Re: [ccp4bb] mtz/cif file for depostion

[Jon Cooper]

From your refmac refinement job in i2, this should give you the combined mtz?

[test.jpg]

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

Sent with [Proton Mail](https://proton.me/) secure email.

On Friday, 9 February 2024 at 17:54, Palm, Gottfried 
 wrote:

> Dear all,
> I have problems preparing my experimental data (XRD) for deposition. I have 
> two mtz files, which work well for refmac5, with an FREER column in one file 
> and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file. I merged 
> them into one mtz file with cad (in ccp4i).
> The validation server doesn't take two separate mtz files, but complains 
> about missing data in the merged file. I guess because FREER ended up in 
> "Columns common to all datasets" and the other columns in "Dataset #1: 
> 356211/DEFAULT/NATIVE".
> Can I somehow move the FREER column to Dataset #1?
> With "Merge experimental data objects to MTZ Export 'old' style MTZ file" in 
> ccp4i2, the problem is the same.
> I also tried converting to cif many ways, but failed.
> I have used OneDep at EBI.
>
> Best Regards
> Gottfried
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] mtz/cif file for depostion

[Jon Cooper]

Hello, there's a way to export all the columns in one file, rather than trying 
to deposit two mini-mtz's. The problem is remembering how when I'm away from 
the computer. It's one of the export options that you find when digging around 
a bit. Maybe it needs a right-click on one of the icons - bit hard for mac 
users, I know ;-0

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

Sent from Proton Mail mobile

 Original Message 
On 9 Feb 2024, 17:54, Palm, Gottfried wrote:

> Dear all,
> I have problems preparing my experimental data (XRD) for deposition. I have 
> two mtz files, which work well for refmac5, with an FREER column in one file 
> and Iplus, SIGIplus, Iminus, SIGIminus columns in the second file. I merged 
> them into one mtz file with cad (in ccp4i).
> The validation server doesn't take two separate mtz files, but complains 
> about missing data in the merged file. I guess because FREER ended up in 
> "Columns common to all datasets" and the other columns in "Dataset #1: 
> 356211/DEFAULT/NATIVE".
> Can I somehow move the FREER column to Dataset #1?
> With "Merge experimental data objects to MTZ Export 'old' style MTZ file" in 
> ccp4i2, the problem is the same.
> I also tried converting to cif many ways, but failed.
> I have used OneDep at EBI.
>
> Best Regards
> Gottfried
>
> ---
>
> 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] mtz/cif file for depostion

[Palm, Gottfried]

Dear all, 
  I have problems preparing my experimental data (XRD) for
deposition. I have two mtz files, which work well for refmac5, with an
FREER column in one file and Iplus, SIGIplus, Iminus, SIGIminus
columns in the second file. I merged them into one mtz file with cad
(in ccp4i). 
The validation server doesn't take two separate mtz files, but
complains about missing data in the merged file. I guess because FREER
ended up in "Columns common to all datasets" and the other columns in
"Dataset #1: 356211/DEFAULT/NATIVE".
Can I somehow move the FREER column to Dataset #1?
With "Merge experimental data objects to MTZ Export 'old' style MTZ
file" in ccp4i2, the problem is the same. 
I also tried converting to cif many ways, but failed. 
I have used OneDep at EBI. 

Best Regards
  Gottfried



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[ccp4bb] R: [ccp4bb] how to use electron scattering factors in REFMAC program?

[BENEDETTA CARROZZINI]

thank you, Robert.
simpler than expected.
 I'll try it right away

Dedi


Da: Roberto Steiner 
Inviato: venerdì 9 febbraio 2024 10:45
A: BENEDETTA CARROZZINI 
Cc: Adedunni Adenuga 
Oggetto: Re: [ccp4bb] how to use electron scattering factors in REFMAC program?

Hi Benedetta

Use an external keyword file that with the line
'source ec mb’

Best
R


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.








On 9 Feb 2024, at 10:30, BENEDETTA CARROZZINI 
mailto:benedetta.carrozz...@cnr.it>> wrote:

You don't often get email from 
benedetta.carrozz...@cnr.it. Learn why this 
is important
Dear CCP4BB community,
I am working on the structural solution of macromolecules via MR using 3D 
electron diffraction data.

I would like to know if it is possible to carry out a preliminary refinement 
(under 'kinematic' conditions) of the MR model with REFMAC.

 If so, what are the options (or rather instructions) I should provide to the 
program to correctly use electron scattering factors (instead of the standard 
X-ray ones)?
 I have searched for this information in the manual and online without success 
and for this reason, I ask for your precious help.

Thanks in advance
Dedi
​


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[ccp4bb] R and TechDev Funding Calls Open for 2024

[ccp4mail]

Dear all,


This is a reminder to apply for the Instruct-ERIC R Pilot Call, and brand new 
TechDev Call!



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pilot research projects in integrated structural biology.



This call is open to all topics within integrated structural biology and offers 
funding of up to a maximum of €15,000 per project. The call will close 15 March 
2024, so submit your 
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Apply to R Call Here



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The new Instruct Technology Development Call is aimed at researchers with a 
proven track record in technology and methods development. This call is open 
for two specific topics for structural biology technology development:

  *   Sample Preparation
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The TechDev call offers funding of up to €30,000 for pilot projects.



Apply to TechDev Call Here




Find out more about the criteria for each call 
here.


Kind regards

Instruct-ERIC Hub Team




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Re: [ccp4bb] Crystals with DNA

[Patrick Shaw Stewart]

Carina, to complement the techniques using sticky ends, etc., you can also
use the "random" microseeding approach that I mentioned to Kavya, see below.

The great advantage in a project like yours, where you have a family of
related constructs, is that you can use cross-seeding - that is, you can
use crushed crystals of one construct to seed other target constructs.  You
can even mix several seed stocks together, although we always keep seed
crystals grown in high-salt conditions separate from those grown in
high-peg conditions.

There are some very nice examples of cross-seeding and mixing seed stocks
in this paper by Obmolova et al.

Obmolova, G., Malia, T.J., Teplyakov, A., Sweet, R.W. and Gilliland, G.L.,
2014. Protein crystallization with microseed matrix screening: application
to human germline antibody Fabs. *Acta Crystallographica Section F:
Structural Biology Communications*, *70*(8), pp.1107-1115.
https://doi.org/10.1107/S2053230X14012552


More info

https://www.douglas.co.uk/mms.htm


Best wishes and good luck!

Patrick
___

Hi Kavya

1. Make a seed stock from the globules or anything else that you think
might be crystalline, and recreen.  In other words, you should add your
seed stock to *random screens* (not optimization experiments).  There could
be many conditions that are in the metastable zone of the phase diagram in
your normal screens - this method can give you crystals in those conditions.

If this works, you'll be in a better position anyway because you'll have
more control - by diluting the seed stock, you can control the number of
crystals per drop.

References:


D'Arcy, A., Villard, F. and Marsh, M., 2007. An automated microseed
matrix-screening method for protein crystallization. *Acta
Crystallographica Section D: Biological Crystallography*, *63*(4),
pp.550-554.

Shaw Stewart, P.D., Kolek, S.A., Briggs, R.A., Chayen, N.E. and Baldock,
P.F., 2011. Random microseeding: a theoretical and practical exploration of
seed stability and seeding techniques for successful protein
crystallization. *Crystal Growth & Design*, *11*(8), pp.3432-3441.


This is how we normally make the seed:


https://www.douglas.co.uk/f_ftp1/rMMS_Procedure.pdf




On Thu, Feb 8, 2024 at 11:26 AM careinaedgo...@yahoo.com <
02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:

>  Hello all.
>
> I am struggling to get defracting crystals with a protein DNA complex. The
> crystals are plentiful but they do not diffract. I am going back to the
> grind stone and relookong at my DNA sequence.
> Is there any wisdom you could give me with regards to what works best with
> DNA in crystals?
> From my reading it seems if the length is a multiple of 7 (for B DNA) and
> blunt ended, it will stretch over the length of the crystal and improve
> crystalisability. But if you want crystals that diffract better, you will
> need to play with length and even making it only one base longer or shorter
> can make a difference, even changing the morphology of the crystal? Longer
> is better than shorter, and overhangs are good for improving diffraction?
> Presumably because they stabilize contacts? It is expensive to synthesize a
> while bunch of sequences so I need to be strategic in my choice. Would
> appreciate any advice.
> Thank you
> Careina.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36



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Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Eleanor Dodson]

If I remember  for coefficients with FOM and a precise PHI calculated, A =
FOM*cos(phi) B = FOM*sin(phi) C=D=0

If you have a probability curve for PHI. 0 to 360  such as you get from
experimental phasing, A B C D mirror this bimodal curve better ..


On Fri, 9 Feb 2024 at 09:58, Nitin Kulhar <
9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear sir
>
> Thank you for clearing that. I checked back to see that HLC/D are
> invariably 0 for all reflections, with the non-zero HLA/B supposedly having
> been originated from the probability distribution of phases *calculated*
> by phaser. Hopefully, I have not misunderstood it.
>
> Thanks and regards
> Nitin Kulhar
>
> On Thu, Feb 8, 2024 at 9:07 PM Randy John Read  wrote:
>
>> Hi,
>>
>> Hendrickson-Lattman coefficients are just a way of storing phase
>> probability information, and they can come from different sources including
>> atomic models. Phaser puts in HL coefficients because they could be handy
>> under some circumstances for combining the phase information from
>> experimental phasing. You might notice that only A and B are non-zero for
>> the molecular replacement HL coefficients. That’s because the phase
>> probability distribution is unimodal for calculated phases, whereas it’s
>> generally bimodal for experimental phases (thus requiring more
>> coefficients).
>>
>> Best wishes,
>>
>> Randy Read
>>
>> > On 8 Feb 2024, at 14:32, Nitin Kulhar <
>> 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:
>> >
>> > Dear all
>> >
>> > Is anomalous diffraction necessary for determining experimental phases
>> and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
>> >
>> > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems
>> to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
>> >
>> > Wavelength:
>> > 1.54179 Angstrom.
>> >
>> > Sample:
>> > •
>> > Protein-small molecule ligand complex crystal.
>> > • No anomalous scatterer in the protein, the ligand, or the
>> crystallization condition.
>> >
>> > Data reduction:
>> > Xtriage and aimless analyses did not indicate significant anomalous
>> signal.
>> >
>> > I would appreciate any help in understanding the reasons for these
>> observations.
>> >
>> > Thanks and regards
>> > Nitin Kulhar
>> > PhD student
>> > c/o Dr Rajakumara Eerappa
>> > Macromolecular Structural Biology Lab
>> > Department of Biotechnology
>> > Indian Institute of Technology Hyderabad
>> > Kandi, Sangareddy
>> > Telangana, India - 502284
>> >
>> > Disclaimer:- This footer text is to convey that this email is sent by
>> one of the users of IITH. So, do not mark it as SPAM.
>> > 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
>> Hills Road   E-mail:
>> rj...@cam.ac.uk
>> Cambridge CB2 0XY, U.K.
>> www-structmed.cimr.cam.ac.uk
>>
>>
> Disclaimer:- This footer text is to convey that this email is sent by one
> of the users of IITH. So, do not mark it as SPAM.
>
> --
>
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Re: [ccp4bb] Crystals with DNA

[Fred Vellieux]

Hello,

Overhanging "sticky" ends are mentioned frequently when it comes to 
obtaining infinite helices that are useful in crystallization. For 
example in 
https://home.ccr.cancer.gov/csb/nihxray/Tips-and-Tricks_Crystallization_Protein-DNA_updated.pdf 
.


Cheers,

Fred.

On 09/02/2024 10:59, careinaedgo...@yahoo.com wrote:

Thank you for this insight, Nicolas. It is very helpful.
Yes I have also had a soccer ball shaped crystal that does not 
diffract as well as, and more recently, many plate like crystals but 
they do not diffract either.
I do know I have both protein and DNA in my crystals but I do not 
know, as you say, exactly what is forming the crystal contacts.
Just to be clear, do you say overhangs are helpful? Surely overhangs 
won't promote an infinite helix? If one wants an infinite helix, would 
the DNA not have to be blunt ended?


Sent from Yahoo Mail on Android 



On Thu, Feb 8, 2024 at 4:59 PM, Nicolas Foos
 wrote:

Hello Careina,

In my hands, DNA protein complex crystals may be frustrating, 
because often we get good looking crystals which don't diffract at
all and are actually not easy to improve.

I remember obtaining a lot of crystal looking a bit like "STOP"
road sign (octogonal shape for one axis) which never diffracts.
(Often containing only DNA not well organized)

So long story short, In my hand (transciption factor bound with
homeodomain for example). I had good results with DNA sequence
which results in hoverhangs. The idea was to bet on a "infinit"
DNA helix which should help the packing.

I strongly encouraged you to rely on any other information  you
can have to be sure of what is the best minimal sequence (like
band shift assay). Also if you can purify the entire complex
before crystallization assay (I don't know your protocol, but
ideally, I would prepare the complex prot-DNA and put it on size
exclusion).

The point is, you don't know /a priori /what kind of crystal
packing you will have. It may be only due to protein protein
contact and not related to the DNA directly.

Also, I often get good results with crystal growing condition
containing MPD or PEG (makes me using PEG screen Familly as first
approach).

I invite you to read the Timothy Richmond teams Papers on 
nucleosome they spend some times improving the resolution on very
large complex. (Luger etal 1997).

There is many parameters, DNA sequence also change a bit the DNA
geometry (look for A-tract), You may want to introduce such
sequence to maybe improve the "rigidity".

Also if your DNA fragment are small, be careful with the
temperature. The annealing and the DNA duplex formation is
critical and you should be careful on your procedure.

I remember that small cation like Li, may help too.

HTH


Nicolas


On 08/02/2024 12:25, careinaedgo...@yahoo.com
 wrote:
 Hello all.

I am struggling to get defracting crystals with a protein DNA
complex. The crystals are plentiful but they do not diffract. I am
going back to the grind stone and relookong at my DNA sequence.
Is there any wisdom you could give me with regards to what works
best with DNA in crystals?
From my reading it seems if the length is a multiple of 7 (for B
DNA) and blunt ended, it will stretch over the length of the
crystal and improve crystalisability. But if you want crystals
that diffract better, you will need to play with length and even
making it only one base longer or shorter can make a difference,
even changing the morphology of the crystal? Longer is better than
shorter, and overhangs are good for improving diffraction?
Presumably because they stabilize contacts? It is expensive to
synthesize a while bunch of sequences so I need to be strategic in
my choice. Would appreciate any advice.
Thank you
Careina.



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-- 
Nicolas Foos PhD - ARISE fellow

https://orcid.org/-0003-2331-8399  


EMBL Grenoble, McCarthy Team

71 av. des Martyrs,
38000 Grenoble FRANCE

+33 4 57 42 84 67





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Re: [ccp4bb] Crystals with DNA

[Nicolas Foos]

Hello,

If you want to promote "infinite" helix, you should go for overhangs 
(sticky end)  with compatible sequence. I try to explain better what I 
have in mind (and I actually did).


example :

5'ATCCCTAAATCGGCGTGTGCT---3'

3'---GGATTTAGCCGCACACGATAG5'

Hoping that this results in something like :

5' ATCCCTAAATCGGCGTGTGCTATCCCTAAATCGGCGTGTGCTATCCCTAAATCGGCGTGTGCT---3'

3' ---GGATTTAGCCGCACACGATAGGGATTTAGCCGCACACGATAGGGATTTAGCCGCACACGATAG5'

With the blunt end, you may have the helix, or not, in my opinion your 
are not really promoting the "infinite helix".


Nicolas

On 09/02/2024 10:59, careinaedgo...@yahoo.com wrote:

Thank you for this insight, Nicolas. It is very helpful.
Yes I have also had a soccer ball shaped crystal that does not 
diffract as well as, and more recently, many plate like crystals but 
they do not diffract either.
I do know I have both protein and DNA in my crystals but I do not 
know, as you say, exactly what is forming the crystal contacts.
Just to be clear, do you say overhangs are helpful? Surely overhangs 
won't promote an infinite helix? If one wants an infinite helix, would 
the DNA not have to be blunt ended?


Sent from Yahoo Mail on Android 



On Thu, Feb 8, 2024 at 4:59 PM, Nicolas Foos
 wrote:

Hello Careina,

In my hands, DNA protein complex crystals may be frustrating, 
because often we get good looking crystals which don't diffract at
all and are actually not easy to improve.

I remember obtaining a lot of crystal looking a bit like "STOP"
road sign (octogonal shape for one axis) which never diffracts.
(Often containing only DNA not well organized)

So long story short, In my hand (transciption factor bound with
homeodomain for example). I had good results with DNA sequence
which results in hoverhangs. The idea was to bet on a "infinit"
DNA helix which should help the packing.

I strongly encouraged you to rely on any other information  you
can have to be sure of what is the best minimal sequence (like
band shift assay). Also if you can purify the entire complex
before crystallization assay (I don't know your protocol, but
ideally, I would prepare the complex prot-DNA and put it on size
exclusion).

The point is, you don't know /a priori /what kind of crystal
packing you will have. It may be only due to protein protein
contact and not related to the DNA directly.

Also, I often get good results with crystal growing condition
containing MPD or PEG (makes me using PEG screen Familly as first
approach).

I invite you to read the Timothy Richmond teams Papers on 
nucleosome they spend some times improving the resolution on very
large complex. (Luger etal 1997).

There is many parameters, DNA sequence also change a bit the DNA
geometry (look for A-tract), You may want to introduce such
sequence to maybe improve the "rigidity".

Also if your DNA fragment are small, be careful with the
temperature. The annealing and the DNA duplex formation is
critical and you should be careful on your procedure.

I remember that small cation like Li, may help too.

HTH


Nicolas


On 08/02/2024 12:25, careinaedgo...@yahoo.com
 wrote:
 Hello all.

I am struggling to get defracting crystals with a protein DNA
complex. The crystals are plentiful but they do not diffract. I am
going back to the grind stone and relookong at my DNA sequence.
Is there any wisdom you could give me with regards to what works
best with DNA in crystals?
From my reading it seems if the length is a multiple of 7 (for B
DNA) and blunt ended, it will stretch over the length of the
crystal and improve crystalisability. But if you want crystals
that diffract better, you will need to play with length and even
making it only one base longer or shorter can make a difference,
even changing the morphology of the crystal? Longer is better than
shorter, and overhangs are good for improving diffraction?
Presumably because they stabilize contacts? It is expensive to
synthesize a while bunch of sequences so I need to be strategic in
my choice. Would appreciate any advice.
Thank you
Careina.



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


-- 
Nicolas Foos PhD - ARISE fellow

https://orcid.org/-0003-2331-8399  


EMBL Grenoble, McCarthy Team

71 av. des Martyrs,
38000 Grenoble 

Re: [ccp4bb] Crystals with DNA

[careinaedgo...@yahoo.com]

Thank you for this insight, Nicolas. It is very helpful.Yes I have also had a 
soccer ball shaped crystal that does not diffract as well as, and more 
recently, many plate like crystals but they do not diffract either.I do know I 
have both protein and DNA in my crystals but I do not know, as you say, exactly 
what is forming the crystal contacts.Just to be clear, do you say overhangs are 
helpful? Surely overhangs won't promote an infinite helix? If one wants an 
infinite helix, would the DNA not have to be blunt ended?

Sent from Yahoo Mail on Android 
 
  On Thu, Feb 8, 2024 at 4:59 PM, Nicolas Foos wrote:
Hello Careina, 
 
 
In my hands, DNA protein complex crystals may be frustrating,  because often we 
get good looking crystals which don't diffract at all and are actually not easy 
to improve. 
 
 
I remember obtaining a lot of crystal looking a bit like "STOP" road sign 
(octogonal shape for one axis) which never diffracts. (Often containing only 
DNA not well organized)
 
 
So long story short, In my hand (transciption factor bound with homeodomain for 
example). I had good results with DNA sequence which results in hoverhangs. The 
idea was to bet on a "infinit" DNA helix which should help the packing. 
 
 
I strongly encouraged you to rely on any other information  you can have to be 
sure of what is the best minimal sequence (like band shift assay). Also if you 
can purify the entire complex before crystallization assay (I don't know your 
protocol, but ideally, I would prepare the complex prot-DNA and put it on size 
exclusion).
 
The point is, you don't know a priori what kind of crystal packing you will 
have. It may be only due to protein protein contact and not related to the DNA 
directly. 
 
Also, I often get good results with crystal growing condition containing MPD or 
PEG (makes me using PEG screen Familly as first approach). 
 
 
I invite you to read the Timothy Richmond teams Papers on  nucleosome they 
spend some times improving the resolution on very large complex. (Luger etal 
1997).
 
There is many parameters, DNA sequence also change a bit the DNA geometry (look 
for A-tract), You may want to introduce such sequence to maybe improve the 
"rigidity". 
 
 
Also if your DNA fragment are small, be careful with the temperature. The 
annealing and the DNA duplex formation is critical and you should be careful on 
your procedure.
 
 
I remember that small cation like Li, may help too.  
 
 
HTH 
 
 

 
 
Nicolas
 
 

 
 On 08/02/2024 12:25, careinaedgo...@yahoo.com wrote:
  
 
  Hello all. 
  I am struggling to get defracting crystals with a protein DNA complex. The 
crystals are plentiful but they do not diffract. I am going back to the grind 
stone and relookong at my DNA sequence. Is there any wisdom you could give me 
with regards to what works best with DNA in crystals? From my reading it seems 
if the length is a multiple of 7 (for B DNA) and blunt ended, it will stretch 
over the length of the crystal and improve crystalisability. But if you want 
crystals that diffract better, you will need to play with length and even 
making it only one base longer or shorter can make a difference, even changing 
the morphology of the crystal? Longer is better than shorter, and overhangs are 
good for improving diffraction? Presumably because they stabilize contacts? It 
is expensive to synthesize a while bunch of sequences so I need to be strategic 
in my choice. Would appreciate any advice. Thank you Careina.  
  
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Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Nitin Kulhar]

Dear sir

Thank you for clearing that. I checked back to see that HLC/D are
invariably 0 for all reflections, with the non-zero HLA/B supposedly having
been originated from the probability distribution of phases *calculated* by
phaser. Hopefully, I have not misunderstood it.

Thanks and regards
Nitin Kulhar

On Thu, Feb 8, 2024 at 9:07 PM Randy John Read  wrote:

> Hi,
>
> Hendrickson-Lattman coefficients are just a way of storing phase
> probability information, and they can come from different sources including
> atomic models. Phaser puts in HL coefficients because they could be handy
> under some circumstances for combining the phase information from
> experimental phasing. You might notice that only A and B are non-zero for
> the molecular replacement HL coefficients. That’s because the phase
> probability distribution is unimodal for calculated phases, whereas it’s
> generally bimodal for experimental phases (thus requiring more
> coefficients).
>
> Best wishes,
>
> Randy Read
>
> > On 8 Feb 2024, at 14:32, Nitin Kulhar <
> 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Dear all
> >
> > Is anomalous diffraction necessary for determining experimental phases
> and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
> >
> > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems
> to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
> >
> > Wavelength:
> > 1.54179 Angstrom.
> >
> > Sample:
> > •
> > Protein-small molecule ligand complex crystal.
> > • No anomalous scatterer in the protein, the ligand, or the
> crystallization condition.
> >
> > Data reduction:
> > Xtriage and aimless analyses did not indicate significant anomalous
> signal.
> >
> > I would appreciate any help in understanding the reasons for these
> observations.
> >
> > Thanks and regards
> > Nitin Kulhar
> > PhD student
> > c/o Dr Rajakumara Eerappa
> > Macromolecular Structural Biology Lab
> > Department of Biotechnology
> > Indian Institute of Technology Hyderabad
> > Kandi, Sangareddy
> > Telangana, India - 502284
> >
> > Disclaimer:- This footer text is to convey that this email is sent by
> one of the users of IITH. So, do not mark it as SPAM.
> > 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
> 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] how to use electron scattering factors in REFMAC program?

[Roberto Steiner]

Hi Benedetta

Use an external keyword file that with the line
'source ec mb’

Best
R


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

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On 9 Feb 2024, at 10:30, BENEDETTA CARROZZINI 
mailto:benedetta.carrozz...@cnr.it>> wrote:

You don't often get email from 
benedetta.carrozz...@cnr.it. Learn why this 
is important
Dear CCP4BB community,
I am working on the structural solution of macromolecules via MR using 3D 
electron diffraction data.

I would like to know if it is possible to carry out a preliminary refinement 
(under 'kinematic' conditions) of the MR model with REFMAC.

 If so, what are the options (or rather instructions) I should provide to the 
program to correctly use electron scattering factors (instead of the standard 
X-ray ones)?
 I have searched for this information in the manual and online without success 
and for this reason, I ask for your precious help.

Thanks in advance
Dedi
​


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[ccp4bb] how to use electron scattering factors in REFMAC program?

[BENEDETTA CARROZZINI]

Dear CCP4BB community,
I am working on the structural solution of macromolecules via MR using 3D 
electron diffraction data.

I would like to know if it is possible to carry out a preliminary refinement 
(under 'kinematic' conditions) of the MR model with REFMAC.

 If so, what are the options (or rather instructions) I should provide to the 
program to correctly use electron scattering factors (instead of the standard 
X-ray ones)?
 I have searched for this information in the manual and online without success 
and for this reason, I ask for your precious help.

Thanks in advance
Dedi
​



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