Re: [ccp4bb] Reg. ITC machine

2023-08-09 Thread Matthew Whitley 
Hello Sivaraman,

We have a Malvern MicroCal PEAQ-ITC system in our lab that is used regularly.  
In general, we are pleased with the machine.  We have experienced no major 
problems with the instrument, the data quality is good, and replicate 
measurements yield very similar results.  I have never used the Affinity ITC 
from TA Instruments, so I cannot comment on that system.

Matthew



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Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

2023-08-09 Thread David Lawson (JIC) 
Thanks both!

Dave

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson 
Email: david.law...@jic.ac.uk


-Original Message-
From: CCP4 bulletin board  On Behalf Of Charles Ballard 
- STFC UKRI
Sent: Wednesday, August 9, 2023 3:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement 
is broken in 0.9.8.7]

In answer to Paul, should be available soon.   Targeting Monday.

-Original Message-
From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 09 August 2023 15:31
To: ccp4bb 
Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement 
is broken in 0.9.8.7]

On 09/08/2023 10:54, David Lawson (JIC) wrote:
> Hi Paul,
>
> Just wondering where we are with this fix.

The blog is generally the place to turn for this sort of thing.

Having said that, I missed the post about 0.9.8.9! But I have added one for 
0.9.8.91 (that revision fixed the missing peptide omega graph and fixes 
"Replace Residue" (needed for the upcoming Summer School)).

As to if/when that gets added to CCP4, that is up to Charles.

> Is it safe to apply the latest CCP4 updates?


Isn't it always?


Paul.


>
> Many thanks
>
> Dave
>
> ---
>
> Prof. David M. Lawson
> Department of Biochemistry and Metabolism, John Innes Centre, Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Web: https://www.jic.ac.uk/people/david-lawson
> Email: david.law...@jic.ac.uk
>
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Paul 
> Emsley
> Sent: Tuesday, July 18, 2023 5:11 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space 
> refinement is broken in 0.9.8.7]
>
> On 18/07/2023 03:55, Mark Saper wrote:
>> I reported this problem to Paul and to the group at least 2-3 months ago.
> Your email didn't arrive.
>
> Just to be clear, Coot's real space refinement is not (was not) broken, the 
> problem is that the version of Coot distributed by CCP4 and the version of 
> the monomer library distributed by CCP4 were not compatible.
>
>> It affects protein as well as [nucleic] acid.  I never heard back 
>> from Paul if a fix was in progress.
> Keitaro Yamashita alerted me to the problem in a timely fashion and an update 
> to Coot was added and documented in early June.
>
>
> [To Charles in particular] My commitments will be out of the way at 
> the end of the week and I hereby commit to making the 0.9.8.9 release 
> early next week.
>
>
> Paul.
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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> ##
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>
>
> --
> CAUTION: This email originated from outside of the LMB.
> Do not click links or open attachments unless you recognize the sender and 
> know the content is safe.
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Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

2023-08-09 Thread Charles Ballard - STFC UKRI 
In answer to Paul, should be available soon.   Targeting Monday.

-Original Message-
From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 09 August 2023 15:31
To: ccp4bb 
Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement 
is broken in 0.9.8.7]

On 09/08/2023 10:54, David Lawson (JIC) wrote:
> Hi Paul,
>
> Just wondering where we are with this fix.

The blog is generally the place to turn for this sort of thing.

Having said that, I missed the post about 0.9.8.9! But I have added one for 
0.9.8.91 (that revision fixed the missing peptide omega graph and fixes 
"Replace Residue" (needed for the upcoming Summer School)).

As to if/when that gets added to CCP4, that is up to Charles.

> Is it safe to apply the latest CCP4 updates?


Isn't it always?


Paul.


>
> Many thanks
>
> Dave
>
> ---
>
> Prof. David M. Lawson
> Department of Biochemistry and Metabolism, John Innes Centre, Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Web: https://www.jic.ac.uk/people/david-lawson
> Email: david.law...@jic.ac.uk
>
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Paul 
> Emsley
> Sent: Tuesday, July 18, 2023 5:11 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space 
> refinement is broken in 0.9.8.7]
>
> On 18/07/2023 03:55, Mark Saper wrote:
>> I reported this problem to Paul and to the group at least 2-3 months ago.
> Your email didn't arrive.
>
> Just to be clear, Coot's real space refinement is not (was not) broken, the 
> problem is that the version of Coot distributed by CCP4 and the version of 
> the monomer library distributed by CCP4 were not compatible.
>
>> It affects protein as well as [nucleic] acid.  I never heard back 
>> from Paul if a fix was in progress.
> Keitaro Yamashita alerted me to the problem in a timely fashion and an update 
> to Coot was added and documented in early June.
>
>
> [To Charles in particular] My commitments will be out of the way at 
> the end of the week and I hereby commit to making the 0.9.8.9 release 
> early next week.
>
>
> Paul.
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
>
>
> --
> CAUTION: This email originated from outside of the LMB.
> Do not click links or open attachments unless you recognize the sender and 
> know the content is safe.
> .-owner-ccp...@jiscmail.ac.uk-.



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Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

2023-08-09 Thread Paul Emsley 

On 09/08/2023 10:54, David Lawson (JIC) wrote:

Hi Paul,

Just wondering where we are with this fix.


The blog is generally the place to turn for this sort of thing.

Having said that, I missed the post about 0.9.8.9! But I have added one 
for 0.9.8.91 (that revision fixed the missing peptide omega graph and 
fixes "Replace Residue" (needed for the upcoming Summer School)).


As to if/when that gets added to CCP4, that is up to Charles.


Is it safe to apply the latest CCP4 updates?



Isn't it always?


Paul.




Many thanks

Dave

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk


-Original Message-
From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: Tuesday, July 18, 2023 5:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is 
broken in 0.9.8.7]

On 18/07/2023 03:55, Mark Saper wrote:

I reported this problem to Paul and to the group at least 2-3 months ago.

Your email didn't arrive.

Just to be clear, Coot's real space refinement is not (was not) broken, the 
problem is that the version of Coot distributed by CCP4 and the version of the 
monomer library distributed by CCP4 were not compatible.


It affects protein as well as [nucleic] acid.  I never heard back from
Paul if a fix was in progress.

Keitaro Yamashita alerted me to the problem in a timely fashion and an update 
to Coot was added and documented in early June.


[To Charles in particular] My commitments will be out of the way at the
end of the week and I hereby commit to making the 0.9.8.9 release early
next week.


Paul.



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--
CAUTION: This email originated from outside of the LMB.
Do not click links or open attachments unless you recognize the sender and know 
the content is safe.
.-owner-ccp...@jiscmail.ac.uk-.




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[ccp4bb] Introducing ‘Covalently Linked Components’ and enriched ligand information at PDBe

2023-08-09 Thread David Armstrong 

Dear all,


We are excited to announce the introduction of Covalently Linked 
Components (CLCs), a new class of reference small molecules that 
facilitates identification of covalently linked multi-component ligands 
across the whole PDB archive. This enhancement vastly improves the 
accessibility and usability of small molecule data for users. Alongside 
CLCs, we have further enriched the existing Peptide-like molecules 
Reference Dictionary (PRD) files by providing additional metadata, such 
as chemical properties and mapping between these molecules and other 
chemical data resources.



As part of the update, we are also making changes to the PDBeChem FTP 
directory structure, aimed at enhancing user experience and making small 
molecule data in the Protein Data Bank in Europe (PDBe) more accessible. 
In this update, we have introduced separate folders for three types of 
reference files: Chemical Components (CCD), Covalently Linked Components 
(CLC), and Peptide-like molecules Reference Dictionary (PRD), making it 
easier for users to access specific data.



The PDBeChem pipeline that powers this process and updates this data 
weekly, uses PDBe CCDUtils as its primary package. PDBe CCDUtils is an 
RDKit-based toolkit for handling and analysing small molecules in the PDB.



For more information about CLC and these changes, 
visit:https://www.ebi.ac.uk/pdbe/news/introducing-covalently-linked-components 




*Urgent Notice:* Effective from January 1st, 2024, we will be retiring 
the top-level sub-directories and files related to CCD (Chemical 
Components) as part of our ongoing updates. This decision has been made 
to streamline our data organisation and improve the user experience. 
Detailed information regarding this change is provided in the 
README.txt, accessible 
at:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/README.txt 
.



We value your cooperation and understanding as we strive to improve our 
data infrastructure and user accessibility. Thankyou for your continued 
support.



Kind Regards,

David

--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK



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Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]

2023-08-09 Thread David Lawson (JIC) 
Hi Paul,

Just wondering where we are with this fix. Is it safe to apply the latest CCP4 
updates?

Many thanks

Dave

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson 
Email: david.law...@jic.ac.uk


-Original Message-
From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: Tuesday, July 18, 2023 5:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is 
broken in 0.9.8.7]

On 18/07/2023 03:55, Mark Saper wrote:
> I reported this problem to Paul and to the group at least 2-3 months ago.

Your email didn't arrive.

Just to be clear, Coot's real space refinement is not (was not) broken, the 
problem is that the version of Coot distributed by CCP4 and the version of the 
monomer library distributed by CCP4 were not compatible.

> It affects protein as well as [nucleic] acid.  I never heard back from 
> Paul if a fix was in progress.

Keitaro Yamashita alerted me to the problem in a timely fashion and an update 
to Coot was added and documented in early June.


[To Charles in particular] My commitments will be out of the way at the 
end of the week and I hereby commit to making the 0.9.8.9 release early 
next week.


Paul.



To unsubscribe from the CCP4BB list, click the following link:
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