Re: [ccp4bb] [EXT] Re: [ccp4bb] Regarding the diffraction image

[kavyashreem]

Dear Ben, 

It was a single crystal that was mounted. I did use IZIT dye, did not
trun blue much. Probably its a TCEp crystal. But I did try a negative
control without protein+ligand and rest everything same, the drop was
clear! 

Thank you 

Regards 

Kavya 

On 2023-02-06 22:49, Ben Bax wrote:

> Hi Kavya, More than one crystal?  
> Epitaxial growth (protein crystal growing on salt crystal or vice versa) 
> Did you try IZIT? 
> (https://hamptonresearch.com/product-Izit-Crystal-Dye-33.html). 
> 
> I have seen salt and protein crystals in the same drop before now - but not 
> growing together. 
> Ben
> 
> On 3 Feb 2023, at 22:15, CRAIG A BINGMAN 
> <21371e2fba31-dmarc-requ...@jiscmail.ac.uk> wrote: 
> 
> Oxidation products of TCEP crystallize in the presence of zinc ions. These 
> crystals fluoresce strongly under UV, which seems like a dirty trick, if your 
> expectation is that only protein crystals can do that. The brightfield white 
> light image of the crystals is also consistent with not-protein crystals, 
> because of the high refractive index contrast between the crystals and the 
> mother liquor. 
> 
> FROM: CCP4 bulletin board  on behalf of kavyashreem 
> 
> DATE: Friday, February 3, 2023 at 2:32 AM
> TO: CCP4BB@JISCMAIL.AC.UK 
> SUBJECT: [ccp4bb] Regarding the diffraction image 
> 
> Dear all, 
> 
> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
> condition 10%PEG3350, 50mM Zinc acetate. 
> 
> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8.  
> 
> Crystal: Crystal:   
> crystal under UV m 
> 
> <8ef9453e.png> 
> 
> When we collected the data at an in-house facility, it looked something like 
> this: 
> 
>  
> 
> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. 
> 
> I have not come across a protein diffraction like this, nor of a salt. When I 
> ran the gel for the incubated protein (protein+ligand), there was no 
> degradation. 
> 
> Although, I was sure there is some problem with this image I tried 
> processing, which could not be, But indexing showed a unit cell  of 11Ang, 
> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not the 
> third. 
> 
> Can anyone please shed some light on this diffraction image? 
> 
> How can it happen? 
> 
> Thank you 
> 
> Regards 
> 
> Kavya 
> 
> -
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> -
> 
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[ccp4bb] Source code for ccp4

[Tsodikov, Oleg V.]

Hello colleagues,

Where can I get the source code for the current version of CCP4 suite? None of 
the links I clicked on seem to be active.

Thanks for your help!
Regards,
Oleg

-
Oleg Tsodikov, Ph.D.
Professor of Pharmaceutical Sciences
University of Kentucky College of Pharmacy
Todd Bldg, Room 425
789 S. Limestone St.
Lexington, KY 40536

phone: 859-218-1687



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[ccp4bb] Post-doc position - Columbia University, New York

[Liang Tong]

A Post-doctoral Research Associate position is available for structural
studies on proteins involved in RNA processing and quality control, and
other projects, using cryo-EM and crystallography. We have extensive
experience in these areas, and have generated many high-impact publications
(for example Science, 367, 700, 2020; Mol. Cell, 77, 800, 2020). Please
visit our home page for more information-



http://tonglab.biology.columbia.edu/

Strong experience in protein biochemistry is required. Prior experience
with cryo-EM and/or X-ray crystallography is desirable.

Please send CV and names of three references to me by email.



Liang Tong
Department of Biological Sciences
Columbia University
New York, NY 10027
Email: lt...@columbia.edu



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[ccp4bb] iNEXT-D hands-on workshop on cryo-FIB lamella preparation & cryo electron tomography 17-21.4.2023

[Bruno KLAHOLZ]

Dear all,

this is to announce the iNEXT-Discovery one-week hands-on workshop on cellular 
cryo-FIB lamella preparation and cryo electron tomography April 17-21 2023.

This is a workshop distributed over several participating centres of the 
iNEXT-Discovery infrastructure 
https://inext-discovery.eu.
Practicals will be run in parallel sessions on each site and shared morning 
lectures on the background and technical aspects will be followed jointly by 
all the participants.
It comprises sample vitrification, focused ion beam milling to obtain lamella 
and cryo-ET data acquisition & evaluation.

If you are interested to join please register here: 
https://inextfibet.sciencesconf.org/

Best regards,

Bruno Klaholz

On behalf of the organizing committee
Bruno Klaholz (CBI/IGBMC), Julia Mahamid (EMBL-HD), Ludo Renault (NeCEN), Jirka 
Novacek (CEITEC)



###
Bruno P. Klaholz
Centre for Integrative Biology
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 1258
1, rue Laurent Fries
BP 10142
67404 ILLKIRCH CEDEX
FRANCE
Tel. from abroad: 0033.369.48.52.78
Tel. inside France: 03.69.48.52.78
websites:
http://www.igbmc.fr/Klaholz
http://www.igbmc.fr/grandesstructures/cbi
https://frisbi.eu
http://instruct-eric.com
https://inext-discovery.eu





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Re: [ccp4bb] Regarding the diffraction image

[Ben Bax]

Hi Kavya,
More than one crystal? 
Epitaxial growth (protein crystal growing on salt crystal or vice versa)
Did you try IZIT? 
(https://hamptonresearch.com/product-Izit-Crystal-Dye-33.html).

I have seen salt and protein crystals in the same drop before now - but not 
growing together.
Ben

On 3 Feb 2023, at 22:15, CRAIG A BINGMAN 
<21371e2fba31-dmarc-requ...@jiscmail.ac.uk> wrote:

Oxidation products of TCEP crystallize in the presence of zinc ions. These 
crystals fluoresce strongly under UV, which seems like a dirty trick, if your 
expectation is that only protein crystals can do that. The brightfield white 
light image of the crystals is also consistent with not-protein crystals, 
because of the high refractive index contrast between the crystals and the 
mother liquor.
 
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of kavyashreem 
mailto:kavyashr...@instem.res.in>>
Date: Friday, February 3, 2023 at 2:32 AM
To: CCP4BB@JISCMAIL.AC.UK  mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Regarding the diffraction image

Dear all,

We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
condition 10%PEG3350, 50mM Zinc acetate.
Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8. 
Crystal: Crystal:   crystal 
under UV m
<8ef9453e.png>
When we collected the data at an in-house facility, it looked something like 
this:

The minimum resolution spot is around 9Ang and maximum ~2.2Ang.
I have not come across a protein diffraction like this, nor of a salt. When I 
ran the gel for the incubated protein (protein+ligand), there was no 
degradation.
Although, I was sure there is some problem with this image I tried processing, 
which could not be, But indexing showed a unit cell  of 11Ang, 11Ang, 46Ang in 
P3. which was quite expected for two of the axes but not the third.
Can anyone please shed some light on this diffraction image?
How can it happen?
 
Thank you
Regards
Kavya
 
 
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[ccp4bb] Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023

[Armando Albert]

Dear all, 

The registration for the next edition of the Macromolecular Crystallography 
School in Madrid from the 8th to the 12th of May 2023 is open. 

The workshop has been organized at Instituto de Química Física Rocasolano CSIC 
since 2010 and it is meant for 25 graduate students or researchers with 
previous expertise in crystallography and/or CryoEM who need a deeper insight 
into the most advanced crystallographic and CryoEM techniques to carry out 
their research projects. The program traditionally covers aspects such as 
sample preparation, structure solution, model building, crystallographic 
refinement, validation, and analysis of the structural results, as well as an 
overview of the newest structural biology technologies. On top of these 
subjects, this year's program will include those aspects related to the impact 
of Artificial Intelligence methods on structure solution and low-resolution 
refinement. In addition, we will cover dynamic crystallography at XFEL and 
synchrotron and ligand building for drug discovery. 
 
You may find further information on our website 
(https://www.xtal.iqfr.csic.es/MCCS2023/index.html 
)
 

Hoping to see you In Madrid
 
Juan and Armando

Armando Albert and Juan A. Hermoso
Departamento de Cristalografía y Biología Estructural
Instituto de Química Física "Rocasolano",
Consejo Superior de Investigaciones Científicas
Serrano 119, 28006 Madrid
Spain


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Re: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

[Julia Griese]

Oh, I hadn’t thought of trying that, that works!

Obviously it would still be great if this issue was fixed (I guess it’s MacOS 
rather than PyMOL that’s to blame here), but this is a decent workaround.

Thanks!

/Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/

From: CCP4 bulletin board  on behalf of Nicholas Clark 

Reply-To: Nicholas Clark 
Date: Monday, February 6, 2023 at 12:46
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2



-- Forwarded message -
From: Nicholas Clark mailto:ndcla...@buffalo.edu>>
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese mailto:julia.gri...@icm.uu.se>>

Julia,

I have the same issue with PyMOL. After it opens the blank session, if you 
return to the file explorer and try to reopen the file it will open the session 
correctly. Seems what you’re trying to open gets “lost” while loading PyMOL.

Best,

Nick Clark

On Mon, Feb 6, 2023 at 5:38 AM Julia Griese 
mailto:julia.gri...@icm.uu.se>> wrote:
Hi all,

I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my 
computer’s nagging) and am now encountering some issues with Coot and PyMOL. 
The issues persist after updating to version 13.2.

Regarding Coot version 0.9.8.7: The rotate/translate zone 
function does not work properly. Everything works when using the slider bars in 
the dialog, and translating with the mouse works, but rotating with the mouse 
does not work. The region to be rotated disappears from view. I can make do 
with the slider bars, but feel that I have much better fine control and it’s 
much faster when using the mouse to rotate. Has anyone else encountered this 
problem and knows of a workaround?
(I’m aware of the workaround for the main window disappearing when you delete 
items.)

Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to 
open any kind of file that is set to open in PyMOL by default (pdb or cif 
coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL 
files through the File Open dialog, having to navigate through the entire 
folder structure first, which obviously takes much longer. Has anyone else 
encountered this issue and knows how to fix it?


Best,

Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/








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--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908
--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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CAUTION: Do not click on links or open attachments unless you recognise the 
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[ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

[Nicholas Clark]

-- Forwarded message -
From: Nicholas Clark 
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese 


Julia,

I have the same issue with PyMOL. After it opens the blank session, if you
return to the file explorer and try to reopen the file it will open the
session correctly. Seems what you’re trying to open gets “lost” while
loading PyMOL.

Best,

Nick Clark

On Mon, Feb 6, 2023 at 5:38 AM Julia Griese  wrote:

> Hi all,
>
>
>
> I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my
> computer’s nagging) and am now encountering some issues with Coot and
> PyMOL. The issues persist after updating to version 13.2.
>
>
>
> *Regarding Coot version 0.9.8.7 :* The rotate/translate
> zone function does not work properly. Everything works when using the
> slider bars in the dialog, and translating with the mouse works, but
> rotating with the mouse does not work. The region to be rotated disappears
> from view. I can make do with the slider bars, but feel that I have much
> better fine control and it’s much faster when using the mouse to rotate.
> Has anyone else encountered this problem and knows of a workaround?
>
> (I’m aware of the workaround for the main window disappearing when you
> delete items.)
>
>
>
> *Regarding PyMOL version 2.5.4 *(had the same issue with 2.4.1): When I
> try to open any kind of file that is set to open in PyMOL by default (pdb
> or cif coordinates, pse), PyMOL opens, but to an empty session. I can only
> open PyMOL files through the File Open dialog, having to navigate through
> the entire folder structure first, which obviously takes much longer. Has
> anyone else encountered this issue and knows how to fix it?
>
>
>
>
>
> Best,
>
>
>
> Julia
>
>
>
> --
>
> Dr. Julia Griese
>
> Assistant Professor/Docent
>
> Department of Cell and Molecular Biology
>
> Uppsala University
>
> BMC, Box 596
>
> SE-75124 Uppsala
>
> Sweden
>
>
>
> email: julia.gri...@icm.uu.se
>
> phone: +46-(0)18-471 4982
>
> http://www.icm.uu.se/structural-biology/griese-lab/
> 
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>
> E-mailing Uppsala University means that we will process your personal
> data. For more information on how this is performed, please read here:
> http://www.uu.se/en/about-uu/data-protection-policy
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908
-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] CCPBioSim Industry Talk

[Sarah Fegan - STFC UKRI]

Dear all,

We are very excited to be hosting Julien Michel for his Industry Talk 
presentation on the 8th March 2023 at 2pm:

"Promoting open collaboration in computer-aided drug design with the OpenBioSim 
Community Interest Company".

You can register for the seminar below:
https://www.ccpbiosim.ac.uk/openbiosim2023

And here is Julien's abstract:
Abstract
OpenBioSim (OBS) is a not-for-profit company that aims to promote and sustain 
the use of open-source chemical research software in academia and industry. OBS 
works with industry partners to integrate open-source software as components of 
technology platforms, and to provide long term support for open-source projects 
that have demonstrated scientific utility.
This webinar will discuss the motivations for setting up OpenBioSim, and 
highlight the work OpenBioSim is currently doing with the open-source projects 
Sire and BioSimSpace to support industrial applications in the domain of 
computer-aided drug design.
www.openbiosim.org

We look forward to seeing you there!!
Sarah Harris, Sarah Fegan and Nicolas Foloppe



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[ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

[Julia Griese]

Hi all,

I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my 
computer’s nagging) and am now encountering some issues with Coot and PyMOL. 
The issues persist after updating to version 13.2.

Regarding Coot version 0.9.8.7: The rotate/translate zone function does not 
work properly. Everything works when using the slider bars in the dialog, and 
translating with the mouse works, but rotating with the mouse does not work. 
The region to be rotated disappears from view. I can make do with the slider 
bars, but feel that I have much better fine control and it’s much faster when 
using the mouse to rotate. Has anyone else encountered this problem and knows 
of a workaround?
(I’m aware of the workaround for the main window disappearing when you delete 
items.)

Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to 
open any kind of file that is set to open in PyMOL by default (pdb or cif 
coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL 
files through the File Open dialog, having to navigate through the entire 
folder structure first, which obviously takes much longer. Has anyone else 
encountered this issue and knows how to fix it?


Best,

Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/








När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
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