, or 360 degrees if you want super anomalous differences. Hope this
helps a bit. 

Jon Cooper

 

On 23 Jun 2020 07:29, Andreas Förster mailto:andreas.foers...@dectris.com> > wrote:

Hi Murpholino,

 

in my opinion (*), the question is neither number of frames nor degrees.
The only thing that matters to your crystal is dose.  How many photons does
your crystal take before it dies?  Consequently, the question to ask is How
best to use photons.  Some people have done exactly that.

https://doi.org/10.1107/S2059798319003528


All best.

 

 

Andreas

 

 

(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to
use them to your advantage.

 

 

 

On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro mailto:murpholi...@gmail.com> > wrote:

Hi. 
Quick question...

I have seen *somewhere* that to get a 'full dataset we need to collect n
frames':

at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 

 

...also...

what other factors can change n... besides symmetry and radiation damage?

 

Thanks

 

  _  

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



-- 

Andreas Förster, Ph.D.

Application Scientist Crystallography, Area Sales Manager Asia & Pacific

Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
andreas.foers...@dectris.com  

DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com  

 

 

  


  

 
 

 

Confidentiality Note: This message is intended only for the use of the named
recipient(s)

and may contain confidential and/or privileged information. If you are not
the 

Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

1/48th of reciprocal space is the minimum in certain SGs..

 

Table 6.6 in BMC or

http://www.ruppweb.org/new_comp/spacegroup_decoder.htm

 

Best, BR

 

 

From: CCP4 bulletin board  On Behalf Of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk
Sent: Tuesday, June 23, 2020 08:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] number of frames to get a full dataset?

 

Someone told me there is a cubic space group where you can get away with 
something like 11 degrees of data. It would be interesting if that's correct. 
These minimum ranges for data collection rely on the crystal being 
pre-oriented, which is unheard-of these days, although they can help if someone 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal, or 360 
degrees if you want super anomalous differences. Hope this helps a bit. 

Jon Cooper

 

On 23 Jun 2020 07:29, Andreas Förster mailto:andreas.foers...@dectris.com> > wrote:

Hi Murpholino,

 

in my opinion (*), the question is neither number of frames nor degrees.  The 
only thing that matters to your crystal is dose.  How many photons does your 
crystal take before it dies?  Consequently, the question to ask is How best to 
use photons.  Some people have done exactly that.

https://doi.org/10.1107/S2059798319003528


All best.

 

 

Andreas

 

 

(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you to 
use them to your advantage.

 

 

 

On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro mailto:murpholi...@gmail.com> > wrote:

Hi. 
Quick question...

I have seen *somewhere* that to get a 'full dataset we need to collect n 
frames':

at least 180 frames if symmetry is X

at least 90 frames if symmetry is Y

at least 45 frames if symmetry is Z

Can somebody point where is *somewhere*? 

 

...also...

what other factors can change n... besides symmetry and radiation damage?

 

Thanks

 

  _  

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



-- 

Andreas Förster, Ph.D.

Application Scientist Crystallography, Area Sales Manager Asia & Pacific

  

Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: 
andreas.foers...@dectris.com  

DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | 
www.dectris.com  

 

 

   


  

   
 

 

Confidentiality Note: This message is intended only for the use of the named 
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intended

recipient, please contact the sender and delete the message. Any unauthorized 
use of

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Re: [ccp4bb] visual mask editor - why

[Bernhard Rupp]

Another brilliant Super-Elf, with a blast from the past - Numerical Recipes FFT 
rules 

 

Many thanks for the excellent explanations,

 

Cheers, BR

 

From: James Holton  
Sent: Saturday, June 13, 2020 17:34
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] visual mask editor - why

 

Bernhard,

Sounds like you are plotting something similar to what I was tinkering with 
once.  A script you may find useful is this one:
https://bl831.als.lbl.gov/~jamesh/bin_stuff/map_func.com

I wrote this because although mapmask, maprot, etc have very useful 
functionalities I found I wanted additional features, such as dividing one map 
by another, or taking a square root.  These are important if you are trying to 
derive the "signal-to-noise ratio", for example.  

 Once you have a map of rho/sigma(rho) you can convert that into a "pobability" 
by passing it through the "erf()" and "pow()" functions.  This can be a good 
way of estimating the "probability something is there" or P(rho) for a given 
map voxel. Specifically: 

P(rho) = 1-pow(erf(abs(rho/sigma(rho))/sqrt(2)),V/2/d^3)

where:
rho is the electron density map value (preferably from a Fo-Fc map)
sigma(rho) is the error on that voxel
V is the unit cell volume (A^3)
d is the resolution in A
erf() is called the "error function"
pow(m,e) is the raise-to-a-power function: m^e

The erf() function by itself turns a rho/sigma(rho)=3 peak into 0.997, and a 
1-sigma peak into 0.683. What that means is: assuming the noise is Gaussian, 
you expect voxels in the range -1-sigma to +1-sigma to be ~68.3% of the total.  
The "probability it isn't noise" (sometimes called a "p-value") is then 1-0.683 
= 0.32.  Seems like a pretty high probability to give to a 1-sigma peak, but 
now remember that the map is not just a single observation but thousands.  So, 
the question you really want to ask is: if I generate 100x100x100 = 1e6 
Gaussian-random numbers, what are the odds that a 4-sigma peak occurred at 
random?  The answer is: pretty much garanteed.  In any collection of 1 million 
Gaussian-random numbers with rms=1 it is virtually impossible to not have at 
least one of them > 4. Trust me, I have tried. This is where the "pow()" 
function comes in.  You need to multiply all the individual voxel probabilities 
together to get the probability of at least one >4-sigma peak happening at 
random.

But, then again, map voxels are hardly independent observations.  Finite 
resolution means that neighboring pixels are highly correlated.  So, rather 
than map grid points, we should be considering "Shannon voxels".  All this is 
is the number of blobs of diameter d, where d is the resolution, that can fit 
into the volume of the map. For example, if we have a 100 A edge on a cubic 
cell and 3 A resolution, then we have about 3.7e4 independent "observations" of 
density, so the probability of a random 4-sigma peak is:
P(rho) = erf(4/sqrt(2))**(((100./3)**3)/2) = 0.31

That is, if you make a zillion maps of random data using different seeds each 
time, 3.7e4 voxels each, and draw from a Gaussian distribution with rms=1, you 
expect 31% of these maps to have a 4-sigma peak. Randomly. The other 69% will 
not have anything > 4.  So, if you see a 4-sigma peak in a map with 3.7e4 
Shannon voxels I'd say it is real about 69% of the time.  You might consider 
0.69 to be a decent "weight" you should give such a 4-sigma peak.  A 5-sigma 
peak under the same circumstances gets P(rho) = 0.989, and a 3-sigma peak gets 
P(rho) = 1e-22.  aka: probaby noise.  It is perhaps worth remembering that at a 
given resolution large-sigma noise peaks are more common in bigger cells than 
small ones.

So, how do you get sigma(rho)?  To be honest, the rms value of the mFo-DFc map 
is a pretty good estimate.  The rms value of the 2mFo-DFc map is not (Lang et 
al. PNAS 2013).  I usually get sigma(rho) empirically.  That is, by making a 
stack of maps: start with your favorite refined structure and introduce random 
noise from whatever source you want to test. I.E. Gaussian error proprotional 
to SigI is an obvious one.  A more realistic on is the Fo-Fc difference itself. 
 After adding this "extra" noise to the data, re-refine the structure and 
generate a 2mFo-DFc map.  Do this ~50 times with different random number seeds. 
Then take those 50 maps and compute the mean and standard deviation of "rho" at 
every voxel.  You can do this with mapmask's ADD, MULT and SCALE features, but 
you can't do the last step, which is taking the square root of the variance.  
Hence: map_func.com

There are lots of other functions supported, including random number genration, 
etc.  Run the script with no arguments to get a list.

Oh, but don't try it on an mtz file!  mtz files are not maps.

-James Holton
MAD Scientist



On 5/28/2020 12:11 PM, Bernhard Rupp

Re: [ccp4bb] visual mask editor - why

[Bernhard Rupp]

Yes I have already pilfered useful parts of it in the scripts.

Thx, BR

 

From: Boaz Shaanan  
Sent: Thursday, May 28, 2020 11:59
To: b...@hofkristallamt.org
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] visual mask editor - why

 

Hi Bernhard,

Did you consider trying 'polder' in the phenix package? 

Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel

 

On May 28, 2020 21:17, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Maybe I should explain an example: Say coot detects an unmodelled blob
(maybe a ligand). Now, I would like to do

a number of things without biasing towards a model. Like comparing these map
regions, excluding

intrusion of a solvent mask, etc.

 

Now could coot for example just generate a mask around what it already knows
are blobs?  

Possible useful items could be a solvent mask not including that regions, or
a density map

that includes only features with a certain boundary around that blob.

 

I pilfered some kludges together from different sources, but let's just say
inelegant would be a compliment.

 

Best, BR



Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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Re: [ccp4bb] visual mask editor - why

[Bernhard Rupp]

Looks like the density manipulation/carving tools might be useful.

Thx, BR

 

From: CCP4 bulletin board  On Behalf Of Jurgen Bosch
Sent: Thursday, May 28, 2020 11:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] visual mask editor - why

 

Give this a shot: https://www.eyesopen.com/afitt

 

At least in Vida from the same suite of programs, you can select such a blob as 
you describe and export it in a useful way.

Jürgen 

___

Jürgen Bosch, Ph.D.

Division of Pediatric Pulmonology and Allergy/Immunology
Case Western Reserve University

2109 Adelbert Rd, BRB 835

Cleveland, OH 44106

Phone: 216.368.7565

Fax: 216.368.4223

https://www.linkedin.com/in/jubosch/





CEO & Co-Founder at InterRayBio, LLC

 

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology





On May 28, 2020, at 2:17 PM, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

 

Maybe I should explain an example: Say coot detects an unmodelled blob (maybe a 
ligand). Now, I would like to do

a number of things without biasing towards a model. Like comparing these map 
regions, excluding

intrusion of a solvent mask, etc.

 

Now could coot for example just generate a mask around what it already knows 
are blobs?  

Possible useful items could be a solvent mask not including that regions, or a 
density map

that includes only features with a certain boundary around that blob.

 

I pilfered some kludges together from different sources, but let’s just say 
inelegant would be a compliment.

 

Best, BR



Brief question: Does something like a visual density mask editor exist?

Thx, BR

------

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> 
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[ccp4bb] visual mask editor - why

[Bernhard Rupp]

Maybe I should explain an example: Say coot detects an unmodelled blob
(maybe a ligand). Now, I would like to do

a number of things without biasing towards a model. Like comparing these map
regions, excluding

intrusion of a solvent mask, etc.

 

Now could coot for example just generate a mask around what it already knows
are blobs?  

Possible useful items could be a solvent mask not including that regions, or
a density map

that includes only features with a certain boundary around that blob.

 

I pilfered some kludges together from different sources, but let's just say
inelegant would be a compliment.

 

Best, BR



Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] visual mask editor?

[Bernhard Rupp]

Yes, there are some ways to do it, more or less cumbersome.

But after being already reprimanded for using old ccp4 stuff I was looking for 
a 21st century solution…sort of matrix-style…put you shades on, wave your 
hands, and done.

 

Cheers, BR

From: CCP4 bulletin board  On Behalf Of Soisson, Stephen 
M
Sent: Thursday, May 28, 2020 09:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] visual mask editor?

 

You used to be able to do this in O (dating myself)

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Bernhard Rupp
Sent: Thursday, May 28, 2020 12:39 PM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: [ccp4bb] visual mask editor?

 

EXTERNAL EMAIL – Use caution with any links or file attachments.

Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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[ccp4bb] visual mask editor?

[Bernhard Rupp]

Brief question: Does something like a visual density mask editor exist?

Thx, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

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[ccp4bb] Map grid passing from ccp4 refmac mask?

[Bernhard Rupp]

Dear Developers,

 

I am wondering if there is a way to entice the REFMAC ccp4i input mask to
accept and hand-off grid parameters into the subsequently

running FFTBIG if I select the 'Generate weighted difference maps' option?

 

Just a convenience issue. I can script it. 

 

Also the map file name despite selection (xyz.ccp4) gets changed to xyz.map
in the actual output.

 

Best, BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

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[ccp4bb] Oddity in CCP4 library signal mtz -error (developers)

[Bernhard Rupp]

Hi Fellows,

 

while reading logs I notice an (apparently inconsequential) error message
using anomalous refinement in Refmac:

 

OPENED INPUT MTZ FILE 

 Logical Name: HKLIN   Filename:
C:/data/Dropbox/Refinements/ABCD\ABCD_anomalous.mtz 

 

>>>>>> CCP4 library signal mtz:File column type different from type expected
by program (Error)

raised in ccp4_lrassn <<<<<<

   From ccp4_lrassn: expected type F does not match file type G for column
F-obs(+)

>>>>>> CCP4 library signal mtz:File column type different from type expected
by program (Error)

raised in ccp4_lrassn <<<<<<

   From ccp4_lrassn: expected type Q does not match file type L for column
SIGF-obs(+)

 

 

The GUI has no problem recognizing/understanding these G and L label types,
though, and Refmac does its job properly producing fine anomalous maps.

 

And oddly enough, for F-obs(-) and SIGF-obs(-)the G and L labels are not
considered offending. 

 

So maybe it's not a real error just expecting F and Q .

 

Best, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

All models are wrong

but some are useful.

--

 




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[ccp4bb] Refmac and hydrogens -developers

[Bernhard Rupp]

Hi Fellows,

 

for an experiment, I am running 0.9 A data with unrestrained Refmac (yes I
know should/could use SHELXL, but let's drop that for now).

 

When I select 'ignore even if present in file' in a PDB that has hydrogens,
I get the identical results than with 'use if present' or 'generate all'.

 

The log informs me that the instructions were properly issued, the output
PDB does not have Hs, but Rs and map are exactly the same 

as with selection of if present or generate all H. Does not seem to make
sense.

 

If I cull the hydrogens from the input PDB and 'use if present' or 'ignore',
the stats and map are different and no H in output as requested -  all as
expected.

 

Maybe that can be reproduced and, if it is not a feature, fixed.

 

Best, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Real knowledge is to know 

the extent of one's ignorance 

--

 




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Re: [ccp4bb] Using SFall for map conversion

[Bernhard Rupp]

Thanks, I would not have the PDP 11 hardware anymore to read the 8” floppies  
No, the problem really was standard sequence of the grid axes sfall expects due 
to SG dependent FFT routines. 

Best, BR

 

From: Philippe BENAS  
Sent: Friday, May 15, 2020 01:23
To: ccp4bb@jiscmail.ac.uk; b...@hofkristallamt.org
Subject: Re: [ccp4bb] Using SFall for map conversion

 

Dear Bernhard,

 

Is it an old map ?

 

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

 

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

 

All the best,

Philippe

 

  _  

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr <mailto:p.be...@ibmc-cnrs.unistra.fr> , 
philippe_be...@yahoo.fr <mailto:philippe_be...@yahoo.fr> 
URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

  _  

 

 

 

Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp mailto:hofkristall...@gmail.com> > a écrit : 

 

 

Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one ***

 

and later

 

>>>>>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job…

 

Many thx, BR

------

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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Re: [ccp4bb] Using SFall for map conversion

[Bernhard Rupp]

Yes, as suggested, it works just fine with maprot and sfall out of the ccp4i 
interface, and the approximate scaling to refence Fo is enough for my hack.

Did not get the Refmac sfall option working but I am still troubleshooting this.

Will transition to clipper tools to avoid age discrimination.

 

Cheers, BR

 

From: CCP4 bulletin board  On Behalf Of Eleanor Dodson
Sent: Friday, May 15, 2020 02:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Using SFall for map conversion

 

maprot will rewrite your map with a changed axis order, as required for sfall.

And grateful as I am to see someone still loyal to sfall, 40+ years after it wa 
written!, there are more modern tools.

In the CCP4I interace go to 

Map & Mask faculities

Clipper Map tools, and there is a map to SFS utility.

 

Eleanor

 

 

 

On Fri, 15 May 2020 at 09:24, Philippe BENAS 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk 
<mailto:0d88e888355a-dmarc-requ...@jiscmail.ac.uk> > wrote:

Dear Bernhard,

 

Is it an old map ?

 

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

 

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

 

All the best,

Philippe

 


  _  


Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr <mailto:p.be...@ibmc-cnrs.unistra.fr> , 
philippe_be...@yahoo.fr <mailto:philippe_be...@yahoo.fr> 
URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/


  _  


 

 

 

Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp mailto:hofkristall...@gmail.com> > a écrit : 

 

 

Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one ***

 

and later

 

>>>>>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job…

 

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 


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Re: [ccp4bb] Using SFall for map conversion

[Bernhard Rupp]

Thanks to all. Mapmask works. Yes the order to change to is ZXY. Map from 
coefficients indeed looks like the directly loaded map, jus the scale is 
different (I supplied no reference PDB)

The remaining issue is  - a pain to automate.

I tried Refmac- there is a mention of an sfall mode and I tried to input the 
map and a reference HKL .. In that case, refmac simply stops after reading the 
map.

If I add a XYZIN to scale the map, I get a mtz but not from the map, which is 
never read.

I am not even sure – this is from the EM part in the instructions – if this is 
intended to work in this fashion.

 

Has somebody tried that successfully with an Xray map?

 

Many thanks again, BR

 

From: CCP4 bulletin board  On Behalf Of Alejandro 
Buschiazzo
Sent: Thursday, May 14, 2020 15:10
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Using SFall for map conversion

 

Oh…maybe I suggested the wrong order then (Y X Z  - for SG 20) ?

 

…I do realize YXZ is not an XYZ cyclic permutation (whereas ZXY is)…I dug it 
from an old script of mine, so now rechecked the FFT doc …but yes, FFT says 
that Y X Z is the std axis ordering for SGs higher-than 18…I’m probably missing 
something silly here (any clue James?)

 

Best, ale





On May 14, 2020, at 6:45 PM, James Holton mailto:jmhol...@lbl.gov> > wrote:

 

Use mapmask first:

echo axis Z X Y |\
mapmask mapin1 old.map mapout new.map

For reasons I'm sure made sense at one time, sfall does not seem to know how to 
automatically re-order the map axes.

Also, it is generally a good idea to expand to P1 first, and use "SFSG 1" in 
sfall.  There are still some "gotcha" space groups in the SFALL code for 
density near cell edges.  I can't remember which ones now because years ago I 
started using SFSG 1 and the problem went away.

-James Holton
MAD Scientist




On 5/14/2020 1:44 PM, Bernhard Rupp wrote:

Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one ***

 

and later

 

>>>>>> CCP4 library signal library_  file:Cannot open file 
>>>>>> (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job…

 

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 


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[ccp4bb] Using SFall for map conversion

[Bernhard Rupp]

Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one
***

 

and later

 

>>>>>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this
spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this
spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job.

 

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

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Re: [ccp4bb] disinfecting keyboards

[Bernhard Rupp]

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

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

HTH BR


> On Apr 29, 2020, at 2:59 PM, Sravya Mounika Kantamneni 
>  wrote:
> 
> How about using keyboard guards and dissecting them as usual?
> 
> Regards,
> Sravya
> 
>> On Apr 29, 2020, at 8:53 PM, Tim Gruene  wrote:
>> 
>> Dear all,
>> 
>> can you make suggestions for how to disinfect computer keyboards, and 
>> instrument panels?
>> 
>> Our facility is going to reboot next week, with shifts so that people 
>> don't meet. The main interface will be the computer keyboards, as 
>> well as the door of our X-ray diffractometer and the mounting of the 
>> crystals.
>> 
>> The keyboard labels may not like alcohols (and the efficiency of 
>> injecting disinfecting through the USB cable is also under 
>> discussion, so I heard).
>> 
>> One way would be to use individual keyboards, and wearing gloves for 
>> replugging, and to use gloves for mounting crystals.
>> 
>> But maybe there are other ways that won't require gloves?
>> 
>> Best regards,
>> Tim
>> 
>> --
>> --
>> Tim Gruene
>> Head of the Centre for X-ray Structure Analysis Faculty of Chemistry 
>> University of Vienna
>> 
>> Phone: +43-1-4277-70202
>> 
>> GPG Key ID = A46BEE1A
>> 
>> #
>> ###
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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> 
> ##
> ##
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Re: [ccp4bb] disinfecting keyboards

[Bernhard Rupp]

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

 

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

 

Cheers, BR

 

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

Dear all,

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

Our facility is going to reboot next week, with shifts so that people
don't meet. The main interface will be the computer keyboards, as well
as the door of our X-ray diffractometer and the mounting of the
crystals.

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

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

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

Best regards,
Tim

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

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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-- 

Eduardo Rodríguez-Román, PhD

ASM, eLIFE & USERN Ambassador

Biotechnology and Plant Virology Lab

Center for Microbiology and Cell Biology

Instituto Venezolano de Investigaciones Científicas

PO Box 20632, Caracas 1020A, Venezuela.

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

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

Cell phone:   +58 (424) 111 0375

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

or erodriguezro...@gmail.com  

Twitter: @erodriguezroman  

      

     


 

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Re: [ccp4bb] on-topic: your opinions requested!

[Bernhard Rupp]

> go the Rupp Route:  Name and Shame!

Thanks for the character reference.

Best, BR



On 07/04/2020 16:08, Artem Evdokimov wrote:

Dear CCP4ers, 

 

I would like to solicit your thoughts on the following (this is a real 
situation, but salient details are changed):

 

Imagine that you're an industrial scientist in a small company, working on the 
Bavarian Sausage (Weisswurst) Esterase project. The overall structure is 
previously unknown, with no good homologs in the PDB, trying to model is "OK 
not great" so the structure is really needed...

 

Then, you find an article from a large commercial competitor, that somehow 
managed to solve the Stadtwurst (Saxony Sausage) Esterase structure (which is a 
very close homolog to the one you need!). 

 

Sounds good - but as you read the paper you realize that the authors managed to 
find a journal that allowed them to publish their work without disclosing 
neither the coordinates of the model, nor even the crystallization conditions 
of the protein - all that's available is a tantalizing still picture of the 
active site in surface mode, with a ball-and-stick ligand positioned such that 
it is impossible to say what it interacts with. 

 

So you sit and ponder - whether to write to the Editor, or maybe to contact the 
authors directly (but then they would know that you're working on this, which 
is not necessarily great since you're competing), or to just buck up and do the 
structure on your own (which feels a bit wasteful). Then, you realize that your 
friends at CCP4 have a lot of wisdom to offer, so you sit down and pen an 
email...

 

Any thoughts?

 

Artem

 

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Re: [ccp4bb] New phasing approach

[Bernhard Rupp]

Hi Fellows,

the idea for this work came from my initial excitement about the FEL, because a 
coherent source of photons
would I principle allow a reflection-wise interference experiment. The reasons 
Ed gave, make this kind
of experiment impractical. The key difference is, that the proposed experiment 
is a single photon experiment, 
and absent some of the instrumental challenges Gerd alluded to, the remaining 
problem is the probe photon
interaction in the delayed-probe experiment (tactfully omitted in fig 1).

I am sure I will have an update in a year from now.

Cheers, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Rosenbaum, Gerold
Sent: Wednesday, April 1, 2020 19:31
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] New phasing approach

The x-ray interferometer is not a joke. In about 1974, Gerd Materlik built one 
for his thesis and inserted it in front of my beamline at the DESY synchrotron. 
The beam splitters and "mirrors" were all carved out of a single block of 
perfect single crystal silicon. He inserted a wedge of plastic in one arm 
acting as a phase shifter and produced dark and white bands in a film. I was 
really, really impressed.

As for the three-beam experiments by Edgar Weckert and K. Hümmer, carried on by 
Bob Sweet, as impressive it is to get precise phase measurements for a 
reflection, there is a practical downsided: the radiation dose for measuring 
one reflection to a few % is as high as the dose for a whole data set from 
which we conventionally extract the phases of all reflection though only at 
about 30% but still good enough to solve the structure.

I have the inkling that Bernhard's phase retrieval would suffer the same death: 
only the ultra-parallel fraction of the x-ray beam passes through the 
interferometer cutting down tremendously the intensity of reflections from 
macromolecular crystals which tend to be far from parallel.

Gerd

On 01.04.2020, 16:02, "CCP4 bulletin board on behalf of Tim Gruene" 
 wrote:

Dear Bernhard,

your paper is actually not so much of a joke. Are you aware of K. Huemmer's 
and E. Weckert's three-beam experiments? See e.g. 

https://link.springer.com/chapter/10.1007/978-1-4615-5879-8_24

Best regards,
Tim

On Wednesday, April 1, 2020 4:00:19 AM CEST Bernhard Rupp wrote:
> Hi Fellows,
> 
> 
> 
> just in time for a little reading during quarantine-induced boredom here
> preprint pages
> 
> (embargoed until 04.01) from my recent Phys. Rev. paper with a different
> take on phasing
> 
> https://tinyurl.com/Phys-Rev-2020
> 
> 
> 
> Enjoy, BR
> 
> --
> 
> Bernhard Rupp
> 
>  <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/
> 
>  <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org
> 
> +1 925 209 7429
> 
> --
> 
> Department of Genetic Epidemiology
> 
> Medical University Innsbruck
> 
> Schöpfstr. 41
> 
> A 6020 Innsbruck
> 
>  <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at
> 
> +43 676 571 0536
> 
> --
> 
> Many plausible ideas vanish
> 
> at the presence of thought
> 
> --
> 
> 
> 
> 
> 
> 
> 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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[ccp4bb] New phasing approach

[Bernhard Rupp]

Hi Fellows,

 

just in time for a little reading during quarantine-induced boredom here
preprint pages 

(embargoed until 04.01) from my recent Phys. Rev. paper with a different
take on phasing

https://tinyurl.com/Phys-Rev-2020

 

Enjoy, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

--

Department of Genetic Epidemiology

Medical University Innsbruck

Schöpfstr. 41

A 6020 Innsbruck

 <mailto:bernhard.r...@i-med.ac.at> bernhard.r...@i-med.ac.at

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Vote for cryoEM

[Bernhard Rupp]

So…Science has come down to a popularity contest on social media.

Best, BR

From: CCP4 bulletin board  On Behalf Of Alessandro 
Vannini
Sent: Tuesday, March 31, 2020 08:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Vote for cryoEM

 

We are head to head with mass-spectrometry in the #JBCMethodsMadness 
CHAMPIONSHIP. This can’t happen! 


Get out and VOTE! 15 min to go!

https://twitter.com/jbiolchem/status/1244655631316987905?s=20



 

Sent from my iPhone

 

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[ccp4bb] [ccp4dev] Broken wiki link to dimple from ccp4i

[Bernhard Rupp]

Dear Developers,

 

from ccp4i classic, the DIMPLE User Guide link (box top right) to 

http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_difference_map_
generation_with_DIMPLE

returns an error message

"Fatal error: Uncaught TypeError: Argument 1 passed to wfReportException()
must be an instance of Exception, instance of Error given, called in
/home/ccp4wiki/public_html/wiki/includes/Exception.php on line 205 and
defined in /home/ccp4wiki/public_html/wiki/includes/Exception.php:168 Stack
trace: #0 /home/ccp4wiki/public_html/wiki/includes/Exception.php(205):
wfReportException(Object(Error)) #1 [internal function]:
wfExceptionHandler(Object(Error)) #2 {main} thrown in
/home/ccp4wiki/public_html/wiki/includes/Exception.php on line 168"

 

Can you reproduce that behavior?

 

Best, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] A question of density

[Bernhard Rupp]

A few figures in BMC re truncation effects:

 

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART2.htm

http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-10.htm

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk
Sent: Thursday, March 5, 2020 12:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A question of density

 

Hello, not sure if anyone has mentioned series termination errors in the 
vicinity of electron dense atoms. The attached is from Glusker & Trueblood and 
might be of interest.

Jon Cooper

 

On 5 Mar 2020 19:00, Jessica Besaw mailto:jbesaw1...@gmail.com> > wrote:

Hello Matthias,

 

Excellent point. Most of the the ordered water are easily visible at 2 rmsd. 
The central disordered (or partially occupied) water becomes visible only at 
1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which I have displayed all of 
the maps). In your opinion, do you think this would be noise? 

 

Jessica

 

On Wed, 4 Mar 2020 at 12:45, Barone, Matthias mailto:bar...@fmp-berlin.de> > wrote:

hey Jessica

a tip that might come up later on anyway: once you put every reasonable bit 
into the desity, what I like to to when facing such blobbs: I take a well 
defined water out to create a diff density at a position where I know it is 
real. Having a feeling of how much you have to contour the diff density at that 
point can give you a good feeling how much of noise is actually in your density 
right in between the waters..?

best, matthias

 

Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Jessica Besaw mailto:jbesaw1...@gmail.com> >
Sent: Wednesday, March 4, 2020 6:42:34 PM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] A question of density 

 

Hey Nukri, 

 

Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure

 

I absolutely agree with you on the refinement. I did previously do that, and I 
attached the picture. 

 

What is the BB?

 

Cheers!

 

Jessica 

 

 

 

 

 

 

On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili mailto:sannu...@gmail.com> > wrote:

Hi Jessica,

You do not say how well is the rest of the structure refined. 

First, you should refine the structure best you can, without placing anything 
in the unclear blob of your interest so to obtain the best possible phases and 
hopefully improve the blob density as well.

Then you should let the BB see what that density looks like. Looking at only 
the list of possibilities has very little value without seeing the density 
itself.

Best wishes,

Nukri

 

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw mailto:jbesaw1...@gmail.com> > wrote:

Hello friends,  

 

I have a "blob" of density in an active site of my protein. 

 

I am struggling to determine if I should place a water in this spot, if I 
should model it as a disordered water, if the density may be a ligand that I 
have not considered, or if it should be left as unaccounted for density. I 
would like to publish this structure without compromising the science.

 

I have attached several possibilities that I have considered below. 

 

Any suggestions would be appreciated.

 

Cheers!

 

Jessica Besaw

 

 

 

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Re: [ccp4bb] refinement of 0.73A data in shelxl

[Bernhard Rupp]

Maybe the figures were just contoured odd...but my recollection of a good
0.8 A map appearance is differentwhich might be consistent with the
high Rf...a look at the high res data or images/stats might help?

Best, br

On Mon, Feb 3, 2020, 14:58 George Sheldrick 
wrote:

> Dear Matthias,
>
>
> That is very strange. First please repeat the shelxl refinement with the
> occupancy of the offending chlorine(s) in the .ins file changed from 11
> (i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If that
> does not help I would be happy to look at it in confidence, I would need
> the .hkl and .ins files.
>
>
> Best wishes, George
>
>
>
>
> On 03.02.20 12:08, Barone, Matthias wrote:
>
> Dear ccp4 community
>
> Im having some problems solving a 0.73A structure. Spacegroup seems to be
> correct, data are not twinned, 95.5% overall completeness, ISa 25.6. Outer
> shell CC1/2 24% and 90.4% complete.
>
> The model is nearly fully built, there is no remaining unmodelled areas.
> However, Rfact is stuck 27% in phenix, with a very distinct artifact in
> the electron map (see phenix.jpg). You can see difference density on
> various well defined sidechain atoms. Notably, they seem to follow a
> pattern: Nearly all Val CG have difference signal, as well as many backbone
> NH. Hence, I suspected that it might be a problem with the SF, since we
> recorded the DS at 0.86A.
>
>
> Hence I gave shelxl a shot:
>
> I used the refined model from phenix, converted it via pdb2ins and pasted
> the restraints created by prodrg.
>
> The shelxl hkl was produced by xdsconv, using the freeR flagging of the
> mtz used by phenix (no merge, friedel false).
>
> Interestingly, shelxl can bring Rfree down to 16% and almost all of
> the diff-density artifacts seen before are gone (shelxl_noSFAC-CL.jpg).
> Except one: the inhibitor contains a chlorinated phenylring (pdb ligand
> 2L5) which now shows massive difference density for Cl.
>
> I therefore suggested that I might deal with a wrong SF for Cl. Funny
> enough, pdb2ins does not produce a DISP line for Cl if converting the pdb
> that contains the inhibitor. Hence, I used pdb2ins and the pdb from
> PRODRG to produce SFAC for the inhibitor Cloride. I then pasted this line
>
> DISP $CL0.188450.21747   1035.16450
>
> into the .res file and updated the UNIT line. Shelxl runs through, and
> the density looks ok on the Chloride now. However Rfree is back up at 24%
> and the artifacts seen by phenix.refine are back (shelxl_SFAC-CL.jpg):
> now, very distincitvly, backbone carbonyls and NHs show difference density.
>
> Am I right in my assumption, that the SFAC of Cloride is not properly
> calculated at the given wavelenght? And if so, how do I guess it correctly?
>
> Thank you very much for your help!
>
> Best, matthias
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry
> University of Goettingen
> Tammannstr.  4
> D37077 Goettingen
> Germany
> Tel: +49 551 3933021 or +49 5594 227312
>
>
> --
>
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[ccp4bb] Remember the turkey?

[Bernhard Rupp]

Hi Fellows - here some light Holiday entertainment (and puzzle) for you:

Remember my thanksgiving posting below?  Meant as  a hoax or satire, it follows 
the 
classical pattern of throwing postmodern Critical Theory gibberish and Social 
Justice key words 
 (successfully deployed by Alan Sokal)
https://en.wikipedia.org/wiki/Sokal_affair
onto an out-of-context situation with the purpose of virtue signaling and 
posturing on moral high ground.

 Well, we just got outdone by a letter in our favorite vanity magazine, Nature: 
https://www.nature.com/articles/d41586-019-03781-0

The parallels are fascinating and it exactly follows the recipe developed above:
" throwing postmodern Critical Theory gibberish and Social Justice key words 
onto an out-of-context situation 
with the purpose to signal virtue and to opportunity for posturing on moral 
high ground"

Now - is this comment (a) meant serious or (b) another successful 
Sokal-Turkey-type hoax?

Cheers, BR

--
It has come to our attention that on this bulletin board insensitive and 
hurtful comments have 
been made towards animals with disability. Particularly concerning is the 
display of white privilege
and racial bias towards a minority individual  given that the turkey is also 
referred to in German as 'Indian'. 
In view of this non-inclusive and divisive display of unwokeness, the faculty 
Bias Response Team 
will contact you shortly and allow you to present your self-critique.
  
We want this board to remain a safe zone inclusive of all animals, complete or 
not.

Stuffed, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Jurgen Bosch
Sent: Thursday, November 28, 2019 13:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?

Think of completeness with an analogy to turkey.
Say you happen to find a one-legged turkey (incomplete by conventional 
standard) you could still stuff it and put it in the oven and enjoy 93% of the 
turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-)

Happy Thanksgiving everyone

Jürgen 



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Re: [ccp4bb] Xray-dataset usable despite low completeness ?

[Bernhard Rupp]

It has come to our attention that on this bulletin board insensitive and 
hurtful comments have 
been made towards animals with disability. Particularly concerning is the 
display of white privilege
and racial bias towards a minority individual  given that the turkey is also 
referred to in German as 'Indian'. 
In view of this non-inclusive and divisive display of unwokeness, the faculty 
Bias Response Team 
will contact you shortly and allow you to present your self-critique.
  
We want this board to remain a safe zone inclusive of all animals, complete or 
not.

Stuffed, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Jurgen Bosch
Sent: Thursday, November 28, 2019 13:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?

Think of completeness with an analogy to turkey.
Say you happen to find a one-legged turkey (incomplete by conventional 
standard) you could still stuff it and put it in the oven and enjoy 93% of the 
turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-)

Happy Thanksgiving everyone

Jürgen 

P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & Kartoffelknödel

> On Nov 28, 2019, at 4:38 PM, Bernhard Rupp  wrote:
> 
> Sorry for being late on this thread -
> 
> but the completeness myth is one of these conventional wisdoms I am 
> seriously questioning and completeness as a global statistic is almost 
> uninformative, short of telling you 'fewer than all recordable reflections up 
> to the reported (likely isotropic) resolution limit given whatever (likely 
> isotropic) cutoff was applied'. Sounds not very clear to me.
> 
> Kay mentioned already that any information is better than no 
> information, with the caveat that you cannot expect map quality (being 
> an upper limit for model quality - not going into precision vs 
> accuracy issue here) corresponding to the highest resolution reported, which 
> is in reality frequently anisotropic (but not reported or reflected 
> adequately in the PDB reports).
> We posted some remarks to this effect recently, pointing out that 
> highly incomplete and anisotropic data can still yield limited but 
> useful information as long as your claim remains correspondingly 
> modest. Section 3.4 in 
> http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html
> 
> Having said that, while random incompleteness is not problematic, 
> systematic reciprocal space incompleteness leads to corresponding 
> systematic real space effects on the map, the simplest being 
> anisotropic data reflecting anisotropic reciprocal map resolution. 
> This is different for example when wedges are missing or absence of serial 
> extinctions makes space group determination more challenging (although we are 
> almost in the age where 'record 360 deg of data and try every SG' works). 
> James Holton has video examples for incompleteness effects and some images 
> are also in my book.
> https://bl831.als.lbl.gov/~jamesh/movies/
> 
> Cheers & Happy Thanksgiving, BR
> 
> PS: A systemic rant regarding data quality representation can be found 
> here
> https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
> 
> --
> Bernhard Rupp
> http://www.hofkristallamt.org/
> b...@hofkristallamt.org
> --
> All models are wrong
> but some are useful.
> --
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kay 
> Diederichs
> Sent: Monday, November 25, 2019 08:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
> 
> Dear Matthias,
> 
> Of course, high completeness is better than low completeness.
> But as long as your low resolution is pretty much complete, there is no such 
> thing as "too low completeness" at high resolution. Each reflection adds 
> information to the map, and serves as a restraint in refinement.
> 
> best,
> Kay
> 
> 
> On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
>  wrote:
> 
>> Dear ccp4 Bulletin Board,
>> 
>> I collected a dataset at a synchrotron beamline and got the 
>> statistics
>> (CORRECT.LP) after processing (using xds) shown in the attached 
>> pdf-file.
>> 
>> Do you think this dataset is usable, due to its low completeness? As 
>> you can see in the attached file the completeness is just 50% in the 
>> highest resolution shell, whereas the I over Sigma is above 2 and 
>> also the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
>> Furthermore the overall statistic are good regarding R factor, CC 

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

[Bernhard Rupp]

Sorry for being late on this thread - 

but the completeness myth is one of these conventional wisdoms I am seriously 
questioning and completeness
as a global statistic is almost uninformative, short of telling you 'fewer than 
all recordable reflections up to the reported 
(likely isotropic) resolution limit given whatever (likely isotropic) cutoff 
was applied'. Sounds not very clear to me. 

Kay mentioned already that any information is better than no information, with 
the caveat that you cannot expect
map quality (being an upper limit for model quality - not going into precision 
vs accuracy issue here) corresponding to 
the highest resolution reported, which is in reality frequently anisotropic 
(but not reported or reflected adequately 
in the PDB reports). 
We posted some remarks to this effect recently, pointing out that highly 
incomplete and anisotropic data can still 
yield limited but useful information as long as your claim remains 
correspondingly modest. Section 3.4 in
http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html

Having said that, while random incompleteness is not problematic, systematic 
reciprocal space incompleteness leads
to corresponding systematic real space effects on the map, the simplest being 
anisotropic data reflecting anisotropic
reciprocal map resolution. This is different for example when wedges are 
missing or absence of serial extinctions makes
space group determination more challenging (although we are almost in the age 
where 'record 360 deg of data and 
try every SG' works). James Holton has video examples for incompleteness 
effects and some images are also in my book.
https://bl831.als.lbl.gov/~jamesh/movies/

Cheers & Happy Thanksgiving, BR

PS: A systemic rant regarding data quality representation can be found here
https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2

------
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
--
All models are wrong
but some are useful.
--

-Original Message-
From: CCP4 bulletin board  On Behalf Of Kay Diederichs
Sent: Monday, November 25, 2019 08:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?

Dear Matthias,

Of course, high completeness is better than low completeness.
But as long as your low resolution is pretty much complete, there is no such 
thing as "too low completeness" at high resolution. Each reflection adds 
information to the map, and serves as a restraint in refinement.

best,
Kay 


On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
 wrote:

>Dear ccp4 Bulletin Board,
>
>I collected a dataset at a synchrotron beamline and got the statistics
>(CORRECT.LP) after processing (using xds) shown in the attached 
>pdf-file.
>
>Do you think this dataset is usable, due to its low completeness? As 
>you can see in the attached file the completeness is just 50% in the 
>highest resolution shell, whereas the I over Sigma is above 2 and also 
>the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
>Furthermore the overall statistic are good regarding R factor, CC 1/2 
>and I over Sigma. The only problem seems to be the completeness. If I 
>would set the cut-off at a lower resolution to get good completeness, I 
>would throw away nearly half of my reflections.
>
>I'm happy to here your opinion. In Addition to that: The space group is 
>orthorhombic and the dataset was collected over 120° using fine slicing 
>(0.1°).
>
>
>Best regards,
>
>Matthias Oebbeke
>
>
>-- 
>Matthias Oebbeke, M.Sc.
>Research Group of Professor Dr. G. Klebe
>Institute of Pharmaceutical Chemistry
>Philipps-University Marburg
>Marbacher Weg 6, 35032 Marburg, Germany
>Phone: +49-6421-28-21392
>Mail: oebbe...@staff.uni-marburg.de
>www.agklebe.de
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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>



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[ccp4bb] Shelx and debian 10

[Bernhard Rupp]

Hi Fellows,

 

we updated to Debian 10 on the local workshop computers, and reinstalled

Coot and ccp4. All fine. 

 

Problem: Shelxc/d/e/  does not run, and

the call exits immediately sans any message.

 

This holds for the binaries included in ccp4 as well as for those from the
SHELX site.

The executables from CCP4 and SHELX site – same file size, probably same -
run fine under Debian 9.

 

I suspect a library problem.

 

Does some kind soul have CDE binaries for Debian 10 to share? 

 

Many thx in advance, BR

 




Bernhard Rupp

Department of Genetics and Pharmacology

Institute of Genetic Epidemiology 

Medical University Innsbruck

Schöpfstrasse 41

A 6020 Innsbruck – Austria

+43 (676) 571-0536

bernhard.r...@i-med.ac.at




k.k. Hofkristallamt

San Diego, CA 92084

001 (925) 209-7429

b...@ruppweb.org

b...@hofkristallamt.org

http://www.ruppweb.org/

---

 




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Re: [ccp4bb] A crystallisation screen pH query.

[Bernhard Rupp]

I would not take that for granted…see the comments by Tom Peat. It is easy to 
measure with some 

coarse and the fine strips both the unbuffered cocktail and drop pH – sometimes 
knowing the drop pH can be 

relevant for the physiological state. Mixing unbuffered cocktail and stock 
buffer also works

to give an initial idea.

 

LGBR

 

From: CCP4 bulletin board  On Behalf Of Jon Cooper
Sent: Sunday, October 6, 2019 00:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A crystallisation screen pH query.

 

Many thanks for the excellent replies. I am very happy with the value of 5.1 
which two of you kindly sent.

 

Best wishes

 

Jon Cooper

 

On 5 Oct 2019 22:51, Bob Cudney mailto:b...@hrmail.com> > 
wrote:

Hello Jon,

 

That JCSG+ reagent is a copy of Hampton Research PEG/Ion reagent 48.  While 
there is no pH adjustment made during the formulation of this reagent, the 20% 
w/v PEG 3350, 0.2 M Ammonium citrate dibasic in deionized water results in a 
measured pH at 25 degrees Celsius of 5.1.  The formulation as well as measured 
pH, refractive index, conductivity and other details can be found here 
https://hamptonresearch.com/product-PEG-Ion-PEG-Ion-2-PEG-Ion-HT-11.html under 
the Support Material(s).  Hope this helps.

 

Kind Regards, Bob Cudney

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Jon Cooper
Sent: Saturday, October 5, 2019 2:10 PM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: [ccp4bb] A crystallisation screen pH query.

 

Does anyone know the pH of JCSG+ condition A3 which is stated as 0.2 M ammonium 
citrate dibasic, 20% (v/v) PEG3350. I can't really measure it myself, so any 
help much appreciated!

 

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Re: [ccp4bb] Figure of merit in refinement

[Bernhard Rupp]

Hi Fellows,

I have tried to summarize these issues James raised, 

in consistent notation in Chapter 12 of BMC of which you can download an 
excerpt here:

https://www.dropbox.com/s/crzwoa5lb8bk3x5/Pages_611-619_from%20BMC_rupp_ch12.pdf?dl=0

> if your R factor is 55% then your phases probably aren't very good either. 

> The phases in your 2mFo-DFc map are identical to those of just an Fc map

> Sometimes you will get a 180 flip to keep the sign of the amplitude positive, 
> but that's it.  

The ultimate summary is in sidebar 12-3 at the end.

Hope this is useful, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

All models are wrong, 

but some are useful.

--

 

 

 




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Re: [ccp4bb] ITC question -dimer vs monomer

[Bernhard Rupp]

Thanks to All for the extended & informative responses. If true
thermodynamic equilibria

are realized, then I would agree that regardless of the pathway the endpoint
(or integrated H)

should be the same.  The actual pathway and cooperativity probably will make
this an 

interesting problem. I may keep bugging selected victims off-board once I
have the first data.

 

Many thanks again, BR

 

From: CCP4 bulletin board  On Behalf Of Barone,
Matthias
Sent: Thursday, October 3, 2019 18:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ITC question -dimer vs monomer

 

As Reza already pointed out, ITC cannot tell you anything about the
sub-processes that underlay an equilibrium, be it complicated like 2A+B2 <->
AB2 + A <-> A2B2, or with (virtually) no intermediate 2A+B2 <-> A2B2 due to
a fast second forward reaction , or a simple one-to-one model A+B2 <-> AB2. 

Given the lack of additional information, its probably good to assume a
simple one-to-one model and titrate either partner to the other.

If you have two separate binding steps (with similar Kd for B2 for A as well
as AB2 for A), you would measure an apparent affinity and would see the
stochiometrics according to  the inflection point (be it around equimolar
excess or at 0.5 or 2, depending on whether you titrate A or B). If the
reaction is more complicated and the the affinities for B2 for A differ
significantly much from the affinity of AB2 for A, then a simple one-to-one
would leave some notable information in the residual standard deviations
(meaning, the residuals would not spread normally around the Regression
line, but should show a wavy pattern). 

Sorry for the long mail..

Matthias

 

Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284

future.

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Bernhard Rupp
Sent: Thursday, October 3, 2019 11:06 AM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: [ccp4bb] ITC question -dimer vs monomer

 

Hi Fellows,

 

please let me ask the respective experts an ITC question: I have 2 proteins,
stable and dialyzed in identical buffer.

A is a monomer and B an obligate dimer. I suspect that eventually a A2B2
dimer will form.

 

Intuitively, it should make a difference whether I titrate the dimer with
the monomer or vice versa.

In the first case, a momomer would initially meet a lot of free dimers, and
I would expect that randomly, a AB2 complex

is more likely to form than a A2B2 (let’s disregard any more complex
colligative/cooperative effects).

 

If I drip the dimer into the monomer pool, it is quite likely that the B
dimer meets 2 free As, and I get right away a higher population of A2B2s.

 

Maybe at dilutions of ITC and with sufficient equilibration that is not an
issue at all (again, absent any cooperative effects that might alter the
first Kd vs. the second, despite the sites on the dimer are at least
initially equivalent).

 

Can someone guide me towards literature about this or perhaps share some
first-hand experience?

 

Many thanks, BR

 

--

Bernhard Rupp

http://www.hofkristallamt.org/
<https://urldefense.com/v3/__http:/www.hofkristallamt.org/__;!oCotSwSxbw8!SE
9mT6grUy1tHFSKLCraXt4bhlDri03OEMEyqQUCLAVSLsg3vwn0GTQtxbStgtNvxBs$> 

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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Re: [ccp4bb] ITC question -dimer vs monomer

[Bernhard Rupp]

I am not looking for anything yet - I wonder what - if any - the
consequences of doing it one way or the other would be.

I am reasonably certain that any difference affects the analysis.

 

Thx, BR

 

From: CCP4 bulletin board  On Behalf Of Keller, Jacob
Sent: Thursday, October 3, 2019 17:41
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ITC question -dimer vs monomer

 

I don't understand what you are trying to do-are you trying to show, by the
difference in ITC response, that the predictions you made about the
oligomerization are true?

 

JPK

 

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

Desk: (571)209-4000 x3159

Cell: (301)592-7004

+

 

The content of this email is confidential and intended for the recipient
specified in message only. It is strictly forbidden to share any part of
this message with any third party, without a written consent of the sender.
If you received this message by mistake, please reply to this message and
follow with its deletion, so that we can ensure such a mistake does not
occur in the future.

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Bernhard Rupp
Sent: Thursday, October 3, 2019 11:06 AM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: [ccp4bb] ITC question -dimer vs monomer

 

Hi Fellows,

 

please let me ask the respective experts an ITC question: I have 2 proteins,
stable and dialyzed in identical buffer.

A is a monomer and B an obligate dimer. I suspect that eventually a A2B2
dimer will form.

 

Intuitively, it should make a difference whether I titrate the dimer with
the monomer or vice versa.

In the first case, a momomer would initially meet a lot of free dimers, and
I would expect that randomly, a AB2 complex

is more likely to form than a A2B2 (let's disregard any more complex
colligative/cooperative effects).

 

If I drip the dimer into the monomer pool, it is quite likely that the B
dimer meets 2 free As, and I get right away a higher population of A2B2s.

 

Maybe at dilutions of ITC and with sufficient equilibration that is not an
issue at all (again, absent any cooperative effects that might alter the
first Kd vs. the second, despite the sites on the dimer are at least
initially equivalent).

 

Can someone guide me towards literature about this or perhaps share some
first-hand experience?

 

Many thanks, BR

 

--

Bernhard Rupp

http://www.hofkristallamt.org/
<https://urldefense.com/v3/__http:/www.hofkristallamt.org/__;!oCotSwSxbw8!SE
9mT6grUy1tHFSKLCraXt4bhlDri03OEMEyqQUCLAVSLsg3vwn0GTQtxbStgtNvxBs$> 

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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[ccp4bb] ITC question -dimer vs monomer

[Bernhard Rupp]

Hi Fellows,

 

please let me ask the respective experts an ITC question: I have 2 proteins,
stable and dialyzed in identical buffer.

A is a monomer and B an obligate dimer. I suspect that eventually a A2B2
dimer will form.

 

Intuitively, it should make a difference whether I titrate the dimer with
the monomer or vice versa.

In the first case, a momomer would initially meet a lot of free dimers, and
I would expect that randomly, a AB2 complex

is more likely to form than a A2B2 (let's disregard any more complex
colligative/cooperative effects).

 

If I drip the dimer into the monomer pool, it is quite likely that the B
dimer meets 2 free As, and I get right away a higher population of A2B2s.

 

Maybe at dilutions of ITC and with sufficient equilibration that is not an
issue at all (again, absent any cooperative effects that might alter the
first Kd vs. the second, despite the sites on the dimer are at least
initially equivalent).

 

Can someone guide me towards literature about this or perhaps share some
first-hand experience?

 

Many thanks, BR

 

--

Bernhard Rupp

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Reg: water pentagon at dimer interface

[Bernhard Rupp]

Indeed they have been observed in quite a number of high resolution structures.

http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-28.htm

 

Chees, BR

 

From: CCP4 bulletin board  On Behalf Of Ronald E. 
Stenkamp
Sent: Friday, September 27, 2019 17:22
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Reg: water pentagon at dimer interface

 

I don’t know about the myth thing, but I remember Martha Teeter describing 
pentagons of waters in crambin.

 

Here’s a reference:

 

Water Structure of a Hydrophobic Protein at Atomic Resolution: Pentagon Rings 
of WaterMolecules in Crystals of Crambin  M. M. Teeter  Proceedings of 
the National Academy of Sciences of the United States of America, 1984, 81(1), 
6014-6018.

 

Ron 

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Vijaykumar Pillalamarri
Sent: Friday, September 27, 2019 4:34 AM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: [ccp4bb] Reg: water pentagon at dimer interface

 

Dear Community,

 

I solved the structure of a protein from vibrio. There are two molecules in the 
asymmetric unit of this protein. At the dimer interface, the C-termini of both 
the chains interact with each other with the help of five water molecules that 
form a pentagon. I have attached an image showing both the chains and stereo 
image of dimer interface in the inset. I was wondering if there is any 
significance to this or if there is any relevant literature that explains this 
behavior.

 

Thank you

Vijaykumar Pillalamarri

C/O: Dr. Anthony Addlagatta

Principal Scientist

CSIR-IICT, Tarnaka

Hyderabad, India-57

Mobile: +918886922975

 

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Re: [ccp4bb] Secrets of ZYMIT

[Bernhard Rupp]

Well, trade secret means exactly what it says. We were equally unable to
extort it from the suppliers.

MS fragment search as suggested might work. 

 

Best, BR 

 

From: CCP4 bulletin board  On Behalf Of Jorg
Stetefeld
Sent: Monday, September 9, 2019 00:02
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Secrets of ZYMIT

 

Hi everyone, 

 

this is Joerg Stetefeld. 

 

I would like to approach the community in a peculiar case of a specific
proteolytic cleavage during crystallization attempts.

Performing several crystallization screens we figured out that ZYMIT
(https://www.ipcol.com/cleaners/zymit-low-foam) is the reason for a highly
specific, but undesireable cleavage of protein components in our setups.
Most remarkably, the cleavage site of our crystallisation target is not
described in any protease database, and is highly inaccessible.

 

 

According to a publication by Naschberger et al, 2014
(doi:10.1107/S2053230X14026053) the authors very nicely describe the
phenomenon. They also describe a very elegant protease removal protocol,
which works in our hands very well. 

At this point, however, I would like to know what is “behind” ZYMIT?
Naschberger et al say “Zymit contains an unspecified‘protease enzyme’ as a
trade secret ( 
http://www.ipcol.com/pdfs/Zymit_msds.pdf)”.

 

Does anyone has more insight into the secrets of ZYMIT? Our attempts to
contact several vendors here in Canada/ abroad failed and a further
characterisation of its nature would help us to understand this particular
phenomenon of proteolytic cleavage.

 

 

Thank you very much in advance- Your advise is appreciated. 

 

js 

 

 

 

 

Jörg Stetefeld

 

https://stetefeldlab.ca/

 

 

 

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[ccp4bb] Disable Phaser anisotropy correction in ccp4i classic

[Bernhard Rupp]

Hi Fellows,

 

for some testing purposes, I'd like to globally disable the Phaser
anisotropy correction 

(without messing anything else up) in MR mode using the classic ccp4i
interface

(not the i2). Do I need to go to the developer options and 

select 'custom', 'anisotropy off' and 'cycles 0'  - or is there a simpler 

external keyword or MODE command I can supply?

 

Many thanks, BR

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

[Bernhard Rupp]

One practically HAS to do what Dale describes. The sigma levels of a difference 
map peak depends on how much it is above the mean noise level of the map. With 
high resolution (and given a cooperating molecule) it is very likely that the 
model is very good and complete, thus low mean map noise level, and anything 
missing will create huge peaks. A forgotten water molecule then can easily have 
difference peak (sigma not absolute) levels in the 20s... 

Best, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Dale Tronrud
Sent: Tuesday, August 6, 2019 00:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

   One thing to remember is that Li+ only has two electrons.  It should be a 
little more than twice the density of an hydrogen (because the charge pulls in 
the electron cloud).  If you are seeing lithium at 8 "sigma" you should be 
seeing the well located hydrogen atoms at 4 "sigma".  Are you?

   I always like controls.  Take out one of the near by water molecules and see 
how that, known, difference peak compares to your mystery peak.
 A Li+ should have about 1/5th the height of an H2O.  If you like the 
hypothesis of two orientations of the PO4 group, the relative height of the two 
peaks will give insight to the occupancy ratio.

   Remember, if the PO4 has two orientations in the crystal, the water 
molecules it (they?) is/are bound to will likely also have alternatives.

Dale Tronrud

On 8/5/2019 6:05 AM, Maria Håkansson wrote:
> Dear CCP4 bulletin board,
> 
> I am working with some lytic enzymes called endolysines, which bind 
> Zn2+ in the active site. I have three homologues protein determined to 
> 1.2 Å each where the Zn2+ is bound to a cystein, two histidines and 
> one phosphate ion added (1.9-2.3 Å binding distances) in the 
> crystallization experiment.
> 
> Now to my question. Close to the phosphate (B-factor=20Å2) ion a 8 
> sigma peak is present in all three endolysines, see below.
> I have modeled it to a Na+ (B-factor= 30 Å2) or a Li+ (B factor = 
> 13Å2) ion.
> Sodium has benn added in the crystallization experiments since sodium 
> potassium phosphate salt has been used. The only reason for including 
> Li+ is that I think the binding distances (1.7-2.0 Å) are too short 
> for Na+.
> 
> I have also tried to make a model with the phosphate in two different 
> conformations but it does not fit.
> 
> Have anyone seen something similar before? What is the most correct 
> way of dealing with unknown densities?
> It is difficult to disregard +8 sigma difference density close to the 
> active site.
> 
> Thanks in advance for any help!
> 
> Best regards,
> Maria
> 
>  
> 
> Maria Håkansson, PhD, Crystallization Facility Manager Principal 
> Scientist
> 
> SARomics Biostructures AB
> Medicon Village
> SE-223 81 Lund, Sweden
> 
> Mobile: +46 (0)76 8585706
> Web: www.saromics.com 
> 
> 
> 
> 
> 
> --
> --
> 
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[ccp4bb] Listserv problem

[Bernhard Rupp]

Dear Guardians of the List:

 

I have been banned from the ccp4bb due to some temporary delivery problems

and I cannot subscribe anymore - can someone please contact me off board
please?

Thx, BR

 

--

Bernhard Rupp

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] challenges in structural biology

[Bernhard Rupp]

> What about 'deep learning' applied to crystallization outcomes? Can it guide 
> individual trials better than intuition? Can it find previously unknown 
> promising combinations on a larger scale?

I think several people were well aware of this need for some sort of sound 
machine learning already 15 years ago but we had no cloud based AI
services thenmaybe it is time to pick this up - particularly if face 
recognition can classify the fine detail in faces maybe we finally could do 
this with drop images as well...

A summary of the state of affairs then is here:
http://www.ruppweb.org/cvs/br/rupp_2004_methods_predictive_models_crystallization.pdf

LG BR


Am 21.07.19 um 23:04 schrieb Artem Evdokimov:
> Dear Kay
>  
> 
> I disagree that 'magic bullet' is impossible. I think the definition is wrong 
> here - magic bullet to me is a rational set of methods that (when executed 
> with precision and care) enable crystallization to the maximum possible 
> benefit. This includes everything - constructs, crystallization design, etc. 
> Part of the magic bullet is also a precise knowledge when crystallization is 
> unlikely (i.e. an actual proven predictor that consistently discriminates 
> between "you're going to succeed if you work hard" and "it's doomed to fail, 
> don't bother" scenarios in crystallization.
> 
> The above is not sexy. It does not present itself as a lovely subject on 
> which to have international cocktail parties with politicians delivering 
> fancy speeches. But that is what is needed, and no one is funding that to the 
> best of my knowledge.
> 
> What needs to be done is a significant amount of testing, standardization, 
> and methods development from the perspective of holistic outcome (i.e. 
> crystals that work) - and none of the previously advertised 'magic bullets' 
> work the way I just described.
> 
> Having written this, I think you're right - this is a bit of a distraction 
> from James' original point. However it's a valid opportunity for a lively 
> discussion on its own :)
> 
> Artem
> 
> - Cosmic Cats approve of this message
> 
> 
> On Sun, Jul 21, 2019 at 4:52 PM Kay Diederichs 
> mailto:kay.diederi...@uni-konstanz.de>> 
> wrote:
> 
> Dear Artem,
> 
> black or white is not my way of thinking, which is why I don't believe in 
> Hannibal's approach when it comes to crystallization.
> 
> None of the magic bullets that were advertised over the past decades have 
> proven generally applicable.  I believe more in incremental improvement which 
> in this case includes a few biophysical characterization methods, possibly 
> improved microfluidics or other apparatus, and expanded screens. And a lot of 
> hard work, perseverance, intuition, frustration
>  tolerance. Nothing that really needs huge funding - of course it does 
> need money, but just a  share of what is anyway needed for the usual lab work 
> including expression, purification, functional characterization, binding 
> studies and the like.
> 
> One area where a huge amount of money was burnt is crystallization in 
> space, on board of e.g. the spacelab and ISS. This is for me an example of a 
> mis-led approach to throw money at a difficult problem, with the expectation 
> of a solution. Science does not work like that, and money in this case seems 
> more to be the problem than the solution.
> 
> This example may illustrate a certain failure of us scientists to resist 
> the temptation to promise unrealistic outcomes when confronted with money 
> provided for political reasons, which ultimately undermines our credibility. 
> But this takes us away from James' points.
> 
> best,
> 
> Kay
> 
> On Sun, 21 Jul 2019 16:06:48 -0400, Artem Evdokimov 
> mailto:artem.evdoki...@gmail.com>> wrote:
> 
> >Dear Kay,
> >
> >Even the small, badly diffracting and 'messed up' crystals are still
> >crystals. There is literally a phase transition (pun very much intended)
> >between growing *usable crystals* versus *having no crystals* (or having
> >crystals that do not qualify as 'diffraction quality' even under the most
> >favorable light). Points 2-9 fall into the 'I have crystals' bucket and
> >everything else is in the 'I have no crystals' bucket.
> >
> >I am being deliberately black and white of course.
> >
> >As to whether huge funding would help to bridge the 'phase gap' - to me
> >this is a purely theoretical question since to the best of my knowledge
> >there never was a 'huge funding' for this particular problem :) And if it
> >is true that the general belief in the art is that crystallization is not
> >worth investing into because there's no hope in it then of course it is a
> >self-fulfilling prophesy.
> >
> >There is an unresolved dichotomy buried in the sentiment above: it seems
> >that we (the community of structural biologists) more or less believe 
> that
> >crystallization research is not 

Re: [ccp4bb] Density questionable?

[Bernhard Rupp]

> Could there be two versions of each model: a "robustly-observed" and a
"most-likely" version?

We tried/suggested something in this spirit once. Not sure how it was
received
http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html

Best, BR
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

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-Original Message-
From: CCP4 bulletin board  On Behalf Of Peer Mittl
Sent: Monday, July 22, 2019 6:05 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Density questionable?

Dear Colleagues,

We are working on a structure where the density for a whole protein chain
(>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3 Ang
resolution). However, the initial difference density map and the feature
enhanced map (normal 2fo-fc map to a minor extend) support the presence of
this chain. Putting the chain seems equally wrong as not putting it. Putting
it reduces Rfree by 0.3%. As a conservative researcher I feel tempted to
deposit the structure without this highly mobile/weakly occupied chain, but
other researchers may say "he has missed something". Handling this chain
like a weakly occupied water is probably wrong, but what is the
optimal/correct way? Is there a general opinion on how the escape this
dilemma?

All the best,
Peer



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Re: [ccp4bb] SA_flag vs PDB

[Bernhard Rupp]

Hmm….this is all a mess. 

 

If the objective is that the users can generate the EXACT map the depositor 
saw, I agree, the output of the Refmac mtz file with the map coefficients would 
be good.

 

Alas, no can do, because the Fs are not the same as in the input file, if I am 
understanding this correctly – reportedly Refmac does something (which is?) to 
them before it dumps them into the output mtz.

 

So I deposit the SA file xyz-staraniso-merged-aniso _free.mtz to get closer to 
the data I used to input into refmac. Bad boy:

 

(a) no can do, PDB no eat SA_flag. Maybe because the FreeR_flag is added as a 
second data set to the xyz-staraniso-merged-aniso.mtz. Ok, fixable.

 

(b) no should do, because we actually want unmerged untruncated and unalterted 
I(obs) – which I agree - and with the XDS_whatever.HKL as close as I can get 
it. 

 

Seems we need a file description that includes all the desired items, and a 
little program the can harvest all that in a single cif file. As I put the 
ASCII XDS*.HKL

file into StarAniso, there seems to be the perfect pre-processing site for all 
our desires. This SuperStar.mtz file then would additionally need only the map 
coefficients for the reflections

actually used by Refmac to generate the map. Might well be that such does 
already exist as some sort of intermediate file. PDB_REPROCESS could take the 
unmerged HKL, process, and F-convert if desired, PDB_REDO could use these data 
then (or the I’s/F’s from SuperStar.mtz). I am sure this does not cover every 
conceivable combination, but it’s worth a discussion. Not that it could ever 
move through glacial committees….

 

In any case, I provide a link to the images for REDO_THE_DARN_JOB_YOURSELF. 

 

Cheers, BR

 

PS: About the deposition read errors on mmcif files later.

 

From: Ian Tickle  
Sent: Monday, July 15, 2019 3:00 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] SA_flag vs PDB

 

 

Hi Bernhard

 

Oh dear, yes that's quite possible.

 

But in any case we recommend _not_ to deposit the output from STARANISO:

 

http://staraniso.globalphasing.org/deposition_about.html

 

Cheers

 

-- Ian

 

 

Cheers

 

-- Ian

 

 

On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Hi Fellows – 

 

wondering if there is a particular reason the PDB cannot process a mtz file 
that in addition to FreeR_flag includes a SA_Flag column from StarAniso?

Can there be no more than one I column type because that is automatically 
interpreted as the free flag??

 

Best, BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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[ccp4bb] SA_flag vs PDB

[Bernhard Rupp]

Hi Fellows - 

 

wondering if there is a particular reason the PDB cannot process a mtz file
that in addition to FreeR_flag includes a SA_Flag column from StarAniso?

Can there be no more than one I column type because that is automatically
interpreted as the free flag??

 

Best, BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] beryllium chloride

[Bernhard Rupp]

The older fellows might well remember the huge Be windows on the ADSC 
multi-wire detectors – 

miraculously we survived them simply by common sense dictating 

(i) don’t eat it, (ii) don’t breathe it,  and (iii) don’t rub your nose in it…. 

 

Cheers, BR

 

 

From: CCP4 bulletin board  On Behalf Of Ian Tickle
Sent: Tuesday, April 2, 2019 5:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

 

 

Yes both soluble beryllium salts and powdered beryllium metal even applied to 
the skin are known to cause sensitization and is a route into the bloodstream 
where it is highly carcinogenic (I am not speaking from experience!).

 

Yet strangely the one source of beryllium that many people (at least the more 
well-off among us) commonly come into contact with, namely the gemstone emerald 
Be3Al2(SiO3)6 obviously has no known toxic effects whatosever!  Apparently even 
gemstone grinders show no ill effects!  I guess it's the free Be2+ ion that's 
so toxic.

 

Cheers

 

-- Ian

 

 

 

On Tue, 2 Apr 2019 at 13:07, Aaron Finke mailto:af...@cornell.edu> > wrote:

1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl- 

 

2. Bob, I studied that page, and couldn’t get past  BeCl2 is known to have a 
“sweetish taste.” I’m very glad chemists no longer characterize chemicals by 
their taste anymore...

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu  


On Apr 1, 2019, at 22:37, Sweet, Robert 
<27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk 
 > wrote:

With all respect, this conversation make my skin crawl a little. I've been 
taught that beryllium salts are EXTREMELY toxic.  Please study this: 
https://pubchem.ncbi.nlm.nih.gov/compound/beryllium_chloride

 

Hopefully, 

 

Bob

 



  Robert M. Sweet   E-Dress:  sw...@bnl.gov 
 

  Deputy Director, LSBR: The Life Science and 

   Biomedical Technology Research Center at NSLS-II 

  Photon Sciences and Biology Dept

  Brookhaven Nat'l Lab. 

  Upton, NY  11973 U.S.A.  

  Phones:631 344 3401  (Office)

 631 338 7302  (Mobile)



 


  _  


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Diana Tomchick mailto:diana.tomch...@utsouthwestern.edu> >
Sent: Monday, April 1, 2019 7:03 PM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] beryllium chloride 

 

No, that should read  

 



 

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 Apr 1, 2019, at 5:54 PM, Keller, Jacob mailto:kell...@janelia.hhmi.org> > wrote:

 

Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion 
with such a charge, well except things like DNA and proteins, but not single 
atoms.

 

JPK

 

+

Jacob Pearson Keller

Research Scientist / Looger Lab

HHMI Janelia Research Campus

19700 Helix Dr, Ashburn, VA 20147

Desk: (571)209-4000 x3159

Cell: (301)592-7004

+

 

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

 

From: CCP4 bulletin board <  
CCP4BB@JISCMAIL.AC.UK> On Behalf Of Aaron Finke
Sent: Monday, April 1, 2019 6:45 PM
To:   CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] beryllium chloride

 

American Elements sells BeCl2 but you’d have to check with them on what scale 
they sell it at. They tend to do custom manufacturing.  

 

  
https://www.americanelements.com/beryllium-chloride-7787-47-5

 

BeCl2 dissociates in aqueous solution to form Be(H2O)4+ 2Cl-. 

 

Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail:   af...@cornell.edu


On Apr 1, 2019, at 17:07, Alexandra Deaconescu < 
 alexandra_deacone...@brown.edu> wrote:

Hello,

Is anyone aware of a company that sells Beryllium chloride in the US? Sigma 
does not carry it any longer, and a quick Google search failed to 

Re: [ccp4bb] Against method: some warnings about model validation

[Bernhard Rupp]

Its still 31st here!

-Original Message-
From: Paul Emsley  
Sent: Sunday, March 31, 2019 6:59 PM
To: b...@hofkristallamt.org
Subject: Re: [ccp4bb] Against method: some warnings about model validation

On 01/04/2019 02:55, Bernhard Rupp wrote:
> I think we can be more specific here: Validation without electron density.
> 
> One cannot wisecrack from the coordinates only.
> 
> Otherwise this will be taken as a carte banc against any sort of validation.

An awful lot of effort for a weird joke, I thought.

P.



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Re: [ccp4bb] Against method: some warnings about model validation

[Bernhard Rupp]

I think we can be more specific here: Validation without electron density. 

One cannot wisecrack from the coordinates only.

 

Otherwise this will be taken as a carte banc against any sort of validation.

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Robbie Joosten
Sent: Sunday, March 31, 2019 2:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Against method: some warnings about model validation

 

Dear CCP4bb-ers, 

 

I'm posting this paper on behalf of Gert Vriend. We need to be critical of 
validation in times like these.

 

Cheers,

Robbie

 

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Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

[Bernhard Rupp]

Hi Fellows,

I'd really like to emphasize the point in the Buster instructions "be
careful when
examining fo-fc at low levels" when solvent is excluded. If the solvent
contribution
is omitted where you suspect the ligand (e.g. occupancy 0.02 in Refmac),
there 
will be a fo contribution there from the solvent that is there.
Particularly if that solvent is a
dense solution, that fo component will show up nicely and at not so low
difference 
map levels, and in the shape of that 'excluded' ligand. 

Figure 2 in link illustrates that. 
https://febs.onlinelibrary.wiley.com/doi/epdf/10./febs.14320

If you start to fill that void with multiple ligands of various low
occupancies, you
are effectively modelling disordered solvent. This is particularly tempting
because 
I found multiple cases where the classical RSR and RSCC measures give 
acceptable stats for such models. The hunt for low occupancy ligands then
quickly 
becomes murky density fishing business...
  
Best, BR


-Original Message-
From: CCP4 bulletin board  On Behalf Of Clemens
Vonrhein
Sent: Friday, February 8, 2019 09:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to
generate Polder maps?

Dear Samuel,

On Mon, Feb 04, 2019 at 11:39:58AM +, Samuel Davis (PG Research) wrote:
> I'm wondering if anyone knows if it is possible to turn off the bulk 
> solvent modelling in Refmac5, for the purpose of generating Polder 
> maps? I know that an option for Polder maps is directly implemented in 
> Phenix, but we ideally want to use Refmac5, as we have used it for the 
> rest of our refinement and want to keep it consistent if possible.

And if you want to try the original implementation of the underlying idea as
an alternative, have a look at the ligand detection mode and maps [1]
produced by BUSTER [2]. See also [3] and some early examples of their
usefulness [4-5].

Cheers

Clemens

[1] https://www.globalphasing.com/buster/wiki/index.cgi?LigandDetectionModes
[2] https://www.globalphasing.com/buster/
[3] Vonrhein, C., & Bricogne, G. (2005). "Automated Structure
Refinement for High-throughput Ligand Detection with
BUSTER-TNT". Acta Crysta A61, C248.
[4] Thoma, Ralf, et al. "Insight into steroid scaffold formation from
the structure of human oxidosqualene cyclase." Nature 432.7013
(2004): 118.
[5] Ekroos, Marika, and Tove Sjogren. "Structural basis for ligand
promiscuity in cytochrome P450 3A4." Proceedings of the National
Academy of Sciences 103.37 (2006): 13682-13687.

-- 

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



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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

[Bernhard Rupp]

The most trivial procedure is probably to generate the symmetry mates in
Coot

(color by symop makes selection easier), pick the ones completing your known
biological 

assembly, and saving those using File/Save Symmetry Coordinates.

 

Once you have the correct model you can superimpose the dimers in Coot and
read the DCM and

the translation vector - if that is what you want. If you click any of the
atoms in a symop-ed

molecule, you get the crystallographic operator and translation. 

 

If you want the crystallographic symops in symbolic and matrix format, you
can use

http://www.ruppweb.org/new_comp/spacegroup_decoder.htm

Standard settings only.

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Klontz, Erik
Sent: Saturday, February 2, 2019 22:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Generating rotation/translation matrices for biological
assemblies

 

Hi all, 

 

I'm working on a protein that I believe is tetrameric based on AUC, gel
filtration, and crystallography. However, although my asymmetric unit has 4
chains, I cannot form the tetramer within the asymmetric unit. Instead, the
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is
completed by pairing up with another half-tetramer from a symmetry mate. If
I load this structure into PISA, it recognizes that each of the 'dimers'
forms a stable assembly, but cannot seem to assemble the tetramer. However,
if I the generate symmetry mates in pymol to create a new PDB for the
biological tetramer and give this to PISA, it recognizes a stable tetramer.

 

Specifically, chains A and C in the original PDB pair with chains A and C of
the second symmetry mate generated in pymol, while chains B and D in the
original pair with chains B and D of the third symmetry mate. How do I use
this knowledge to generate a 3x4 rotation with translation matrix for PDB
deposition?

 

Thanks, 
Erik Klontz

 

 

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