Re: [ccp4bb] Issues in new Mac version 10.15

[Xavier Brazzolotto]

Hi Rachel,

Did you try to reinstall XQuartz ?
https://www.xquartz.org/

> Le 16 oct. 2019 à 01:50, Werther, Rachel A  a écrit :
> 
> Hello All,
>  
> I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t 
> open on my computer.
>  
> Phenix opened as usual.  I use the GUI, and the button that says “Open in 
> COOT” was not greyed out, but would not launch the window.  When I tried to 
> open it directly from Finder, it also failed to open.  The cartoon coot 
> appeared on my recently opened section of my bottom-of-screen toolbar, but 
> nothing happened.
>  
> Next I downloaded the latest CCP4-7.0.077, and followed the instructions to 
> remove the extended attributes:
> ATTENTION: If you are planning to install CCP4 from a tarball on Mac OS X 
> version 10.13 or later (10.12 was not tested), you will have to remove 
> extended attributes from the tar-gz-file before unpacking it, otherwise the 
> app icons will not be functional (and you will be able to launch the CCP4 
> apps including ccp4i and ccp4i2 from the command line only). The extended 
> attributes can be removed from the file _file_ using the command "xattr -c 
> _file_". For example: xattr -c ccp4-7.0.065-macosx64.tar.gz
>  
> But when I try to open CCP4, I get this message:
> Ccp4 cannot be opened because of a problem.
> Check with the developer to make sure ccp4 works with this version of macOS. 
> You may need to reinstall the application. Be sure to install any available 
> updates for the application and macOS.
> Click Report to see more detailed information and send a report to Apple.
>  
> And when I try to open Coot from the Finder, I again just see the icon in my 
> recently opened section of my bottom-of-screen toolbar, but it doesn’t open.
>  
> Any advice?
>  
> Many thanks,
> Rachel
>  
> Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / 
> Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org 
>  / 206-667-4066
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 
Xavier Brazzolotto, PhD
xavier.brazzolo...@chemdef.fr





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

[ccp4bb] Issues in new Mac version 10.15

[Werther, Rachel A]

Hello All,

I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t open 
on my computer.

Phenix opened as usual.  I use the GUI, and the button that says “Open in COOT” 
was not greyed out, but would not launch the window.  When I tried to open it 
directly from Finder, it also failed to open.  The cartoon coot appeared on my 
recently opened section of my bottom-of-screen toolbar, but nothing happened.

Next I downloaded the latest CCP4-7.0.077, and followed the instructions to 
remove the extended attributes:
ATTENTION: If you are planning to install CCP4 from a tarball on Mac OS X 
version 10.13 or later (10.12 was not tested), you will have to remove extended 
attributes from the tar-gz-file before unpacking it, otherwise the app icons 
will not be functional (and you will be able to launch the CCP4 apps including 
ccp4i and ccp4i2 from the command line only). The extended attributes can be 
removed from the file _file_ using the command "xattr -c _file_". For example: 
xattr -c ccp4-7.0.065-macosx64.tar.gz

But when I try to open CCP4, I get this message:

Ccp4 cannot be opened because of a problem.

Check with the developer to make sure ccp4 works with this version of macOS. 
You may need to reinstall the application. Be sure to install any available 
updates for the application and macOS.

Click Report to see more detailed information and send a report to Apple.

And when I try to open Coot from the Finder, I again just see the icon in my 
recently opened section of my bottom-of-screen toolbar, but it doesn’t open.

Any advice?

Many thanks,
Rachel

Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / Fred 
Hutchinson Cancer Research Center / 
rwert...@fredhutch.org / 206-667-4066



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

Re: [ccp4bb] Crystal screen for DNA binding proteins

[Newman, Janet (Manufacturing, Parkville)]

And if you log in to C6 (c6.csiro.au -  one can use the guest account: click on 
"Or click here to try guest account") - navigate to "screens list"=>"commercial 
screens" => KERAfast => and if you click on the screen then it will come up 
with a description of what is in every well, and (most) of the conditions will 
also have recipes of how to make that condition.

Cheers, Janet

Janet Newman
Principal Scientist / Director, Collaborative Crystallisation Centre (C3)
CSIRO Material Science and Engineering
343 Royal Parade
Parkville.  VIC. 3052
Australia
Tel +613 9662 7326
Email janet.new...@csiro.au


From: CCP4 bulletin board  on behalf of Guillaume 
Gaullier 
Sent: Wednesday, October 16, 2019 1:45 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Crystal screen for DNA binding proteins

Hi Sylvia,

A screen specifically designed to crystallize protein-DNA complexes is 
described in this paper: https://www.ncbi.nlm.nih.gov/pubmed/22869139

Back when it was just published, I manually prepared the 48 conditions and it 
was not too difficult (each one is a combination of one buffer, one or two 
salts, and one PEG). Now you can buy it pre-made from at least one supplier 
(possibly available elsewhere too, I haven’t checked): 
https://www.kerafast.com/product/287/protein-nucleic-acid-complex-crystal-screen

Good luck with your project!

Guillaume


On Oct 15, 2019, at 01:48, Sylvia Fanucchi 
mailto:sylvia.fanuc...@wits.ac.za>> wrote:


Hi
Can anyone recommend a good crystal screen to use to crystalise protein-NA 
complexes?

Kind Regards
Sylvia
This communication is intended for the addressee only. It is confidential. If 
you have received this communication in error, please notify us immediately and 
destroy the original message. You may not copy or disseminate this 
communication without the permission of the University. Only authorised 
signatories are competent to enter into agreements on behalf of the University 
and recipients are thus advised that the content of this message may not be 
legally binding on the University and may contain the personal views and 
opinions of the author, which are not necessarily the views and opinions of The 
University of the Witwatersrand, Johannesburg. All agreements between the 
University and outsiders are subject to South African Law unless the University 
agrees in writing to the contrary.



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




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



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

Re: [ccp4bb] Crystal screen for DNA binding proteins

[chitra latka]

Hey,

You can try these two screens -

1. Qiagen's Nucleix screen and

2. Jena Biosciences JBScreen nuc-pro

Best of luck !

On Tue, Oct 15, 2019, 1:18 PM Sylvia Fanucchi 
wrote:

>
>
> Hi
>
> Can anyone recommend a good crystal screen to use to crystalise protein-NA
> complexes?
>
>
>
> Kind Regards
>
> Sylvia
> This communication is intended for the addressee only. It is confidential.
> If you have received this communication in error, please notify us
> immediately and destroy the original message. You may not copy or
> disseminate this communication without the permission of the University.
> Only authorised signatories are competent to enter into agreements on
> behalf of the University and recipients are thus advised that the content
> of this message may not be legally binding on the University and may
> contain the personal views and opinions of the author, which are not
> necessarily the views and opinions of The University of the Witwatersrand,
> Johannesburg. All agreements between the University and outsiders are
> subject to South African Law unless the University agrees in writing to the
> contrary.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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

Re: [ccp4bb] Crystal screen for DNA binding proteins

[Guillaume Gaullier]

Hi Sylvia,

A screen specifically designed to crystallize protein-DNA complexes is 
described in this paper: https://www.ncbi.nlm.nih.gov/pubmed/22869139 
 

Back when it was just published, I manually prepared the 48 conditions and it 
was not too difficult (each one is a combination of one buffer, one or two 
salts, and one PEG). Now you can buy it pre-made from at least one supplier 
(possibly available elsewhere too, I haven’t checked): 
https://www.kerafast.com/product/287/protein-nucleic-acid-complex-crystal-screen
 


Good luck with your project!

Guillaume


> On Oct 15, 2019, at 01:48, Sylvia Fanucchi  wrote:
> 
>  
> Hi
> Can anyone recommend a good crystal screen to use to crystalise protein-NA 
> complexes?
>  
> Kind Regards
> Sylvia
> This communication is intended for the addressee only. It is confidential. If 
> you have received this communication in error, please notify us immediately 
> and destroy the original message. You may not copy or disseminate this 
> communication without the permission of the University. Only authorised 
> signatories are competent to enter into agreements on behalf of the 
> University and recipients are thus advised that the content of this message 
> may not be legally binding on the University and may contain the personal 
> views and opinions of the author, which are not necessarily the views and 
> opinions of The University of the Witwatersrand, Johannesburg. All agreements 
> between the University and outsiders are subject to South African Law unless 
> the University agrees in writing to the contrary.
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
> 



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

[ccp4bb] PhD position - Ghent University, Belgium

[Kristof Van Hecke]

Dear, 

I would like to draw your attention to this vacancy for a PhD position at the 
Department of Chemistry, Ghent University, Belgium. 

https://edit.ugent.be/en/work/vacancies/scientific/phd-student-l83o2/ 


https://www.ugent.be/en/ghentuniv 


We are looking for a highly motivated candidate to perform academic research to 
study the crystallization process of specific compounds using state-of- the-art 
nonlinear optical scattering techniques, combined with small angle X-ray 
scattering (SAXS) techniques. 

Prior experience with small angle X-ray scattering (SAXS) techniques is highly 
recommended.

We can offer a funded PhD position for a period of four years in total, with 
expected starting date of 01/01/2020.


Regards

Kristof Van Hecke


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

Re: [ccp4bb] Crystal screen for DNA binding proteins

[Rajiv gandhi.s]

This following screen Is generally used for DNA but one can give a try for
dna-protein complex as well.


https://hamptonresearch.com/product-Individual-Natrix-Natrix-2-Natrix-HT-Reagents-512.html

https://www.jenabioscience.com/crystallography-cryo-em/screening/crystal-screens/jbscreen-nuc-pro

Best regards
Rajiv

On Tue, Oct 15, 2019, 1:19 PM Sylvia Fanucchi 
wrote:

>
>
> Hi
>
> Can anyone recommend a good crystal screen to use to crystalise protein-NA
> complexes?
>
>
>
> Kind Regards
>
> Sylvia
> This communication is intended for the addressee only. It is confidential.
> If you have received this communication in error, please notify us
> immediately and destroy the original message. You may not copy or
> disseminate this communication without the permission of the University.
> Only authorised signatories are competent to enter into agreements on
> behalf of the University and recipients are thus advised that the content
> of this message may not be legally binding on the University and may
> contain the personal views and opinions of the author, which are not
> necessarily the views and opinions of The University of the Witwatersrand,
> Johannesburg. All agreements between the University and outsiders are
> subject to South African Law unless the University agrees in writing to the
> contrary.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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

[ccp4bb] Crystal screen for DNA binding proteins

[Sylvia Fanucchi]

Hi
Can anyone recommend a good crystal screen to use to crystalise protein-NA 
complexes?

Kind Regards
Sylvia
This communication is intended for the addressee only. It is confidential. If 
you have received this communication in error, please notify us immediately and 
destroy the original message. You may not copy or disseminate this 
communication without the permission of the University. Only authorised 
signatories are competent to enter into agreements on behalf of the University 
and recipients are thus advised that the content of this message may not be 
legally binding on the University and may contain the personal views and 
opinions of the author, which are not necessarily the views and opinions of The 
University of the Witwatersrand, Johannesburg. All agreements between the 
University and outsiders are subject to South African Law unless the University 
agrees in writing to the contrary.



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