Re: [ccp4bb] (R)MS

[zbyszek]

B-factors are definitely a measure of uncertainty in variance (square) 
units. The crystal lattice has multiple occurrence of the atoms that are 
equivalent by crystal symmetry. They will have the same fractional 
coordinates within the uncertainty of their position relative to the 
crystal lattice orientation definition. B-factors are the measure of 
this uncertainty (variance) in somewhat unusual units (Angstrom squared 
/ (8*pi*pi)). The fact that you can directly measure uncertainty by 
observing the width of the profile of the atomic distribution (shape of 
the uncertainty function) does not negate that this function represents 
uncertainty of atomic position relative to the crystal lattice.


As a comment: uncertainty of the centroid of the uncertainty 
distribution is a second order or recursive uncertainty. As this 
centroid is deposited as atomic coordinates in pdb files, its 
uncertainty is a separate subject from the uncertainty (variation) of 
the atom position in the crystal lattice. Unfortunately theories of 
uncertainty estimates of uncertainty estimates is more complex and for 
this reason crystallographers rarely deal productively with uncertainty 
of the x,y,z coordinates deposited.


A second comment: the B-factor really represents the sum of two 
uncertainties. One is the uncertainty of atom positions in the crystal 
lattice. The second is our experimental uncertainty about the knowledge 
of atom position. The first one has a physical interpretation. The 
second represents our data and analysis, e.g. phasing.


For these reasons, saying that the B-factor represents uncertainty 
estimates is very productive because it is all about uncertainty. 
Independent uncertainties are convolved with each other to produce a 
final uncertainty function. In terms of the width squared of that 
function, it represents the sum of the widths squared of the 
contributors. In fact this observation is behind the Central Limit 
Theorem.


Zbyszek

On 2021-05-28 19:05, James Holton wrote:

I feel I should point out here that B-factors are NOT a measure of
uncertainty.  They are a width.  This width itself may be uncertain,
as may be the position of the center of the peak, but just because
your peak is broad doesn't mean you don't know where the middle of it
is.

As for why leave the mean variation squared?  I expect it is because
it is supposed to be proportional to temperature. Hence the name
"temperature factor".

-James Holton
MAD Scientist

On 5/27/2021 11:09 AM, Gergely Katona wrote:


Dear Jonathan,

In 1D sd may be intuitive, but in 3D it is not so much. The square
root of a symmetric covariance matrix is not universally defined and
it is not intuitive to me.

Best wishes,

Gergely

Gergely Katona, Professor, Chairman of the Chemistry Program Council


Department of Chemistry and Molecular Biology, University of
Gothenburg

Box 462, 40530 Göteborg, Sweden

Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910

Web: http://katonalab.eu, Email: gergely.kat...@gu.se

From: CCP4 bulletin board  On Behalf Of
Hughes, Jonathan
Sent: 27 May, 2021 18:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] (R)MS

hey!

thank y'all for the informative (and swift!) answers! but, if the B
factor (as defined) appears in a mathematical formulation, that
doesn't make it an "appropriate" parameter for mobility/uncertainty.
wouldn't √B be better, in the same way that, for humans, standard
deviation (RMSD) is a more appropriate parameter of variability than
variance? or am i missing something?

cheers

j

Von: Ian Tickle 
Gesendet: Donnerstag, 27. Mai 2021 18:32
An: Hughes, Jonathan 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] (R)MS

Hi Jonathan

It's historical, it's simply how it appears in the expression for
the Debye-Waller factor, i.e. exp(-B sin^2(theta)/lambda^2).  So it
must have the same units as lambda^2.

Cheers

-- Ian

On Thu, 27 May 2021 at 13:25, Hughes, Jonathan
 wrote:

o yes! but maybe the crystal people could explain to me why the B
factor is the variance (with units of Ų) rather than the standard
deviation (i.e. RMS, with units of Å) when, to my simple mind, the
latter would seem be the more appropriate description of variability
in space?

cheers

jon

Von: CCP4 bulletin board  Im Auftrag von
Pearce, N.M. (Nick)
Gesendet: Donnerstag, 27. Mai 2021 12:38
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Analysis of NMR ensembles

If you want something comparable to B-factors don’t forget to put
the MSF in the B-factor column, not the RMSF. Will change the
scaling of the tube radius considerably!

Nick

On 27 May 2021, at 11:16, Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

Cool…

Purely for visualisation this does look like the approved CCP4 way -




Harry

On 27 May 2021, at 10:01, Stuart McNicholas
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:

Drawing style (right menu in display table) -> Worm scaled by ->
Worm
scaled by NMR variability

Re: [ccp4bb] (R)MS

[James Holton]

I feel I should point out here that B-factors are NOT a measure of 
uncertainty.  They are a width.  This width itself may be uncertain, as 
may be the position of the center of the peak, but just because your 
peak is broad doesn't mean you don't know where the middle of it is.


As for why leave the mean variation squared?  I expect it is because it 
is supposed to be proportional to temperature. Hence the name 
"temperature factor".


-James Holton
MAD Scientist

On 5/27/2021 11:09 AM, Gergely Katona wrote:


Dear Jonathan,

In 1D sd may be intuitive, but in 3D it is not so much. The square 
root of a symmetric covariance matrix is not universally defined and 
it is not intuitive to me.


Best wishes,

Gergely

Gergely Katona, Professor, Chairman of the Chemistry Program Council

Department of Chemistry and Molecular Biology, University of Gothenburg

Box 462, 40530 Göteborg, Sweden

Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910

Web: http://katonalab.eu, Email: gergely.kat...@gu.se

*From:*CCP4 bulletin board  *On Behalf Of 
*Hughes, Jonathan

*Sent:* 27 May, 2021 18:53
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] AW: [ccp4bb] (R)MS

hey!

thank y'all for the informative (and swift!) answers! but, if the B 
factor (as defined) appears in a mathematical formulation, that 
doesn't make it an "appropriate" parameter for mobility/uncertainty. 
wouldn't √B be better, in the same way that, for humans, standard 
deviation (RMSD) is a more appropriate parameter of variability than 
variance? or am i missing something?


cheers

j

*Von:*Ian Tickle mailto:ianj...@gmail.com>>
*Gesendet:* Donnerstag, 27. Mai 2021 18:32
*An:* Hughes, Jonathan >

*Cc:* CCP4BB@JISCMAIL.AC.UK 
*Betreff:* Re: [ccp4bb] (R)MS

Hi Jonathan

It's historical, it's simply how it appears in the expression for the 
Debye-Waller factor, i.e. exp(-B sin^2(theta)/lambda^2).  So it must 
have the same units as lambda^2.


Cheers

-- Ian

On Thu, 27 May 2021 at 13:25, Hughes, Jonathan 
> wrote:


o yes! but maybe the crystal people could explain to me why the B
factor is the variance (with units of Ų) rather than the standard
deviation (i.e. RMS, with units of Å) when, to my simple mind, the
latter would seem be the more appropriate description of
variability in space?

cheers

jon

*Von:*CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von *Pearce, N.M. (Nick)
*Gesendet:* Donnerstag, 27. Mai 2021 12:38
*A**n:*CCP4BB@JISCMAIL.AC.UK 
*Betreff:* Re: [ccp4bb] Analysis of NMR ensembles

If you want something comparable to B-factors don’t forget to put
the MSF in the B-factor column, not the _R_MSF. Will change the
scaling of the tube radius considerably!

Nick

On 27 May 2021, at 11:16, Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk
> wrote:

Cool…

Purely for visualisation this does look like the approved CCP4
way -



Harry

On 27 May 2021, at 10:01, Stuart McNicholas
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk
> wrote:

Drawing style (right menu in display table) -> Worm scaled
by -> Worm
scaled by NMR variability

in ccp4mg?

This changes the size of the worm but not the colour.

On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk
> wrote:


Anyway, thanks to all those who answered my original
question - especially

       Tristan: Chimerax (+ his attached script)
       Michal, Scott: Theseus
(https://theobald.brandeis.edu/theseus/
)
       Bernhard: Molmol
(https://pubmed.ncbi.nlm.nih.gov/8744573/
)
       Rasmus CYRANGE
(http://www.bpc.uni-frankfurt.de/cyrange.html
) and
https://www.ccpn.ac.uk/ (of
course…)
       Andrew (uwmn - not sure if this is buildable on
a modern box)
       Smita: PyMol (not sure if I’m allowed to say
that on ccp4bb…)

or I could script it and use Gesamt or Superpose for
the superposition if I wanted to stay in the ccp4
universe and had the time to spare ;-)

[ccp4bb] Research Associate position at SSRL-SMB

[Artem Lyubimov]

The Structural Molecular Biology (SMB) Division at the Stanford Synchrotron
Radiation Lightsource (SSRL) is seeking a Research Associate with a strong
background in X-ray diffraction data processing and/or software
development. A successful candidate will work with an interdisciplinary
group of crystallographers, engineers, and software developers on
analytical pipelines and frameworks for processing large volumes of
crystallographic data at SSRL, with emphasis on serial crystallography.

Note: This is a 2-year termed PhD-level appointment.

See the full job posting here:
https://erp-hprdext.erp.slac.stanford.edu/psp/hprdext/EMPLOYEE/HRMS/c/HRS_HRAM_FL.HRS_CG_SEARCH_FL.GBL?Page=HRS_APP_JBPST_FL=U=Applicant=1=4476=1

If you have any questions about the position, please contact Art Lyubimov (
lyubi...@stanford.edu) or Aina Cohen (aco...@slac.stanford.edu).



-- 
Art Lyubimov, PhD
Staff Scientist
SSRL SMB Crystallography
2525 Sand Hill Road mail stop 99
Menlo Park, CA 94025-7015
(415) 325-2057



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Re: [ccp4bb] Analysis of NMR ensembles

[John R Helliwell]

Dear Rasmus,
Thankyou for your very useful summary of NMR being “more complex than 
flexibility”.
The complementary roles of NMR and crystallography are important and I very 
recently provided a resume in section 2.3 of my Acta Cryst A article 
https://journals.iucr.org/a/issues/2021/03/00/ae5100/index.html 
which I imagine will be of keen interest.
The IUCr has established a Commission on NMR Crystallography and Related 
Methods:- https://www.iucr.org/iucr/commissions/nmr-crystallography 
Best wishes,
John 

Emeritus Professor John R Helliwell DSc




> On 27 May 2021, at 10:35, Rasmus Fogh  wrote:
> 
> Dear Dale,
> 
> It is more complex than just 'flexibility', but then it is always more 
> complicated. Here are the main possibilities for undetermined regions:
> 
> -1- fast, free movement - signals are easy to see, have 'random-coil' 
> chemical shifts, often overlap, and there are no  NOEs
> -2-  intermediate-range exchange between several different conformations, 
> free/bound etc. Signals are broadened and harder to observe, NOEs even more 
> so.
> -3-  The molecule is too big and slow-moving - you might be able to observe a 
> domain linked by a flexible linker to a huge and invisible protein (or virus, 
> ...)
> -4- Proximity to lanthanides or other kinds of unpaired electrons.
> -5- Missing observations, due to overlapped signals combined with barely 
> adequate S/N ratio.
> 
> Arguably 1) and 2) are both movement, just in different time scales - 1) can 
> be identified from relaxation measurements and/or chemical shifts, which 
> should be pretty routine.
> 3) and 4) you would know about.
> 5) you could check by looking at, essentially, completeness.
> 
> Yours,
> Rasmus
> 
>> On 26/05/2021 22:06, Dale Tronrud wrote:
>> Dear Boaz,
>>   We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) 
>> arise from their flexibility, ..."  This makes it sound like you agree that 
>> these deficiencies in other regions may be caused by properties other than 
>> flexibility.
>>   As an extreme example, the N-terminal region of a protein may have a broad 
>> distribution in the ensemble model either because this region experiences 
>> many conformations in solution, or because this peptide was cleaved from the 
>> protein at some earlier time and its absence was not recognized by the 
>> experimentalist.
>> Dale Tronrud
>>> On 5/26/2021 1:06 PM, Boaz Shaanan wrote:
>>> Hi Dale and Cecil,
>>> 
>>> This is quite a circular argument, isn't it? Deficient NOE's for some 
>>> regions (e.g. loops) arise from their flexibility, hence they are not as 
>>> well resolved as other (e.g. internal ) regions for which the number of NOE 
>>> is large. So they are flexible by all accounts and, not surprisingly, align 
>>> usually with high B-factor regions in the corresponding crystal structures. 
>>> In cases where such flexible regions are held by crystal contacts the 
>>> situations would likely be different.
>>> 
>>> Cheers,
>>> 
>>> Boaz
>>> 
>>> 
>>> /Boaz Shaanan, Ph.D.
>>> Dept. of Life Sciences
>>> Ben-Gurion University of the Negev
>>> Beer-Sheva 84105
>>> Israel
>>> 
>>> E-mail: bshaa...@bgu.ac.il
>>> Phone: 972-8-647-2220
>>> Fax:   972-8-647-2992 or 972-8-646-1710 /
>>> //
>>> //
>>> /
>>> 
>>> /
>>> 
>>> *From:* CCP4 bulletin board  on behalf of Dale 
>>> Tronrud 
>>> *Sent:* Wednesday, May 26, 2021 10:46 PM
>>> *To:* CCP4BB@JISCMAIL.AC.UK 
>>> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles
>>>  I agree with Dr Breyton. The variability in an NMR ensemble does not
>>> reflect "mobility" but simply "uncertainty" in conformation.  The spread
>>> in coordinates in some regions simply reflects the lack of experimental
>>> data which could define a single conformation.  There are many reasons
>>> why these data are be absent and high mobility is only one.
>>> 
>>> Dale Tronrud
>>> 
>>> On 5/26/2021 8:45 AM, Cécile Breyton wrote:
 Hello,
 
 In my understanding of NMR, the loops and terminii that adopt very 
 different conformations in the structure ensemble rather reflect the fact 
 that for those residues, the number of constraints is lower, thus the 
 number of structures that fulfil the constraints is larger A dynamics 
 study of the protein will be much more informative.
 
 Cécile
 
 Le 26/05/2021 à 17:29, S. Mohanty a écrit :
> Hi Harry,
> 
> The superpose/overlay of all the structures in PyMol should inform you 
> the rigid part of the protein as well as the flexible part. The rigid 
> part would have very low backbone RMSD or overlay tightly and the 
> flexible part (loops, N-term and C-term etc.) would not superpose 
> tightly. If you check literature, the dynamics of the protein may have 
> been studied through NMR relaxation.
> 
> Smita
> 
> 
> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry 

Re: [ccp4bb] Senior scientist RNA crystallographer position at Evotec

[Stephanie Duclos]

Dear CCP4 community,

We currently have a crystallographer position open in our structural biology 
team, with strong focus on RNA crystallography.
If you are interested, please apply using this link:
https://evotecgroup.wd3.myworkdayjobs.com/Evotec_Career_Site/job/Abingdon/RNA-Crystallography-Senior-Scientist_REQ-03367

Best wishes,

Stephanie

[cid:image002.png@01D41934.D23B4340]
Stephanie Duclos, Ph.D.
Team Leader, Structural Biology
+44 (0)1235 44 1548  (Direct)
stephanie.duc...@evotec.com
www.evotec.com

Evotec (UK) Ltd.
114 Innovation Drive,
Milton Park
Abingdon
Oxfordshire
OX14 4RZ, UK



Please find our information on data protection 
here.

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Registration number:2674265.  Registered Office:  114 Innovation Drive, Milton 
Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom

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If received in error, please notify us immediately by reply email and then 
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[ccp4bb] (R)MS

[David A Case]

On Fri, May 28, 2021, Hughes, Jonathan wrote:


if you just see the B factor as a number, ok, you can do the √ in your
head, but if it's visualized as in pymol/putty larger uncertainties become
exaggerated – which is another word for "misrepresented".


Two points that haven't yet been raised:

1. Crystallographers have a half-century of experience in "seeing the B
factor as a number", and many have a good intuitive feeling for how these
numbers are affected by secondary structure, resolution, and so on.

2. B-factors are really refinement parameters, and can serve to account for
errors or uncertainties in other parts of data processing or refinement.
Stated in another way: the simple atomic model of xyz coordinates + ADPs
is generally not sufficient to represent what is really going on at the
atomic level.  The connection to  is a rough one: especially for large
B-factors (relative to the average) using the simple formula to estimate
 often underestimates the atomic fluctuations that are actually present.

dac



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[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Hughes, Jonathan]

hi ian,
yes, that aspect was in my mind, a bit, but i wanted to keep it simple. my 
point wasn't really how the "uncertainty" parameter is derived but rather its 
units. i can imagine that uncertainty in 3D could be expressed in ų (without 
helping the naïve user much) or in Å (which to me at least seems useful), but 
Ų (i.e. the B factor) seems neither logical nor helpful in this context, 
irrespective of its utility elsewhere. if you just see the B factor as a 
number, ok, you can do the √ in your head, but if it's visualized as in 
pymol/putty larger uncertainties become exaggerated – which is another word for 
"misrepresented".
cheers
j

Von: Ian Tickle 
Gesendet: Freitag, 28. Mai 2021 12:10
An: Hughes, Jonathan 
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS


Hi Jonathan

On Thu, 27 May 2021 at 18:34, Hughes, Jonathan 
mailto:jon.hug...@bot3.bio.uni-giessen.de>> 
wrote:

 "B = 8π2  where u is the r.m.s. displacement of a scattering center, and 
<...> denotes time averaging"

Neither of those statements is necessarily correct: u is the _instantaneous_ 
displacement which of course is constantly changing (on a timescale of the 
order of femtoseconds) and cannot be measured.  So u2 is the squared 
instantaneous displacement,   is the mean-squared displacement, and so the 
root-mean-squared displacement (which of course is amenable to measurement) is 
sqrt(), not the same thing at all as u.

Incidentally, the 8π2 constant factor comes from Fourier-transforming the 
Debye-Waller factor expression I mentioned earlier.

Also for crystals at least, the averaging is not only over time, it's over all 
unit cells, i.e. the displacements are not only thermal in origin but also due 
to spatial static disorder (instantaneous differences between unit cells).


it would seem to me that we would be able to interpret things MUCH more easily 
with u rather than anything derived from u².
So then I think what you mean is sqrt() rather than , which seems not 
unreasonable.

Cheers

-- Ian







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Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] (R)MS

[Randy John Read]

It’s also important to keep in mind that, in this equation, u is the component 
of the displacement *in the direction of the diffraction vector*.  If you 
assume isotropic displacements and you know the mean-squared value of the 
overall xyz vector displacement, you have to divide that mean-squared value by 
3 to get the variance in any particular direction.  This is a source of 
considerable confusion in crystallography textbooks!

Best wishes,

Randy Read

> On 28 May 2021, at 11:09, Ian Tickle  wrote:
> 
> 
> Hi Jonathan
> 
> On Thu, 27 May 2021 at 18:34, Hughes, Jonathan 
>  wrote:
> 
>  "B = 8π2  where u is the r.m.s. displacement of a scattering center, and 
> <...> denotes time averaging"
> 
> Neither of those statements is necessarily correct: u is the _instantaneous_ 
> displacement which of course is constantly changing (on a timescale of the 
> order of femtoseconds) and cannot be measured.  So u2 is the squared 
> instantaneous displacement,   is the mean-squared displacement, and so 
> the root-mean-squared displacement (which of course is amenable to 
> measurement) is sqrt(), not the same thing at all as u.
> 
> Incidentally, the 8π2 constant factor comes from Fourier-transforming the 
> Debye-Waller factor expression I mentioned earlier.
> 
> Also for crystals at least, the averaging is not only over time, it's over 
> all unit cells, i.e. the displacements are not only thermal in origin but 
> also due to spatial static disorder (instantaneous differences between unit 
> cells).
> 
> it would seem to me that we would be able to interpret things MUCH more 
> easily with u rather than anything derived from u².
> 
> So then I think what you mean is sqrt() rather than , which seems not 
> unreasonable.
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

[Ian Tickle]

Hi Jonathan

On Thu, 27 May 2021 at 18:34, Hughes, Jonathan <
jon.hug...@bot3.bio.uni-giessen.de> wrote:

 "B = 8π2  where u is the r.m.s. displacement of a scattering center,
and <...> denotes time averaging"

Neither of those statements is necessarily correct: u is the
_instantaneous_ displacement which of course is constantly changing (on a
timescale of the order of femtoseconds) and cannot be measured.  So u2 is
the squared instantaneous displacement,   is the mean-squared
displacement, and so the root-mean-squared displacement (which of course is
amenable to measurement) is sqrt(), not the same thing at all as u.

Incidentally, the 8π2 constant factor comes from Fourier-transforming the
Debye-Waller factor expression I mentioned earlier.

Also for crystals at least, the averaging is not only over time, it's over
all unit cells, i.e. the displacements are not only thermal in origin but
also due to spatial static disorder (instantaneous differences between unit
cells).

it would seem to me that we would be able to interpret things MUCH more
> easily with u rather than anything derived from u².
>
So then I think what you mean is sqrt() rather than , which seems
not unreasonable.

Cheers

-- Ian



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Re: [ccp4bb] PDB-REDO question

[Robbie Joosten]

Hi Joern,

Yes, these values are all stored in a file called data.json that each entry 
has. The keys that are most relevant are:
BLTBEST (geometric restraint weight)
BBEST (B-factor restraint weight)
BREFTYPE (B-factor model)
DOTLS (Whether or not TLS refinement is used)
ISTWIN (Whether or not the data are perceived as twinned)
RSHRINK (Solvent mask shrinkage)
VDWPROBE (Solvent mask probe)
IONPROBE (Solvent mask ion probe)

Feel free, to ask what the other keys mean. Most of them are model statistics, 
there are a lot of them.

HTH,
Robbie



> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Joern
> Krausze
> Sent: Friday, May 28, 2021 10:26
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB-REDO question
> 
>   Dear all,
> 
> 
> I want to do the following: I want to download several structures from
> PDB-REDO and pipe them into Refmac5 for re-refinement, replacing the
> restraints dictionary of a certain ligand with a customized one. The
> refinement settings I want to keep otherwise unchanged. We are talking
> about a few hundred structures here, so I prefer to do this via a shell
> script.
> 
> Are the Refmac5 settings that PDB-REDO used for redoing the deposited
> structures to be found somewhere? For my own structures, I get a
> *.refmac file that I can directly pipe into Refmac5. However, I didn't
> find such a file for the deposited structures. Is there a way to get my
> hands on it?
> 
> 
> Thanks in advance & best wishes,
> 
> Joern
> 
> --
> *
> Address:
> 
> Joern Krausze
> Braunschweig University of Technology
> Institute of Plant Biology
> Spielmannstr. 7
> 38106 Braunschweig
> Germany
> 
> Email:  j.krau...@tu-braunschweig.de
> Phone:  +49 (0)531 3915858
> *
> 
> ###
> #
> 
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[ccp4bb] Two positions available at BioMAX (MAX IV)

[Ana Gonzalez]

We are currently advertising two positions at the BioMAX beamline:  a beamline 
scientist (see https://lu.varbi.com/en/what:job/jobID:404484/) and a postdoc 
(https://lu.varbi.com/en/what:job/jobID:40/ )

BioMAX  is the first macromolecular crystallography beamline at MAX IV. It  
started user operation in 2017.  BioMAX  is a state-of-the-art beamline  with 
high performance x-ray optics and control systems.  It is geared towards 
high-throughput  protein crystallography and it can handle conventional MX 
experiments as  well as microfocus applications. For more information, see 
https://maxiv.lu.se/biomax.  BioMAX is operated by the international and 
interdisciplinary team, which is part of the MX group. The MX group is also  
developing MicroMAX, a serial crystallography beamline for studying  protein 
dynamics and it manages a crystallographic fragment screening  facility,  
FragMAX.

The successful candidates will be involved in the in-house research program and 
development of the beamline instrumentation, software  and methods to enhance 
the user facilities at BioMAX , with emphasis on  beamline automation, 
multi-crystal  experiments and room temperature data collection.

The application deadline is August 15th 2021

For  any inquiries about the positions, please contact Ana Gonzalez  
(ana.gonza...@maxiv.lu.se)  or Thomas Ursby (thomas.ur...@maxiv.lu.se)
   



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Re: [ccp4bb] Analysis of NMR ensembles

[Harry Powell - CCP4BB]

This even seems to have a”batch” mode (similar to the well-known homology 
modelling server Phyre2) that might accept a zip file containing multiple PDBs. 
If it does, and if it will take my ~700 PDBs, then that would save me a little 
bit of scripting.

Harry

> On 27 May 2021, at 22:03, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> A bit late, I know, but a bit more googling gave me this site which I don't 
> think has been mentioned so far:
> 
> http://old.protein.bio.unipd.it/mobi/
> 
> Given the pdb code, it is a one click job to get a pdb file with the 
> "B-factors changed to averaged Scaled Distance x 100" and the resulting 
> picture (attached) looks about right, I think/hope.
> 
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
> 
> Sent with ProtonMail Secure Email.
> 
> ‐‐‐ Original Message ‐‐‐
> On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB 
>  wrote:
> 
>  Hi Jon
> 
>  The RMSD data (also NOEs, chemical shifts, etc) are not in the original 
> PDB so I would have to calculate them - which takes me to my original 
> question!
> 
>  Harry
> 
>   On 26 May 2021, at 17:22, Jon Cooper jon.b.coo...@protonmail.com 
> wrote:
>   Hello Harry,
>   Looking at:
>   http://www.mcgnmr.mcgill.ca/ProtSkin/
>   It says: "If your input is a plain file containing your scalar data 
> to map, such as heteronuclear NOE or chemical shift differences, ensure the 
> first column in your file contains residue numbers and the second column 
> contains the values to map, then click the Browse button to retrieve this 
> file and select "Plain list of scores"
>   If you can get the residue number and rmsd data into columns in a 
> file, it should map them onto a pdb file for one monomer as pseudo-B-factors.
>   HTH, Jon.C.
>   Sent from ProtonMail mobile
>    Original Message 
>   On 26 May 2021, 16:51, Harry Powell - CCP4BB  
> hrp-ccp...@virginmedia.com wrote:
>   Yes, Jon, but I was hoping I wasn’t the first person to ever want 
> this…
>   Harry
>  
>On 26 May 2021, at 16:34, Jon Cooper 
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk wrote:
>The hard bit is to get the rmsd's into the B-factor column, 
> but it shouldn't stretch you too much, Harry ;-
>There is ProtSkin on the web which does something similar with 
> sequence alignments.
>Sent from ProtonMail mobile
> Original Message 
>On 26 May 2021, 16:28, Harry Powell - CCP4BB  
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote:
>Hi Jurgen
>NMR structures don’t appear to have B_factors, or at least not 
> meaningful ones (e.g. in 2kv5 they’re all 0.00…).
>thanks for the response, though
>Harry
>   
> On 26 May 2021, at 16:21, Jurgen Bosch jxb...@case.edu 
> wrote:
> How about color by B-factor and look for the cold areas 
> and hot areas?
> Jürgen
>
>  On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB 
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk wrote:
>  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
>  
> 
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>  
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[ccp4bb] PDB-REDO question

[Joern Krausze]

 Dear all,


I want to do the following: I want to download several structures from 
PDB-REDO and pipe them into Refmac5 for re-refinement, replacing the 
restraints dictionary of a certain ligand with a customized one. The 
refinement settings I want to keep otherwise unchanged. We are talking 
about a few hundred structures here, so I prefer to do this via a shell 
script.


Are the Refmac5 settings that PDB-REDO used for redoing the deposited 
structures to be found somewhere? For my own structures, I get a 
*.refmac file that I can directly pipe into Refmac5. However, I didn't 
find such a file for the deposited structures. Is there a way to get my 
hands on it?



Thanks in advance & best wishes,

Joern

--
*
Address:

Joern Krausze
Braunschweig University of Technology
Institute of Plant Biology
Spielmannstr. 7
38106 Braunschweig
Germany

Email:  j.krau...@tu-braunschweig.de
Phone:  +49 (0)531 3915858
*



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[ccp4bb] Postdoc in Hamburg (CFEL/HARBOR @ DESY) developing statistical crystallography

[TJ Lane]

Uncovering protein dynamics: developing statistical crystallography
Postdoctoral Position
Center for Free Electron Laser Science (CFEL), Hamburg, Germany [DESY Campus]

Protein motion is at the heart of life, but remains challenging to witness 
firsthand. Proteins move to reading and copying DNA, convert sunlight into 
chemical energy, and transmit signals between cells, yet our ability to image 
these functions is limited by the technology we have to image protein dynamics. 

A new opportunity to meet this challenge is emerging, however, as 
crystallographic methods advance. We can now collect data from thousands to 
millions of crystals of the same protein, and it is clear no two crystals are 
identical. Thus, analyzing their distribution may reveal protein structural 
fluctuations directly. Can we develop a statistical crystallography to turn 
these large datasets into knowledge about protein dynamics? Can we use 
statistical analysis of crystal-to-crystal variation to separate signal from 
noise in time resolved experiments, revealing protein motion induced by mixing 
with a ligand or excitation with a pump laser? We seek a computational 
scientist who will answer these questions.

As the ideal candidate, you will have the following key attributes:

•   A doctoral degree in physics, biophysics, chemistry, applied 
mathematics or a related field
•   Working knowledge of macromolecular crystallographic methods and 
software
•   A track record of scientific computing and programming
•   The ability to drive your work independently and show initiative

And you will be excited to take on the following responsibilities:

•   Mathematical modeling of protein dynamics and protein crystal 
diffraction data
•   Interpretation and analysis of experimental results
•   Open-source development to make your insights available to the broader 
scientific community
•   Presenting your work in written and oral form to the scientific 
community
•   Helping to foster an environment conductive to collaboration, learning, 
growth, and fun

Available immediately is a two-year contract with a competitive salary and the 
opportunity to work and live in the beautiful and vibrant city of Hamburg, 
Germany. The group is housed at the Center for Free Electron Laser Science on 
the vibrant DESY campus (Luruper Chaussee 149, 22761 Hamburg, Germany).

This position is funded through the Advanced Imaging of Matter Cluster of 
Excellence (https://www.cui-advanced.uni-hamburg.de/en.html). The successful 
candidate will become a fellow of the cluster and have access to career 
support, training opportunities, and an engaging scientific network via the 
cluster. The candidate will have additional technical and mentorship support 
from partners Andrea Thorne, Arwen Pearson, and Nicholas Pearce and their 
groups during the course of the project.

We are an equal opportunity employer. Women and minorities are encouraged to 
apply and handicapped persons will be preferred given equal qualifications.

Application deadline: 17 June 2021
Applications should include a cover letter, a tabular curriculum vitae, and 
copies of degree certificate(s). Please send applications by email to: 


For more details, write directly to TJ: 
Also see our website: pbio.cfel.de




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