Re: [ccp4bb] CryoEM map refinements in coot

[Krieger, James M]

I guess you mean that you’ve done an initial global rigid body fit and you 
still want to do some refinement to get better local fits?

Refmac servalcat is a good option and uses two half maps in MRC format. It 
comes as part of ccpem but does require ccp4 to be installed too

Or alternatively, you could use phenix, which has a real space refinement 
option for cryo-EM.

Best wishes
James

> On 18 Dec 2024, at 21:04, Paul Emsley  wrote:
>
> On 18/12/2024 18:17, tim smith wrote:
>> Hi all,
>>
>> Can you please advise once we fit the map and open in coot. What is next 
>> step to do in coot.
>
> I am somewhat confused. Once you have done the fitting then you're done. 
> Right? You can run your model through (another) refinement program before you 
> analyse and deposit - servalcat springs to mind.
>
>> I tried refmac but that required ccp4 file which doesn't have.
>
> Refmac is part of the CCP4 Suite. You need CCP4 to get Refmac.
>
> One can build Servalcat from source - https://github.com/keitaroyam/servalcat 
> - and that doesn't need CCP4 - however I doubt that is easy for "newbies."
>
>> Please some one can help in elaborating and sharing any tutorial would be 
>> helpful. I'm new bie and first time I am trying model building.
>
> There are some cryo-EM tutorial on my blog:
>
> https://pemsley.github.io/coot/blog/
>
> e..g this one:
>
> https://pemsley.github.io/coot/blog/2022/08/27/Coot-Cryo-EM-Tutorial-Part-1.html
>
> There are some tutorials on YouTube (e.g. sbgrid) I should make more.
>
> Paul
>
> 
>
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[ccp4bb] CryoEM map refinements in coot

[tim smith]

Hi all,

Can you please advise once we fit the map and open in coot. What is next
step to do in coot. I tried refmac but that required ccp4 file which
doesn't have. Please some one can help in elaborating and sharing any
tutorial would be helpful. I'm new bie and first time I am trying model
building. Any help would be really appreciated. Thank you so much
Best wishes

Tim



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[ccp4bb] Two beamline scientist positions open for the Swiss Light Source 2.0

[Leonarski Filip]

Dear All,

We have two openings for tenure-track beamline scientists in our group to 
develop software and methods for crystallography beamlines at the upgraded 
Swiss Light Source 2.0 synchrotron.

The positions offer a unique opportunity to explore novel methods such as 
dynamic crystallography and SAS tensor tomography. You will have access to 
state-of-the-art X-ray detectors and cutting-edge instrumentation, while also 
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Jobs | 
PSI
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PSI

For further information, please contact Dr Meitian Wang, e-mail 
meitian.w...@psi.ch, or myself, e-mail 
filip.leonar...@psi.ch.

With best regards,
Filip
__
Paul Scherrer Institut
Dr Filip Leonarski (he/him)
WSLA/223
Forschungsstrasse 111
5232 Villigen PSI
Schweiz

E-Mail: filip.leonar...@psi.ch
Page: https://www.psi.ch/en/people/filip-leonarski




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Re: [ccp4bb] Recommendations for crystallization screens

[Ben Bax]

Hi Saniya,
   Another place to start is molecular dimensions - they say for
'your initial crystallisation screen, please use our Screen Selection
Guide and Screen Redundancy Guide to maximise the crystallisation
chemical space sampled and increase your crystallisation success rate'
- I have not tried these yet.
Minimizing the amount of floppy DNA not bound by the protein is often
important in getting high resolution crystal structures. When I worked
for GSK we eventually gel purified and crystallised a DNA complex with
a new class of antibiotic [described in Bax, B. D., Chan, P. F.,
Eggleston, D. S., Fosberry, A., Gentry, D. R., Gorrec, F., ... &
Gwynn, M. N. (2010). Type IIA topoisomerase inhibition by a new class
of antibacterial agents. Nature, 466(7309), 935-940.]. The success of
this work very much depended on excellent work by Claus Spitzfaden who
developed a gel filtration assay that ran on 6uls of protein
(automatically injected from a 96 well plate). This assay was used to
optimize the length of the DNA, the DNA sequence, and the metal ions
used - it is described in the supplementary material to the Nature
article.
Best regards, Ben Bax

On Tue, Dec 17, 2024 at 5:30 PM Debanu  wrote:
>
> Hi Saniya,
>
> Open up the catalog/website of Hampton Research and you will find screens 
> recommended for these different kinds of samples of protein-ligand complexes, 
> where ligand=protein, nucleic acid, etc. Depending on the ligand, screens 
> include components of buffers/salts/precipitants that are less likely to 
> destabilize the complex and aid in crystallization (for example, high salts 
> can destabilize protein-DNA complexes). Then you can also cross check with 
> other crystallization screens/companies to get a sense of other options. Many 
> of these screens are built from published papers on suitability of components 
> for specific types of complexes.
>
> Generally speaking, while it could be useful to screen with whatever you have 
> easily available, and to be very thorough screen with all screens you can get 
> your hands on, in reality, this could be limited by available of 
> samples/complexes, and also the effort of screening, imaging, monitoring, 
> following up on hits for optimization, etc.
>
> Best regards,
> Debanu
> --
> Debanu Das, Ph.D.
> bio.site/debanu_das
>
>
>
> On Sun, Dec 15, 2024 at 3:16 AM Saniya Dubey 
>  wrote:
>>
>> Dear All,
>>
>> We're exploring suitable crystallization screens for different types
>> of complexes, including:
>>
>> 1) Protein-nucleic acid complexes
>> 2) Protein-protein complexes
>> 3) Protein-ligand complexes
>>
>> We would appreciate any recommendations you might have of specific
>> screens that work well for these types of samples.
>>
>> Thank You for your insights!
>>
>> Regards,
>> Saniya Dubey
>> PhD Student
>> Macromolecular Structural Biology Lab,
>> Indian Institute of Technology, Hyderabad
>>
>> --
>>
>>
>> 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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[ccp4bb] PhD positions at the International Max Planck School of Cellular Biophysics in Frankfurt, Germany

[MPI-Biophys-PR]

We are pleased to announce that the new application cycle of the International 
Max Planck Research School on Cellular Biophysics (IMPRS-CBP) is now open! We 
are looking for excellent students in natural sciences to apply for fully 
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**
Dr. Pamela Ornelas
Graduate Education Coordinator
Max Planck Institute of Biophysics
Frankfurt am Main, Germany




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Re: [ccp4bb] CryoEM map refinements in coot

[Paul Emsley]

On 18/12/2024 18:17, tim smith wrote:

Hi all,

Can you please advise once we fit the map and open in coot. What is 
next step to do in coot.


I am somewhat confused. Once you have done the fitting then you're done. 
Right? You can run your model through (another) refinement program 
before you analyse and deposit - servalcat springs to mind.



I tried refmac but that required ccp4 file which doesn't have.


Refmac is part of the CCP4 Suite. You need CCP4 to get Refmac.

One can build Servalcat from source - 
https://github.com/keitaroyam/servalcat - and that doesn't need CCP4 - 
however I doubt that is easy for "newbies."


Please some one can help in elaborating and sharing any tutorial would 
be helpful. I'm new bie and first time I am trying model building.


There are some cryo-EM tutorial on my blog:

https://pemsley.github.io/coot/blog/

e..g this one:

https://pemsley.github.io/coot/blog/2022/08/27/Coot-Cryo-EM-Tutorial-Part-1.html

There are some tutorials on YouTube (e.g. sbgrid) I should make more.

Paul



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