[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre – deadline extended to 24th June

[David Lawson (JIC)]

Hi All,

The John Innes Centre in Norwich (UK) will be hosting this year’s CCP4-BCA 
Protein Crystallography Summer School.

We will cover the range of techniques required for a protein structure solution 
from protein expression through to structure validation. We have a great 
line-up of tutors and a full programme of lectures, practicals and social 
events. You will interact with experts in the field and will have the 
opportunity to get help with analysing your own data.

Please follow this link for more details and to apply:
https://www.jic.ac.uk/event/ccp4-bca-protein-crystallography-summer-school-2024/

Best wishes

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





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[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre

[David Lawson (JIC)]

Hi All,

The deadline for applications is rapidly approaching – please apply by 10th 
June.

Dave

-

Hi All,

The John Innes Centre in Norwich (UK) will be hosting this year’s CCP4-BCA 
Protein Crystallography Summer School.

Please follow this link for more details and to apply:
https://www.jic.ac.uk/event/ccp4-bca-protein-crystallography-summer-school-2024/

Best wishes

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





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[ccp4bb] CCP4-BCA Protein Crystallography Summer School (1st – 6th Sept 2024) hosted by the John Innes Centre

[David Lawson (JIC)]

Hi All,

The John Innes Centre in Norwich (UK) will be hosting this year’s CCP4-BCA 
Protein Crystallography Summer School.

Please follow this link for more details and to apply:
https://www.jic.ac.uk/event/ccp4-bca-protein-crystallography-summer-school-2024/

Best wishes

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





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[ccp4bb] Structural Biology Facility Manager vacancy at the John Innes Centre, Norwich UK

[David Lawson (JIC)]

Dear All,

We have a vacancy for a Structural Biology Facility Manager at the John Innes 
Centre.

The John Innes Centre is an independent, international centre of excellence in 
plant and microbial sciences. We nurture a creative, curiosity-led approach to 
answering important questions in bioscience, and translate that knowledge into 
societal benefits. Recent investment from the UKRI Infrastructure Fund will 
ensure the JIC's ability to contribute cutting-edge, world-leading research 
into the future, underpinned by excellent facilities. We are an equal 
opportunities employer, actively supporting inclusivity and diversity, and we 
provide support for ongoing career development.

We are looking for someone with extensive postdoctoral expertise in protein 
crystallography; experience of cryo-EM and SAXS would also be advantageous. The 
successful applicant will oversee the Facility and contribute to a wide variety 
of projects. The post holder will be expected to provide training and to ensure 
financial sustainability of the Facility though usage recharges and funding 
applications.

Closing date - 7th March 2024.
Salary - £43,550 - £54,900
Contract - indefinite, full-time

For further details, please visit our website http://jobs.jic.ac.uk or contact 
the Human Resources team on 01603 450814 or nbi.recruitm...@nbi.ac.uk quoting 
reference 1004561.

Best Wishes,

Dave Lawson

---

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





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[ccp4bb] Structural Biology Facility Manager vacancy at the John Innes Centre, Norwich UK

[David Lawson (JIC)]

Dear All,

We have a vacancy for a Structural Biology Facility Manager at the John Innes 
Centre.

The John Innes Centre is an independent, international centre of excellence in 
plant and microbial sciences. We nurture a creative, curiosity-led approach to 
answering important questions in bioscience, and translate that knowledge into 
societal benefits. Recent investment from the UKRI Infrastructure Fund will 
ensure the JIC's ability to contribute cutting-edge, world-leading research 
into the future, underpinned by excellent facilities. We are an equal 
opportunities employer, actively supporting inclusivity and diversity, and we 
provide support for ongoing career development.

We are looking for someone with extensive postdoctoral expertise in protein 
crystallography; experience of cryo-EM and SAXS would also be advantageous. The 
successful applicant will oversee the Facility and contribute to a wide variety 
of projects. The post holder will be expected to provide training and to ensure 
financial sustainability of the Facility though usage recharges and funding 
applications.

Closing date - 3rd December 2023.
Salary - £43,550 - £54,900
Contract - indefinite, full-time

For further details, please visit our website http://jobs.jic.ac.uk or contact 
the Human Resources team on 01603 450814 or nbi.recruitm...@nbi.ac.uk quoting 
reference 1004561.

Best Wishes,

Dave Lawson

---

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





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Re: [ccp4bb] re-open the results from a previous DIALS User Interface session in CCP4 cloud?

[David Lawson (JIC)]

Hi both,

Thanks for the suggestions. I will see if I can find a workable solution based 
on what you say.  

Best wishes

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 Maria Fando
Sent: Thursday, August 17, 2023 7:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] re-open the results from a previous DIALS User Interface 
session in CCP4 cloud?

Hi Luiso,


All correct, thank you for replying 


Cheers,
Maria



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[ccp4bb] re-open the results from a previous DIALS User Interface session in CCP4 cloud?

[David Lawson (JIC)]

Hi All,

In CCP4i2 it is possible to re-open the results from a previous DUI session by 
cloning the job and selecting the "Continue from previous dials session" option 
from the drop-down. I'm trying to find a way to do this in CCP4 cloud for a 
tutorial - perhaps it's not possible?

Any suggestions?

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





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

[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:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
>
> ##
> ##
>
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>
> 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]

[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.



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Re: [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL?

[David Lawson (JIC)]

Hi Eugene,

Many thanks – that’s sorted it!

Best wishes

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<mailto:david.law...@jic.ac.uk>


From: Eugene Pichkur 
Sent: Monday, July 17, 2023 11:59 AM
To: David Lawson (JIC) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL?

You don't often get email from 
eugene.pich...@gmail.com<mailto:eugene.pich...@gmail.com>. Learn why this is 
important<https://aka.ms/LearnAboutSenderIdentification>
Hi!

Yes, it's been broken for a long time, but it will be fixed in Coot very soon 
[https://pemsley.github.io/coot/blog/2023/06/05/AA-RNA.html].
A workaround is to downgrade to CCP4 v. 8.0.006 (Coot v. 0.9.8.5) through the 
CCP4 Update Manager.

Best,
Eugene

On Mon, Jul 17, 2023 at 1:45 PM David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:
Hi All,

Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am 
seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an 
M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and 
finding that often when I do real space refinement (well, I mostly use tandem 
refinement) the atoms just shoot off in one direction to give a very scrambled 
structure, even if I am just doing final tweaks on a close to final structure. 
I don’t know if it has something to do with the DNA restraints, because 
refining the protein in regions distant from the DNA seems fine, whereas 
working on protein regions close to the DNA, or on the DNA itself, generally 
results in a mess.

However, if I revert to COOT 0.9.6 EL (as distributed with CCP4-7) with the 
same input files, the problem goes away.

Any help much appreciated,

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<mailto:david.law...@jic.ac.uk>





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[ccp4bb] real space refinement broken in COOT 0.9.8.8 EL?

[David Lawson (JIC)]

Hi All,

Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am 
seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an 
M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and 
finding that often when I do real space refinement (well, I mostly use tandem 
refinement) the atoms just shoot off in one direction to give a very scrambled 
structure, even if I am just doing final tweaks on a close to final structure. 
I don't know if it has something to do with the DNA restraints, because 
refining the protein in regions distant from the DNA seems fine, whereas 
working on protein regions close to the DNA, or on the DNA itself, generally 
results in a mess.

However, if I revert to COOT 0.9.6 EL (as distributed with CCP4-7) with the 
same input files, the problem goes away.

Any help much appreciated,

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





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Re: [ccp4bb] Unidentified density

[David Lawson (JIC)]

Hi Zeya,

Did you cryoprotect with glycerol perhaps?

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


From: CCP4 bulletin board  On Behalf Of zeyaul islam
Sent: 21 February 2023 11:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified density

You don't often get email from zeya1...@gmail.com. 
Learn why this is important
Dear all
 We have solved the structure of nanobody at 1.25 angstrom. We observe some 
unidentified density near the serine. Please have a look at the figures. 
Protein was purified in PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 
2 mM KH2PO4) and the crystallisation condition has 0.1 M BIS-TRIS pH 5.5, 2.0 M 
ammonium sulfate. Any ideas what this could be? I tried SO4 and PO4 but didn’t 
satisfy the observed electron density.
I appreciate any help you can provide.
Thanks
Zeya
Zeyaul Islam, PhD
QBRI - Qatar Biomedical Research Institute
P.O. Box: 34110
Doha – Qatar
Tel: +974 445 46690




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[ccp4bb] Application deadline approaching - Virtual CCP4 Protein Crystallography Summer School 2021 (6th-10th September)

[David Lawson (JIC)]

Dear colleagues,

We are pleased to announce the Virtual CCP4 Protein Crystallography Summer 
School 2021 to be hosted by the John Innes Centre (Norwich, UK).

The school will take place from Monday 6 September – Friday 10 September 
inclusive and is intended for students and researchers new to crystallography. 
Its dual aims are to provide comprehensive training in crystallography and to 
promote best practice. The lectures cover the range of techniques required for 
protein structure solution, from protein expression through to structure 
validation. Intensively supervised computer tutorials enable students to relate 
the theory presented in the lectures to practice.

The application deadline is Thursday 5 August 2021
(don’t leave it to the last minute – your application needs to be supported by 
your supervisor or line manager)

For further information and to apply please follow this link:
https://www.jic.ac.uk/training-careers/summer-schools/ccp4-protein-crystallography-summer-school/

Best wishes,

Dave, Clare, Julia, Naomi and Sarah (organisers)




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[ccp4bb] Virtual CCP4 Protein Crystallography Summer School 2021 (6th-10th September) - applications open

[David Lawson (JIC)]

Dear colleagues,

We are pleased to announce the Virtual CCP4 Protein Crystallography Summer 
School 2021 to be hosted by the John Innes Centre (Norwich, UK).

The school will take place from Monday 6 September – Friday 10 September 
inclusive and is intended for students and researchers new to crystallography. 
Its dual aims are to provide comprehensive training in crystallography and to 
promote best practice. The lectures cover the range of techniques required for 
protein structure solution, from protein expression through to structure 
validation. Intensively supervised computer tutorials enable students to relate 
the theory presented in the lectures to practice.

The application deadline is Thursday 5 August 2021

For further information and to apply please follow this link:
https://www.jic.ac.uk/training-careers/summer-schools/ccp4-protein-crystallography-summer-school/

Best wishes,

Dave, Clare, Julia, Naomi and Sarah (organisers)




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Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

[David Lawson (JIC)]

…and make this the default 

Garib and Rob cc’d…

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
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

From: Eleanor Dodson 
Sent: 09 February 2021 13:33
To: David Lawson (JIC) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

Yes, I agree.. garish? Rob Nichols?? Can you email this to them directly? E

On Tue, 9 Feb 2021 at 13:28, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:
Hi Eleanor,

I’m glad it’s not just me then.
I too tried the grepping option, but my recollection was that that didn’t go 
too well either. It doesn’t help that I’m not very comfortable with MMCIF 
format yet…
Also, I forgot to mention, but was just reminded that you can change “Output 
calculated riding hydrogens to file” to “No” in the Output tab of REFMAC, but 
it still writes them to the MMCIF!
Without wishing to start a lengthy email discussion, can’t we just have the 
option to write an MMCIF without hydrogens from REFMAC?

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
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<mailto:david.law...@jic.ac.uk>

From: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Sent: 09 February 2021 13:15
To: David Lawson (JIC) mailto:david.law...@jic.ac.uk>>
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>
Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

I took this up with pdbe but what with lock down and all I am not too sure what 
the decision was ( or whether there was one) maybe you could start a chat to 
the pdbe lot
Our code was d- 1292109592.

It was a mess - tony Wilkinson was depositing the data from the labs, I had 
been doing refinement from home so we didn’t have a proper deposition 
directory. And then they grumbled about hydrogens with zero occupancy. I 
grepped them out of the Mcciff file but it isn’t the best silution
On Tue, 9 Feb 2021 at 12:29, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:
Hi All,

By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens 
during refinement. It then writes out a PDB file without the hydrogens and an 
MMCIF file that retains these hydrogens. In the latter, you end up with mostly 
hydrogens with unit occupancy and a few with zero occupancy. Upon further 
investigation it seems the latter are mostly polar hydrogens, but some sit at 
the end of side-chains that have been truncated (I don’t want restart the 
discussion about whether you should or should not truncate side-chains). As a 
result, if you use the latter for deposition, which is the only option if you 
use the CCP4I2 “New Deposition Task”, you run into trouble. So my question is: 
how can I stop REFMAC from writing the hydrogens to the MMCIF file (I also 
don’t want to restart the discussion about whether you should or should not 
deposit hydrogens)? The alternative is that I revert to using the more tedious 
option of the pdb_extract server since that works with a PDB file.

Thanks in advance,

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
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<mailto:david.law...@jic.ac.uk>




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Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

[David Lawson (JIC)]

Hi Eleanor,

I’m glad it’s not just me then.
I too tried the grepping option, but my recollection was that that didn’t go 
too well either. It doesn’t help that I’m not very comfortable with MMCIF 
format yet…
Also, I forgot to mention, but was just reminded that you can change “Output 
calculated riding hydrogens to file” to “No” in the Output tab of REFMAC, but 
it still writes them to the MMCIF!
Without wishing to start a lengthy email discussion, can’t we just have the 
option to write an MMCIF without hydrogens from REFMAC?

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
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

From: Eleanor Dodson 
Sent: 09 February 2021 13:15
To: David Lawson (JIC) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

I took this up with pdbe but what with lock down and all I am not too sure what 
the decision was ( or whether there was one) maybe you could start a chat to 
the pdbe lot
Our code was d- 1292109592.

It was a mess - tony Wilkinson was depositing the data from the labs, I had 
been doing refinement from home so we didn’t have a proper deposition 
directory. And then they grumbled about hydrogens with zero occupancy. I 
grepped them out of the Mcciff file but it isn’t the best silution
On Tue, 9 Feb 2021 at 12:29, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:
Hi All,

By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens 
during refinement. It then writes out a PDB file without the hydrogens and an 
MMCIF file that retains these hydrogens. In the latter, you end up with mostly 
hydrogens with unit occupancy and a few with zero occupancy. Upon further 
investigation it seems the latter are mostly polar hydrogens, but some sit at 
the end of side-chains that have been truncated (I don’t want restart the 
discussion about whether you should or should not truncate side-chains). As a 
result, if you use the latter for deposition, which is the only option if you 
use the CCP4I2 “New Deposition Task”, you run into trouble. So my question is: 
how can I stop REFMAC from writing the hydrogens to the MMCIF file (I also 
don’t want to restart the discussion about whether you should or should not 
deposit hydrogens)? The alternative is that I revert to using the more tedious 
option of the pdb_extract server since that works with a PDB file.

Thanks in advance,

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
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<mailto:david.law...@jic.ac.uk>




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[ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

[David Lawson (JIC)]

Hi All,

By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens 
during refinement. It then writes out a PDB file without the hydrogens and an 
MMCIF file that retains these hydrogens. In the latter, you end up with mostly 
hydrogens with unit occupancy and a few with zero occupancy. Upon further 
investigation it seems the latter are mostly polar hydrogens, but some sit at 
the end of side-chains that have been truncated (I don't want restart the 
discussion about whether you should or should not truncate side-chains). As a 
result, if you use the latter for deposition, which is the only option if you 
use the CCP4I2 "New Deposition Task", you run into trouble. So my question is: 
how can I stop REFMAC from writing the hydrogens to the MMCIF file (I also 
don't want to restart the discussion about whether you should or should not 
deposit hydrogens)? The alternative is that I revert to using the more tedious 
option of the pdb_extract server since that works with a PDB file.

Thanks in advance,

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
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




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[ccp4bb] running the CCP4i2 export utility from the command line?

[David Lawson (JIC)]

Hi All,

I would like to run the CCP4i2 export utility from the command line (on a Mac) 
to produce a zip file from a project directory that can then be imported in the 
normal way using the CCP4i2 GUI. I assume this is possible?

Thanks in advance

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
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




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Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Lawson (JIC)]

Just to follow up on this one...

The problem was at my end, there was an issue with the upload from my iMac 
(possibly something to do with the system's proxy server settings). When I 
switched to using a PC, everything works as it should.
N.B. when providing a scaled but unmerged mtz, it is important to have the 
"Check here if the data are unmerged but already scaled ..." button checked.

Thanks to Ian and Clemens at Global Phasing for help with troubleshooting.

Dave

---

Prof. David M. Lawson
Department of Biological Chemistry,
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<mailto:david.law...@jic.ac.uk>

From: CCP4 bulletin board  On Behalf Of David Waterman
Sent: 14 January 2020 11:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

Hi Eleanor,

MTZ history is still useful, so from a recent xia2 run I can see (with mtzdmp):

 * HISTORY for current MTZ file :

 From DIALS 2.0.1-gb22bab67b-release, run on 2019-11-21 at 10:59:17 GMT

It isn't possible to tell that the data were actually scaled in DIALS too 
though, apart from the lack of POINTLESS and AIMLESS lines within the history. 
As Graeme says, I think there are opportunities here for more sophisticated 
tracking of provenance - certainly going back as far as telling us where and 
when the images were collected would be most useful.

Cheers
-- David


On Tue, 14 Jan 2020 at 11:04, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Not quite relevent but is there some way of stamping these files with a record 
of where they were generated ?
I used to use my ability to read - name them myself as
SAMPLEX-dialsprocessing-unmerged.mtz then
SAMPLEX-dialsprocessing-unmerged-staranisod.mtz

and there is an mtz feature which wrote a history with dates as well but now 
with automated file naming it is hard to keep track of how a file was generated.


It seems likely that lots of Table !s do not describe the data set that was 
actually used for structure solution and deposition!

Eleanor

On Tue, 14 Jan 2020 at 10:11, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:
Dear  Dave, Star Aniso Developers,

If this turns out to be because we are “missing something” i.e. there is an 
expectation on a property being present in the output files but it’s not there 
in our MTZ output, please let us know :-)

Best wishes Graeme


On 14 Jan 2020, at 09:06, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an “Internal Server Error” after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don’t get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
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<mailto:david.law...@jic.ac.uk>




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[ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

[David Lawson (JIC)]

Dear ccp4bb

I am trying to get the staraniso server to accept a scaled but unmerged mtz 
file from DIALS processing, but it reports an "Internal Server Error" after 
thinking about it for a while. Should this be possible? The file is 31 MB, so 
not huge.

It works fine for a merged mtz from DIALS, but this is not the preferred option 
and I don't get the full statistics I need for Table 1.

Thanks in advance

Dave Lawson

---

Prof. David M. Lawson
Department of Biological Chemistry,
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




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[ccp4bb] Warning - ccp4 update 7.0.069 breaks ccp4i2 on MacBook running Mojave (v 10.14.2)

[david lawson (JIC)]

Hi All,

I installed the latest ccp4 update on my MacBook through the CCP4i2 update 
manager. After doing so, refmac appeared to be broken. I tried to restart the 
I2 GUI but it refused to even after a reboot.
Eventually I got running again by uninstalling this update through the CCP4i 
update manager (i.e. the old GUI). After cloning my failed refmac job in 
CCP4i2, it ran without a hitch.

Dave

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk




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Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

[david lawson (JIC)]

Hi All,

In a similar vein, does anyone have a photo of the eight cassette carousel 
(ideally in situ on a beamline) that was used to collect data on film at 
Daresbury?

Many thanks,

Dave

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk

From: CCP4 bulletin board  On Behalf Of Harry Powell
Sent: 27 November 2018 12:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

Hi Elspeth

That's brilliant - no, it's not too late by any means. Photos of other obsolete 
detectors are also welcome!


On 27 Nov 2018, at 12:40, Elspeth Garman wrote:


I have one of the LMB Cambridge one.
Can dig it out for you but not till Monday. Is that too late?
Elspeth
Sent from my iPhone

On 27 Nov 2018, at 12:35, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi

I was wondering if anyone out there has a decent-quality photograph of an 
Enraf-Nonius FAST detector that I could use? I believe that one was installed 
at SRS Daresbury in 1983...

Harry
--
Dr Harry Powell





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[ccp4bb] Name that protein!

[david lawson (JIC)]

Hi All,

Many thanks to those who responded. The general opinion is that it is some sort 
of pore/channel, possibly a voltage-gated potassium or sodium channel.

Best wishes,

Dave



Hi All

Apologies for the off-topic question.

The attached image has been hanging on the wall at our institute for several 
years and nobody knows what it is or who generated it.

If anyone recognises it, please let me know.

Many thanks

Dave Lawson

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk




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[ccp4bb] Name that protein!

[david lawson (JIC)]

Hi All

Apologies for the off-topic question.

The attached image has been hanging on the wall at our institute for several 
years and nobody knows what it is or who generated it.

If anyone recognises it, please let me know.

Many thanks

Dave Lawson

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk




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Re: [ccp4bb] restraints for pseudo-amino acids within a peptide chain

[david lawson (JIC)]

Hi Robbie,

That works!

If I call one C-alpha "CA", I can use the standard TRANS definition in 
mon_lib_list.cif for the LINKR record. To restrain the other, I duplicated the 
TRANS section in this file and called it TRANS2. Then I replaced the 
appropriate CA entries with the name of my second C-alpha (CA2) and used the 
TRANS2 definition for the LINKR record for this peptide linkage.

Thanks very much,

Dave

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk>

From: Robbie Joosten [mailto:robbie_joos...@hotmail.com] On Behalf Of Robbie 
Joosten
Sent: 27 September 2017 17:04
To: david lawson (JIC) <david.law...@jic.ac.uk>; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] restraints for pseudo-amino acids within a peptide chain

Hi David,

You can copy the TRANS definition from the CCP4 dictionary and hack it to match 
your atom names. It's in a file called mon_lib_list.cif

Cheers,
Robbie

Sent from my Windows 10 phone

From: david lawson (JIC)<mailto:david.law...@jic.ac.uk>
Sent: woensdag 27 september 2017 17:44
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] restraints for pseudo-amino acids within a peptide chain

Hi All,

I am having issues with getting pseudo-amino acids to behave in refmac such 
that they correctly form peptide bonds with standard residues before and after 
them. The problem I have is that when naming atoms forming the peptide bonds, 
there are effectively two C-alpha atoms, as shown below, where the pseudo-amino 
acid is contained within the square brackets:

standard_aminoacid-[N-CA-some_stuff-CA-CO]-standard_aminoacid (both CA 
atoms have R groups, but I have not shown them)

I have inserted the "L-peptide" line into the cif dictionary for the 
pseudo-amino acid, but in order to get the correct geometry, in particular the 
planarity of the peptide bond, the C-alpha atoms need to be called "CA", but I 
can only use that label once per residue.

I did wonder whether it's possible to create some special TRANS definitions to 
use in LINKR lines in the pdb header, but I can't figure out how to do that.

Any suggestions?

Many thanks

Dave Lawson

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk>

[ccp4bb] restraints for pseudo-amino acids within a peptide chain

[david lawson (JIC)]

Hi All,

I am having issues with getting pseudo-amino acids to behave in refmac such 
that they correctly form peptide bonds with standard residues before and after 
them. The problem I have is that when naming atoms forming the peptide bonds, 
there are effectively two C-alpha atoms, as shown below, where the pseudo-amino 
acid is contained within the square brackets:

standard_aminoacid-[N-CA-some_stuff-CA-CO]-standard_aminoacid (both CA 
atoms have R groups, but I have not shown them)

I have inserted the "L-peptide" line into the cif dictionary for the 
pseudo-amino acid, but in order to get the correct geometry, in particular the 
planarity of the peptide bond, the C-alpha atoms need to be called "CA", but I 
can only use that label once per residue.

I did wonder whether it's possible to create some special TRANS definitions to 
use in LINKR lines in the pdb header, but I can't figure out how to do that.

Any suggestions?

Many thanks

Dave Lawson

---

Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.law...@jic.ac.uk

[ccp4bb] SUMMARY: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

[david lawson (JIC)]

Dear All,

Thanks to Bill Scott, James Stroud and Jürgen Bosch for their responses.

Here is the original email:


We have recently bought a few iMacs for crystallography. I'm not keen on the 
supplied mighty mouse so I have switched to using a microsoft 3-button wheel 
mouse. I would like to configure it so that it behaves as it would with other 
unix systems such as RH Linux.

i.e.
(1) double-clicking with LH button on a file name selects ALL of the file name, 
not just up to the first full stop.
(2) clicking the scroll wheel pastes the selected text AND it can be done 
multiple times without re-selecting.
(2) I would like these functions to work in terminal windows, the ccp4i gui and 
web pages (and probably a few other things I haven't thought of
yet!) AND be able to transfer the selected text between applications.

I have installed the microsoft intellipoint drivers that seem to give more 
control over configuring the various buttons through system preferences, but 
I still can't get what I want.

Any help would be much appreciated.

Many thanks

Dave Lawson

---

Here are the responses:

--
Bill:
--

Hi David:

david lawson (JIC) wrote:
 Dear All,

 Sorry for the slightly off-topic subject.

 We have recently bought a few iMacs for crystallography. I'm not keen 
 on the supplied mighty mouse

May I have them?

 so I have switched to using a microsoft 3-button wheel mouse. I would 
 like to configure it so that it behaves as it would with other unix 
 systems such as RH Linux.

You managed to use Microsoft, behaved and Linux (albeit RH) all in one 
sentence without a hint of irony.



 i.e.
 (1) double-clicking with LH button on a file name selects ALL of the 
 file name, not just up to the first full stop.

Although your choice of Microsoft products shows dedication to a company with a 
firm reputation for placing the customizability needs of its customers ahead of 
its own desire to make profits, the first thing to realize is that you should 
never ever ever install their drivers. Ever. So if you did, take them out, now, 
and reboot. I'll wait.  It is still early Sunday morning here.


 (2) clicking the scroll wheel pastes the selected text AND it can be 
 done multiple times without re-selecting.

When you've gotten rid of the drivers, this should now work. In Apple's 
Terminal program (as of 10.5) and iTerm (as of 1215), you just set the 
preference to do middle-button-paste and left-button select, and Blair's your 
uncle. Unfortunately, in pretty much every other application I can think of on 
OS X, this, sadly, does not work, and there is nothing Steve Gates will let you 
do about it.


 (2) I would like these functions to work in terminal windows, the 
 ccp4i gui and web pages (and probably a few other things I haven't 
 thought of
 yet!) AND be able to transfer the selected text between applications.

I'd like to be at my ideal high-school weight, be paid more than a postdoc, 
and, well ...  Getting the OS X gui to play nice with X11 is sometimes 
challenging.  With the exception of Terminal and iTerm, you have to explicitly 
put stuff in the copy/paste buffer (command-C) before it is in the system 
clipboard.  Then you can paste to X11 programs with a middle-button click, but 
this only works if you uninstalled that viral driver. Going from X11 to aqua 
programs requires selecting the text in the usual X11 manner but explicitly 
issuing the paste command (command-p).  If you are using KDE X11 applications, 
you are really in for headaches.

To get whole-string selection in iTerm or Terminal, there is a preference 
setting that allows you to input which characters you want to have considered 
parts of a word for click-to-select purposes.  Unfortunately, pretty much 
every other application lacks this customizability, and I know of no 
system-wide preference setting that would enable you to do this globally.

Aqua simply behaves by slightly different rules.  Although I am a slobbering OS 
X fan, this lack of customizability to me, as well as a lack of 
focus-follows-mouse, it a negative.

If you really need the canonical linux behavior, you can install gnome, xfce4, 
KDE, enlightenment, or any number of other window managers via fink. I've found 
KDE buggy and the XFCE4 is way out of date.  Gnome is probably the best bet, 
and there is a major effort now to bring it completely up to date in fink.


 I have installed the microsoft intellipoint drivers that seem to give 
 more control over configuring the various buttons through system 
 preferences, but I still can't get what I want.

Therein lies the problem, I am afraid. OS X will behave better using the 
default settings.  It may be possible to tinker around with the driver, 
including separate settings in X11, to recover canonical behavior, but for 
purposes of sanity, uninstall them first, get everything working as best as 
possible, verify middle-button-paste

[ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

[david lawson (JIC)]

Dear All,

Sorry for the slightly off-topic subject.

We have recently bought a few iMacs for crystallography. I'm not keen on
the supplied mighty mouse so I have switched to using a microsoft
3-button wheel mouse. I would like to configure it so that it behaves as
it would with other unix systems such as RH Linux.

i.e.
(1) double-clicking with LH button on a file name selects ALL of the
file name, not just up to the first full stop.
(2) clicking the scroll wheel pastes the selected text AND it can be
done multiple times without re-selecting.
(2) I would like these functions to work in terminal windows, the ccp4i
gui and web pages (and probably a few other things I haven't thought of
yet!) AND be able to transfer the selected text between applications.

I have installed the microsoft intellipoint drivers that seem to give
more control over configuring the various buttons through system
preferences, but I still can't get what I want.

Any help would be much appreciated.

Many thanks

Dave Lawson

---

Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: [EMAIL PROTECTED]
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm 
 

Re: [ccp4bb] Popularity of Stereo graphics in crystallography

[david lawson (JIC)]

I haven't used stereo since the last millenium - I don't miss it. You don't 
really need it and it's not worth the expense/hassle to set up. In my opinion 
it's just something to impress visitors! 

Dave


---

Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: [EMAIL PROTECTED]
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm 
 
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Roger Rowlett
Sent: 20 June 2007 20:27
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography

I've found that many of my undergraduates like the stereo capability, although 
I personally rarely use it. So I guess it's worth the pain of getting the 
stereo hardware to play nice with the OS and specialized applications. We put 
the cheapest stereo-ready cards available at the time(Quadro 980XGL) in our 
Linux workstations, along with NuVision 60GX glasses, and none of the 
workstations cost more than $2000 to build. If you don't need stereo, clearly 
almost any reasonable PC will do. Even the lowliest of Nvidia or ATI graphics 
cards are more than ample for running O, Coot, Pymol, etc.

Cheers,

___
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]


-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Santarsiero, 
Bernard D.
Sent: Wednesday, June 20, 2007 1:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Popularity of Stereo graphics in crystallography


I agree with Kevin. We have stereo on about half of our workstations, and no 
one has used them in about three years. We typically use O.

Also, we have three large servers which are relatively fast. So the main 
purpose of a workstation is building, not computing here. That way you can 
easily work on multiple structures on a workstation at the same time, while 
you're refining and building them. We have a few people that use PC's and Coot 
as well.

Bernie


On Wed, June 20, 2007 11:45 am, P Hubbard wrote:
 Hi,

 Thanks for the e-mail. The current results of the survey would 
 certainly put you in the minority! Stereo graphics are not dead after 
 all.

 I have used systems with and without stereo graphics. I personally 
 prefer them, and think they are great for helping newbies refine, and 
 for non-structural biologists and students to look at molecular 
 architecture. It seems a lot of other people, for whatever reason, 
 like them too.

 Paul


From: Kevin Cowtan [EMAIL PROTECTED]
Reply-To: Kevin Cowtan [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Survey on computer usage in crystallography
Date: Wed, 20 Jun 2007 17:27:04 +0100

More likely the issue is that some of us do not find stereo to be 
necessary of beneficial for crystallographic model building.

In which case, given the power of modern PCs and graphics cards, a 
basic off-the-shelf PC costing $1000/£500 is completely adaquate for 
typical structure solution and model building problems.

I use coot a lot and I haven't even bothered installing the graphics 
drivers for my graphics card. All the 3D stuff gets gone in software, 
and most of the graphics hardware sits around doing nothing. If I 
needed the performance, it would be a 5 minute job to install the 
drivers, but I haven't needed it.

Kevin

P Hubbard wrote:
I am sorry you are unhappy with the questions, David.

As I am sure you know, I half-decent system with stereo graphics 
doesn't come cheap, and if you price things together to make 
something that performs well I doubt you'll get much change out of 
$2000.

I am aware of other 3D systems (such as those listed on 
www.stereo3d.com). However, the price of peripherals like a 3D LCD 
monitor are  prohibitively expensive (and the quality of the images 
is supposed to be poor). Do you know of a relatively inexpensive way 
of displaying 3D images on PCs?

Any other comments would be greatly appreciated.

Paul

 _
 Get a preview of Live Earth, the hottest event this summer - only on 
 MSN http://liveearth.msn.com?source=msntaglineliveearthhm

[ccp4bb] INDEPENDENT RESEARCH FELLOWSHIPS CONFERENCE 4/5 June 2007, John Innes Centre UK

[david lawson (JIC)]

Dear All,

Apologies for the non-CCP4 related post. 

Please can you bring the following ad to the attention of researchers
who either hold, or wish to apply for Independent Research Fellowships. 

-

INDEPENDENT RESEARCH FELLOWSHIPS CONFERENCE 4/5 June 2007

The John Innes Centre (JIC), Norwich, UK is a world-leading centre of
excellence in plant and microbial sciences based on the Norwich Research
Park.  We are inviting applications from outstanding researchers who
either hold, or wish to apply for Independent Research Fellowships, to
attend a Conference at the JIC on 4/5 June 2007; all expenses will be
covered.  At the meeting you will be able to present a talk about your
proposed area of research and to discuss your proposals, the development
of your group and your future career plans in depth with senior JIC
Scientists.

After the Conference we will select and mentor outstanding candidates in
writing Fellowship applications and/or offer the opportunity to move
existing Fellowships to the JIC.

Further details and particulars can be found at
http://www.jic.ac.uk/corporate/opportunities/vacancies/fellows.htm

Please e-mail a 2-page summary of your research plan, a copy of your CV
and arrange for three letters of recommendation to be emailed to:
[EMAIL PROTECTED] by Friday 20th April 2007.

The John Innes Centre is a registered charity (No223852) grant-aided
by the Biotechnology and Biological Sciences Research Council and is
an Equal Opportunities Employer.



I am happy to deal with any informal enquiries. 

Many thanks,

Dave Lawson

---

Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: [EMAIL PROTECTED]
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm