Re: [ccp4bb] quantifying electron density

[Alexandre Ourjoumtsev]

Dear Sriram, dear Jon, 

The sum of values of a map (always calculated at some finite resolution) is not 
the same as a sum of density values. 
In such maps, a contribution of each atom is a function oscillating with the 
distance to the atomic center. 
Even when the height of these ripples is relatively small, surprisingly, the 
sum (integral) of the map values converges very-very slowly (not like for a 
density itself!) with the radius at which you truncate you sum. See for example 
§3.2 and Figs. 3-4 in a our recent article in Acta Cryst D (2022), D78, 
1451-1468. 

So one should be very careful with interpretations of such formally calculated 
sums (again, even when you have F000, absolute scale etc). 

With best wishes, 

Sacha Urzhumtsev 

- Le 29 Juin 23, à 3:10, sriram raghavan  a écrit 
: 

> Dear Pavel,

> I came across an example of calculating "electron_sums_around_atom" in [
> https://github.com/cctbx/cctbx_project/blob/master/cctbx/examples/fft_map_electron_density_around_atom.py
> | cctbx ] . If we don't zero the F000 or if we normalize the density of the
> real-space map by the unit cell volume and the scattering factor of the unit
> cell (F000), we can obtain the value of the density and sum the values of the
> positions of the obtained grid points on the map. This approach will yield the
> electron density sum across the volume, correct?

> Additionally, there is a tool called [
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236894 |
> PDB-EDA ] that performs a similar calculation but not on selected volume.

> Best regards,
> S. Sriram

> On Thu, Jun 29, 2023 at 4:03 AM Pavel Afonine < [ mailto:pafon...@gmail.com |
> pafon...@gmail.com ] > wrote:

>> Hi Jon,
>> not really the answer to your question but.. This may be very tricky to do
>> because what you look at is not an electron density map but its Fourier image
>> of finite resolution phased by crystal model (that has errors), plus
>> experimental errors, and missing F000 (which is not measured as part of your
>> diffraction experiment). So.. if such a software exists I'd be very cautious
>> interpreting the results you get from it!
>> Pavel

>> On Wed, Jun 28, 2023 at 9:16 AM Hughes, Jonathan < [
>> mailto:jon.hug...@bot3.bio.uni-giessen.de | 
>> jon.hug...@bot3.bio.uni-giessen.de
>> ] > wrote:

>>> hello everyone,
>>> is there software that can use an electron density map to quantify the 
>>> number of
>>> electrons in a selected volume somewhere in a protein?
>>> cheers
>>> jon

>>> --
>>> Professor Jon Hughes, BSc, PhD
>>> Department of Physics
>>> Free University of Berlin
>>> Arnimallee 14
>>> 14195 Berlin
>>> Germany
>>> mobile: (+49/0)1757929098
>>> email: [ mailto:lv...@posteo.de | lv...@posteo.de ]
>>> homepage:
>>> [ http://www.uni-giessen.de/fbz/fb08/Inst/pflphys |
>>> http://www.uni-giessen.de/fbz/fb08/Inst/pflphys ]
>>> Sent without the use of Apple products

>>> 

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> --
> With Regards

> S.Sriram

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Re: [ccp4bb] quantifying electron density

[sriram raghavan]

Dear Pavel,

I came across an example of calculating "electron_sums_around_atom" in cctbx
.
If we don't zero the F000 or if we normalize the density of the real-space
map by the unit cell volume and the scattering factor of the unit cell
(F000), we can obtain the value of the density and sum the values of the
positions of the obtained grid points on the map. This approach will yield
the electron density sum across the volume, correct?

Additionally, there is a tool called PDB-EDA

that performs a similar calculation but not on selected volume.

Best regards,
S. Sriram


On Thu, Jun 29, 2023 at 4:03 AM Pavel Afonine  wrote:

> Hi Jon,
> not really the answer to your question but.. This may be very tricky to do
> because what you look at is not an electron density map but its Fourier
> image of finite resolution phased by crystal model (that has errors), plus
> experimental errors, and missing F000 (which is not measured as part of
> your diffraction experiment). So.. if such a software exists I'd be very
> cautious interpreting the results you get from it!
> Pavel
>
>
> On Wed, Jun 28, 2023 at 9:16 AM Hughes, Jonathan <
> jon.hug...@bot3.bio.uni-giessen.de> wrote:
>
>> hello everyone,
>> is there software that can use an electron density map to quantify the
>> number of electrons in a selected volume somewhere in a protein?
>> cheers
>> jon
>>
>> --
>> Professor Jon Hughes, BSc, PhD
>> Department of Physics
>> Free University of Berlin
>> Arnimallee 14
>> 14195 Berlin
>> Germany
>> mobile:   (+49/0)1757929098
>> email: lv...@posteo.de
>> homepage:
>> http://www.uni-giessen.de/fbz/fb08/Inst/pflphys
>> Sent without the use of Apple products
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
With Regards

S.Sriram



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Re: [ccp4bb] quantifying electron density

[Pavel Afonine]

Hi Jon,
not really the answer to your question but.. This may be very tricky to do
because what you look at is not an electron density map but its Fourier
image of finite resolution phased by crystal model (that has errors), plus
experimental errors, and missing F000 (which is not measured as part of
your diffraction experiment). So.. if such a software exists I'd be very
cautious interpreting the results you get from it!
Pavel


On Wed, Jun 28, 2023 at 9:16 AM Hughes, Jonathan <
jon.hug...@bot3.bio.uni-giessen.de> wrote:

> hello everyone,
> is there software that can use an electron density map to quantify the
> number of electrons in a selected volume somewhere in a protein?
> cheers
> jon
>
> --
> Professor Jon Hughes, BSc, PhD
> Department of Physics
> Free University of Berlin
> Arnimallee 14
> 14195 Berlin
> Germany
> mobile:   (+49/0)1757929098
> email: lv...@posteo.de
> homepage:
> http://www.uni-giessen.de/fbz/fb08/Inst/pflphys
> Sent without the use of Apple products
>
> 
>
> 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
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[ccp4bb] Two postdoctoral openings in structural biochemistry of fertilization at Karolinska Institutet

[Luca Jovine]

Our research group at Karolinska Institutet (http://jovinelab.org) is looking 
for two ambitious postdoctoral fellows who would like to spearhead our future 
steps towards unveiling the molecular basis of gamete recognition and fusion 
through the evolutionary tree.

For more information and to submit an application (deadline 31 July 2023), 
please visit:

Integrative Structural Biology of Fertilization
https://ki.varbi.com/se/what:job/jobID:637984

Biochemistry of Fertilization
https://ki.varbi.com/se/what:job/jobID:639567

Of course, you are also always welcome to contact me directly for informal 
queries.

We look forward to receiving your application!

With best regards,

Luca

--

Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
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[ccp4bb] REMINDER: CBMS Lecture Series - Dominique Bourgeois - June 28, 13:30

[Stojanoff, Vivian]

You are cordially invited to join ……..



Dominique Bourgeois


Institut de Biologie Structurale J-P. Ebel, GRENOBLE



Wednesday, June 28, 2023, 13:30 EDT (New York time)



STRUCTURAL PHOTOPHYSICS OF FLUORESCENT PROTEINS USED IN SUPER RESOLUTION 
MICROSCOPY


https://bnl.zoomgov.com/meeting/register/vJIsf-2orTkoHue9RhbBuN5K0UKRrafNNTk



Abstract

Phototransformable fluorescent proteins (PTFPs) are widely used in many 
advanced fluorescence microscopy methods, notably in the super-resolution 
field. A plethora of PTFPs have been engineered in the last years, which 
display a variety of photoactivation, photoconversion, photoswitching, 
photoblinking and photobleaching properties that can be used at advantage in 
many super-resolution schemes, but that are also at the origin of significant 
complications and artifacts, making these fascinating genetically encoded 
labels still far from ideal. In this talk, I will review how (kinetic) X-ray 
crystallography, optical spectroscopy, multidimensional NMR and molecular 
dynamics simulations can be combined with single-molecule investigations to 
reveal phototransformation mechanisms of PTFPs at the near-atomic level.



 Graphical Abstract:


[cid:653945e9-d41c-4f3d-bb0a-2b57aba4efed]



===



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Education, Training, Outreach

User Program

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Supporting Grants: CBMS is supported by NIH-NIGMS #P30GM133893, and by the 
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[ccp4bb] CCP4 Summer School 2023: deadline approaching!

[Jon Agirre]

Dear CCP4bb subscribers,

As you may know, the CCP4 Summer School is returning to York after a 4-year
hiatus – this is a continuation of the excellent work done by our
colleagues at St. Andrews pre-2019.

We've got an exciting programme prepared for the students, including
lectures not just on macromolecular crystallography but also Cryo-EM, NMR
and protein fold prediction – please have a look at our website here:
https://www.ccp4.ac.uk/schools/ccp4-summer-school/index.php

There will be a few social events, including a ceilidh and school dinner
in/on a unique venue (!).

As you will see, the BBSRC is generously funding fees for up to 10
students, while the BCA is also providing some bursaries. These bursaries
are meant for UK-based students only, but our school is open to anyone.

*Registration closes on the 5th of July (next week).*
Places are limited.

Many thanks,
Johan Turkenburg, Jon Agirre and Paul Bond
-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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[ccp4bb] quantifying electron density

[Hughes, Jonathan]

hello everyone,
is there software that can use an electron density map to quantify the number 
of electrons in a selected volume somewhere in a protein?
cheers
jon 

--
Professor Jon Hughes, BSc, PhD
Department of Physics
Free University of Berlin
Arnimallee 14
14195 Berlin
Germany
mobile:   (+49/0)1757929098
email: lv...@posteo.de 
homepage:
http://www.uni-giessen.de/fbz/fb08/Inst/pflphys
Sent without the use of Apple products



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Re: [ccp4bb] Binding affinity in AutoDock Vina

[Robbie Joosten]

Are you doing self-docking or are you analysing the models as-is? Not all binding poses in the PDB are realistic and things like atomic clashes have a massive energy penalty.Have you looked at the model in the electron density? You can also try the pdb-redo version op the same pdb entry to see if that gives a more sensitive binding energy.HTH,RobbieOn 28 Jun 2023 17:39, Thripthi Shenoy  wrote:I am performing docking studies for some of the protein structures from PDB using AutoDock Vina. Some of the ligands are giving binding energy as positive integers (eg. 435 kcal/mol). I tried rectifying the issue best to my knowledge. I would be grateful if someone could explain to me the reason for such a result.Thanking in advance,Thripthi S.


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[ccp4bb] Binding affinity in AutoDock Vina

[Thripthi Shenoy]

I am performing docking studies for some of the protein structures from PDB
using AutoDock Vina. Some of the ligands are giving binding energy as
positive integers (eg. 435 kcal/mol). I tried rectifying the issue best to
my knowledge. I would be grateful if someone could explain to me the
reason for such a result.

Thanking in advance,
Thripthi S.



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Re: [ccp4bb] Peculiar issue with C2 datasets

[Eleanor Dodson]

C2 Cell :



Average unit cell:   119.05   84.31  107.99   90.00   91.50   90.00

Space group: C 1 2 1


C2 shift ( if I have read your image correctly..)

60.32 2.137. 0.088 In fractions 60.32/119.05 2.137/84.31 0.00. = 0.504
0.023 0.00


See this site C121 has alt origin 1/2, ?,0 so your solutions A 7 B are more
or less equivalent.

(Molecular replacement programs are happy to select ANY origin..)

Maybe you needed to start your refinement from the original model by some
rigid body cycles to adjust for the 1/2A shift?


*See https://saf.bio.caltech.edu/hhmi_manuals/ccp4/alternate_origins.html
*

C 1 2 1 SG No: 5 (Standard short HM symbol: C2)

Number of alternate origins: *4*

This is a *polar spacegroup*: the origin is not fixed along the *B* axis
N*origin*XoYoZo
1 0. ?? 0.
2 0. ?? 0.5000
3 0.5000 ?? 0.
4 0.5000 ?? 0.5000

On Wed, 28 Jun 2023 at 10:14, Nichols, Charlie 
wrote:

> Hi,
>
>
>
> I am running an XChem / PanDDA based study and have collected ~2000
> datasets.
>
>
>
> ~100 of these behave anomalously and I am struggling to understand what is
> going on – any advice / comment appreciated (symmetry maths not my greatest
> strength )
>
>
>
> For manually processed datasets I am running Aimless via CCP4i GUI with
> ‘customised symmetry determination’ / ‘match index to reference’ and a
> previous hi-res dataset used as ‘reference MTZ’ so all datasets index
> consistently with the beta angle >90 solution.
>
>- Within XCE / PanDDA system auto-processed data are similarly
>re-indexed by Dimple to give a consistent population
>
>
>
> In most cases the hi-res model can then be refined against these data –
> solution-A
>
>
>
> With ~1 in 20 datasets however you get an Rfree of 30-45% but if you run
> Phaser and then refine then the Rfree drops to <25% - solution-B.
>
>
>
> Loading the two solutions into Coot shows solution-B appears to be a
> simple translation along the A-axis:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> SSM alignment output:
>
>
>
> In some cases, I have two crystals from the same drop soaked with the same
> ligand where one is ‘solution-A’ and the other ‘solution-B’
>
>
>
> Sample Aimless summaries pasted at end of this communication – B and C
> cell dimensions do vary a bit but there are solution-A datasets with
> greater shifts than observed between the sample datasets illustrated here.
>
>
>
> Are the two populations fundamentally different, or  is there a way to
> reindex the solution-B population so they can be included in the solution-A
> PanDDA runs?
>
>
>
> Thanks for your help,
>
> Take care, Charlie.
>
>
>
> (P.S. unable to share actual data due to client confidentiaility)
>
>
>
>
>
>
>
>
>
>
>
> *Aimless Summary – sample solution-A data*
>
>Overall  InnerShell  OuterShell
>
> Low resolution limit   68.11 68.11  2.49
>
> High resolution limit   2.40  8.98  2.40
>
>
>
> Rmerge  (within I+/I-) 0.082 0.057 0.734
>
> Rmerge  (all I+ and I-)0.094 0.067 0.877
>
> Rmeas (within I+/I-)   0.114 0.080 1.018
>
> Rmeas (all I+ & I-)0.113 0.082 1.056
>
> Rpim (within I+/I-)0.079 0.056 0.703
>
> Rpim (all I+ & I-) 0.063 0.047 0.581
>
> Rmerge in top intensity bin0.065- -
>
> Total number of observations  128856  2463 13718
>
> Total number unique40921   823  4270
>
> Mean((I)/sd(I))  5.9  15.2   0.9
>
> Mn(I) half-set correlation CC(1/2) 0.980 0.950 0.649
>
> Completeness99.9  99.7  99.7
>
> Multiplicity 3.1   3.0   3.2
>
> Mean(Chi^2) 0.66  0.77  0.54
>
>
>
> Anomalous completeness  90.6  92.7  90.9
>
> Anomalous multiplicity   1.5   1.7   1.6
>
> DelAnom correlation between half-sets -0.034-0.035-0.063
>
> Mid-Slope of Anom Normal Probability   0.780   - -
>
>
>
> The anomalous signal appears to be weak so anomalous flag was left OFF
>
>
>
> Estimates of resolution limits: overall
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  ==
> maximum resolution
>
>from Mn(I/sd) >  1.50: limit =  2.60A
>
>from Mn(I/sd) >  2.00: limit =  2.70A
>
>
>
> Estimates of resolution limits in reciprocal lattice directions:
>
>   Along0.99 a* + 0.15 c*
>
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.88A
>
>from Mn(I/sd) >  1.50: limit =  2.99A
>
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[ccp4bb] LINXS Structure-Based Drug Discovery Symposium and course on Fragment Based Lead Discovery!

[Raminta Venskutonyte]

Dear all,

I would like to draw your attention to the upcoming symposium on 
Structure-Based Drug Discovery followed by a course for young researchers with 
focus on Fragment-Based Lead Discovery, that will take place in September in 
Lund, Sweden. Hope it can be of interest!

Welcome to register at 
https://www.linxs.se/events/2023/09/18-22/spdd-symposium-phd-course


Best,
Raminta

Raminta Venskutonytė, PhD
Associate researcher | Dept. of Experimental Medical Science | Lund University
BMC C13 | Office C1320b | SE - 221 84 Lund | Sweden

LINXS - LINXS Institute of advanced Neutron and X-ray Science
https://www.linxs.se/integrative-pharmacology-and-drug-discovery



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LINXS]





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Welcome to LINXS Structure-Based Drug Discovery Symposium and course on 
Fragment Based Lead Discovery


Where: LINXS and MAX IV, Lund, Sweden (online participation also possible)

Symposium, 18/9

The symposium aims to provide an overview of the current situation, challenges 
and future perspectives within structure-based drug discovery. The program 
gathers keynote talks by eminent speakers, from both academia and the 
pharmaceutical industry, covering all the areas of structure - based drug 
design with a special focus on Fragment Based Lead Discovery, FBLD.

Fragment Based Lead Discovery Course, 19-22/9

  *   Lectures: 19-20/9, open for everyone.
  *   Practicals: 21-22/9, for selected participants in the full course - for 
early career scientists.
The course is aimed at PhD students, postdocs, and early-career scientists who 
are broadly working within the area of structure-based drug discovery and who 
want to learn more about fragment screening, FBLD, and how they can use MAX IV 
Laboratory and other Swedish infrastructures to drive their research using 
structural data.


18-22

September



Register











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 | i...@linxs.lu.se | Phone: +46 70 575 2244

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Re: [ccp4bb] Win 10 DHCP-Server to assign fixed IP-address

[Pedro Matias]

Hi Tim,

Why do you need a DHCP server? Can't you configure a fixed IP address on 
the Oxford Cryo 800? Check out this site for a possible alternative: 
https://www.dhcpserver.de/cms/


But if you can connect via USB instead, it's probably better to buy a 
cable. We have an older 700 and it is connected to our Bruker PC via a 
serial cable on a COM port.


Best,

Pedro

On 28/06/2023 09:13, Tim Gruene wrote:

Hello everyone,

we connected an Oxford Cryo 800 with the windows PC of our Bruker
Diffractometer via network cable (as I didn't have a USB-cable at hand).

The Oxford Cryo 800 runs a dhcp-client. Is it possible to set up a
local dhcp-server with Win 10 in order to assign a local IP-address to
the Oxford Cryo 800? Unfortunately, there is no linux computer nearby.

I search up and down, but it seems that it requires a Windows Server
installation to enable a dhcp-server?

Cheers,
Tim

P.S.: I posted this on the Bruker mailing list last Friday, but heard
no response, hence this cross-post.


--
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
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Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8



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Re: [ccp4bb] Need suggestion

[Kirtishila Sonkar]

Dear Afsan,


Based on the information you provided, it's possible that the crashing
issue in COOT when attempting to merge the monomers could be due to several
reasons. Here are a few suggestions and potential workarounds you can try:

Either Update COOT or Import monomers as coordinates: Instead of using the
"Get monomer" option in COOT, you can try importing the monomers as
separate coordinate files. You can save the Glycerol or BCT coordinates in
a PDB or CIF file format and then import them into COOT using the "File"
menu or drag-and-drop functionality. This approach bypasses any potential
issues with the "Get monomer" option.

I hope these suggestions help you overcome the crashing issue in COOT while
adding monomers to your cryo-EM data.

Best regards,

Kirti



On Tue, Jun 27, 2023 at 4:01 PM Afshan Begum <
01d12a434d1a-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear expert,
>
> I am currently working on building my cryo-EM data using COOT. However, I
> have encountered an issue when trying to add monomers such as Glycerol or
> BCT using their letter code from the "Get monomer" option in COOT. Whenever
> I attempt to merge them into my coordinate, COOT crashes.
>
> I would greatly appreciate any suggestions or advice on how to overcome
> this issue. I am currently using version 0.9.8.5 of COOT on a Mac operating
> system. I am unsure if this is a bug or if there is a specific workaround
> for this situation.
>
> Thank you for your assistance.
>
> Best Regards
> ===
>  Afshan Begum
> 
>
>
> --
>
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>


-- 
With best regards,
Kirti Sonkar
Molecular Pathology Group
International Center for Genetic Engineering and Biotechnology (ICGEB)
AREA Science Park ,
Padriciano 99, 34149
Trieste, Italy



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[ccp4bb] Win 10 DHCP-Server to assign fixed IP-address

[Tim Gruene]

Hello everyone,

we connected an Oxford Cryo 800 with the windows PC of our Bruker
Diffractometer via network cable (as I didn't have a USB-cable at hand).

The Oxford Cryo 800 runs a dhcp-client. Is it possible to set up a
local dhcp-server with Win 10 in order to assign a local IP-address to
the Oxford Cryo 800? Unfortunately, there is no linux computer nearby.

I search up and down, but it seems that it requires a Windows Server
installation to enable a dhcp-server?

Cheers,
Tim

P.S.: I posted this on the Bruker mailing list last Friday, but heard
no response, hence this cross-post.

-- 
--
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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