Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Nicholas Clark]

Hi Paul,

Thank you for providing that information. Editing the restraints for CSO
corrected the issue! Your assistance is greatly appreciated. I figured I
was missing something :)

Best,

Nick Clark

On Fri, May 26, 2023 at 10:55 PM Paul Emsley 
wrote:

>
> On 27/05/2023 03:46, Nicholas Clark wrote:
>
> Paul,
>
> Yes, it appears that the upper level group is "NON-POLYMER". However,
> there is an alias at the bottom that does state polymer.
>
>
> Hi Nick,
>
>
> In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to
> "peptide" and press enter in the entry, then "Apply"
>
> Now you can refine your CSO in Coot.
>
> Paul.
>
>
>
> Best,
>
> Nick Clark
>
>
> On Fri, May 26, 2023 at 10:37 PM Paul Emsley 
> wrote:
>
>>
>> On 27/05/2023 03:23, Nicholas Clark wrote:
>>
>> Hey Paul,
>>
>> I found the dictionary entry for CSO, it appears to be in the "peptide"
>> group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
>>
>> "loop_
>> _chem_comp_alias.comp_id
>> _chem_comp_alias.group
>> _chem_comp_alias.atom_id
>> _chem_comp_alias.atom_id_standard
>> CSO *peptide* HN2 H2"
>>
>>  I've attached the file I have for your reference, as I may not be
>> looking in the correct place. Also, if I'm looking in the wrong file
>> location, please let me know.
>>
>>
>> Due to other priorities, Coot is not up to speed with the developments of
>> my colleagues:
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/
>> 
>> (Section 2)
>>
>> What is the value of _chem_comp.group ? That is (for the moment) what
>> Coot cares about.
>>
>>
>> Paul.
>>
>>
>
> --
> 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
>
> --
>
> 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



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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Paul Emsley]

On 27/05/2023 03:46, Nicholas Clark wrote:

Paul,

Yes, it appears that the upper level group is "NON-POLYMER". However, 
there is an alias at the bottom that does state polymer.



Hi Nick,


In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to 
"peptide" and press enter in the entry, then "Apply"


Now you can refine your CSO in Coot.

Paul.




Best,

Nick Clark


On Fri, May 26, 2023 at 10:37 PM Paul Emsley 
 wrote:



On 27/05/2023 03:23, Nicholas Clark wrote:

Hey Paul,

I found the dictionary entry for CSO, it appears to be in the
"peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):

"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
CSO *peptide* HN2 H2"

 I've attached the file I have for your reference, as I may not
be looking in the correct place. Also, if I'm looking in the
wrong file location, please let me know.



Due to other priorities, Coot is not up to speed with the
developments of my colleagues:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/


(Section 2)

What is the value of _chem_comp.group ? That is (for the moment)
what Coot cares about.


Paul.




--
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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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Nicholas Clark]

Paul,

Yes, it appears that the upper level group is "NON-POLYMER". However, there
is an alias at the bottom that does state polymer.

Best,

Nick Clark


On Fri, May 26, 2023 at 10:37 PM Paul Emsley 
wrote:

>
> On 27/05/2023 03:23, Nicholas Clark wrote:
>
> Hey Paul,
>
> I found the dictionary entry for CSO, it appears to be in the "peptide"
> group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
>
> "loop_
> _chem_comp_alias.comp_id
> _chem_comp_alias.group
> _chem_comp_alias.atom_id
> _chem_comp_alias.atom_id_standard
> CSO *peptide* HN2 H2"
>
>  I've attached the file I have for your reference, as I may not be looking
> in the correct place. Also, if I'm looking in the wrong file location,
> please let me know.
>
>
> Due to other priorities, Coot is not up to speed with the developments of
> my colleagues:
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/
> 
> (Section 2)
>
> What is the value of _chem_comp.group ? That is (for the moment) what Coot
> cares about.
>
>
> Paul.
>
>

-- 
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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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Paul Emsley]

On 27/05/2023 03:23, Nicholas Clark wrote:

Hey Paul,

I found the dictionary entry for CSO, it appears to be in the 
"peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):


"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
CSO *peptide* HN2 H2"

 I've attached the file I have for your reference, as I may not be 
looking in the correct place. Also, if I'm looking in the wrong file 
location, please let me know.




Due to other priorities, Coot is not up to speed with the developments 
of my colleagues:


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/ (Section 2)

What is the value of _chem_comp.group ? That is (for the moment) what 
Coot cares about.



Paul.




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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Nicholas Clark]

Hey Paul,

I found the dictionary entry for CSO, it appears to be in the "peptide"
group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):

"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
CSO *peptide* HN2 H2"

 I've attached the file I have for your reference, as I may not be looking
in the correct place. Also, if I'm looking in the wrong file location,
please let me know.

Best,

Nick Clark

On Fri, May 26, 2023 at 10:04 PM Nicholas Clark 
wrote:

> Hey Paul,
>
> I'm not sure how to check that? Would you be able to provide a resource to
> check this?
>
> Best,
>
> Nick Clark
>
> On Fri, May 26, 2023 at 9:21 PM Paul Emsley 
> wrote:
>
>>
>> On 27/05/2023 00:43, Nicholas Clark wrote:
>>
>> I have a cysteine residue that is oxidized and needs to be modeled as
>> CSO. In the past, when "replace residue" was used to substitute for CSO,
>> the CSO would "behave" during real-space refinement and essentially take
>> the place of the Cys. However, when Cys is replaced by CSO now the CSO is
>> behaving as an "external ligand" and does not maintain covalent bonds to
>> the residue before or after (repulsion between CSO & preceding and
>> subsequent residue). The only way I can get it to maintain covalent bonds
>> in Coot is to add CSO as a monomer and place it before merging into the
>> chain and renumbering the residue (afterwards, real space refinement
>> behaves the same as direct replacement of CYS->CSO). Similarly, during
>> refinement with Refmac, only one of the CSO conformations will maintain its
>> position, the alternate conformation breaks the linkage to the preceding
>> residue.
>>
>> *TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as
>> external ligand*.
>>
>>
>> As you may know the monomer library has been undergoing substantial
>> reworking over the last several months. Is the group of the CSO in your
>> dictionary "peptide"?
>>
>> Paul.
>>
>>
>>
>
> --
> 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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CSO.cif
Description: Binary data

Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Nicholas Clark]

Hey Paul,

I'm not sure how to check that? Would you be able to provide a resource to
check this?

Best,

Nick Clark

On Fri, May 26, 2023 at 9:21 PM Paul Emsley 
wrote:

>
> On 27/05/2023 00:43, Nicholas Clark wrote:
>
> I have a cysteine residue that is oxidized and needs to be modeled as CSO.
> In the past, when "replace residue" was used to substitute for CSO, the CSO
> would "behave" during real-space refinement and essentially take the place
> of the Cys. However, when Cys is replaced by CSO now the CSO is behaving as
> an "external ligand" and does not maintain covalent bonds to the residue
> before or after (repulsion between CSO & preceding and subsequent residue).
> The only way I can get it to maintain covalent bonds in Coot is to add CSO
> as a monomer and place it before merging into the chain and renumbering the
> residue (afterwards, real space refinement behaves the same as direct
> replacement of CYS->CSO). Similarly, during refinement with Refmac, only
> one of the CSO conformations will maintain its position, the alternate
> conformation breaks the linkage to the preceding residue.
>
> *TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as
> external ligand*.
>
>
> As you may know the monomer library has been undergoing substantial
> reworking over the last several months. Is the group of the CSO in your
> dictionary "peptide"?
>
> Paul.
>
>
>

-- 
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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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Paul Emsley]

On 27/05/2023 00:43, Nicholas Clark wrote:
I have a cysteine residue that is oxidized and needs to be modeled as 
CSO. In the past, when "replace residue" was used to substitute for 
CSO, the CSO would "behave" during real-space refinement and 
essentially take the place of the Cys. However, when Cys is replaced 
by CSO now the CSO is behaving as an "external ligand" and does not 
maintain covalent bonds to the residue before or after (repulsion 
between CSO & preceding and subsequent residue). The only way I can 
get it to maintain covalent bonds in Coot is to add CSO as a monomer 
and place it before merging into the chain and renumbering the residue 
(afterwards, real space refinement behaves the same as direct 
replacement of CYS->CSO). Similarly, during refinement with Refmac, 
only one of the CSO conformations will maintain its position, the 
alternate conformation breaks the linkage to the preceding residue.


*TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as 
external ligand*.




As you may know the monomer library has been undergoing substantial 
reworking over the last several months. Is the group of the CSO in your 
dictionary "peptide"?


Paul.




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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Nicholas Clark]

Hi Jon,

Thanks for the reply. They’re going in as HETATMs. I didn’t try changing
them to ATOMs because I checked my previous structure’s PDB file (one that
worked fine) and they were in it as HETATMs.

I have changed them to ATOMs and it’s still “misbehaving” in real space
refinement but shows a “link line” to the preceding and subsequent residue.
But that appears to be due the linkage lines I previously entered into the
header, as removing them removed this behavior.

I put the file with the CSO as ATOMs through Refmac refinement and the same
behavior occurs, loss of one conformation’s covalent bond to the preceding
residue. They are changed back to HETATOMs by Refmac.

Best,

Nick Clark

On Fri, May 26, 2023 at 8:14 PM Jon Cooper 
wrote:

> Hello, is the CSO going into the PDB file as ATOM'S or HETATM's?
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 27 May 2023, 00:43, Nicholas Clark < ndcla...@buffalo.edu> wrote:
>
>
> I have a cysteine residue that is oxidized and needs to be modeled as CSO.
> In the past, when "replace residue" was used to substitute for CSO, the CSO
> would "behave" during real-space refinement and essentially take the place
> of the Cys. However, when Cys is replaced by CSO now the CSO is behaving as
> an "external ligand" and does not maintain covalent bonds to the residue
> before or after (repulsion between CSO & preceding and subsequent residue).
> The only way I can get it to maintain covalent bonds in Coot is to add CSO
> as a monomer and place it before merging into the chain and renumbering the
> residue (afterwards, real space refinement behaves the same as direct
> replacement of CYS->CSO). Similarly, during refinement with Refmac, only
> one of the CSO conformations will maintain its position, the alternate
> conformation breaks the linkage to the preceding residue.
>
> *TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as
> external ligand*.
>
> I've tried adding a "Link" definition to the header for both conformations
> but this does not fix it. Any suggestions on how to resolve this issue?
>
> Best regards,
>
> Nick Clark
>
> --
> 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
>
>
> --
>
> 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



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Re: [ccp4bb] Issue with CSO in Coot & Refmac

[Jon Cooper]

Hello, is the CSO going into the PDB file as ATOM'S or HETATM's?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 27 May 2023, 00:43, Nicholas Clark wrote:

> I have a cysteine residue that is oxidized and needs to be modeled as CSO. In 
> the past, when "replace residue" was used to substitute for CSO, the CSO 
> would "behave" during real-space refinement and essentially take the place of 
> the Cys. However, when Cys is replaced by CSO now the CSO is behaving as an 
> "external ligand" and does not maintain covalent bonds to the residue before 
> or after (repulsion between CSO & preceding and subsequent residue). The only 
> way I can get it to maintain covalent bonds in Coot is to add CSO as a 
> monomer and place it before merging into the chain and renumbering the 
> residue (afterwards, real space refinement behaves the same as direct 
> replacement of CYS->CSO). Similarly, during refinement with Refmac, only one 
> of the CSO conformations will maintain its position, the alternate 
> conformation breaks the linkage to the preceding residue.
>
> TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as 
> external ligand.
>
> I've tried adding a "Link" definition to the header for both conformations 
> but this does not fix it. Any suggestions on how to resolve this issue?
>
> Best regards,
>
> Nick Clark
>
> --
>
> 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
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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[ccp4bb] Issue with CSO in Coot & Refmac

[Nicholas Clark]

I have a cysteine residue that is oxidized and needs to be modeled as CSO.
In the past, when "replace residue" was used to substitute for CSO, the CSO
would "behave" during real-space refinement and essentially take the place
of the Cys. However, when Cys is replaced by CSO now the CSO is behaving as
an "external ligand" and does not maintain covalent bonds to the residue
before or after (repulsion between CSO & preceding and subsequent residue).
The only way I can get it to maintain covalent bonds in Coot is to add CSO
as a monomer and place it before merging into the chain and renumbering the
residue (afterwards, real space refinement behaves the same as direct
replacement of CYS->CSO). Similarly, during refinement with Refmac, only
one of the CSO conformations will maintain its position, the alternate
conformation breaks the linkage to the preceding residue.

*TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as
external ligand*.

I've tried adding a "Link" definition to the header for both conformations
but this does not fix it. Any suggestions on how to resolve this issue?

Best regards,

Nick Clark

-- 
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



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Re: [ccp4bb] British X-ray Crystallographers

[Jon Cooper]

I've just registered as a non-member and there's no fee, right?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 24 May 2023, 09:26, Harry Powell wrote:

> Hi Jon “Preaching to the choir”! Harry > On 23 May 2023, at 23:16, Jon Cooper 
> wrote: > > I am biased, but this looks like an interesting meeting: > > 
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers > > 
> Best wishes, Jon Cooper. > jon.b.coo...@protonmail.com > > Sent with Proton 
> Mail secure email. > > To unsubscribe from the CCP4BB list, click the 
> following link: > 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
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[ccp4bb] Postdoc position at SBBS, QMUL

[Vidya Darbari]

A Postdoctoral Research Assistant position in Structural Biology is available 
at Queen Mary University of London (QMUL) to work with Professor Richard 
Pickersgill. This project is in collaboration with Professor Martin Warren and 
colleagues at the Quadram Institute,  also in collaboration with Dr Arianna 
Fornili (QMUL) on the computational aspects of the work. The post-holder will 
be funded by BBSRC on a project entitled “Vitamin scavenging in the gut: 
Structure/function of the tight-binding B12 foraging machinery in Bacteroides – 
and its biotechnological applications”.

The successful candidate should have a PhD (or close to completion) in 
structural biology, biophysics, biochemistry, or a related field. The candidate 
should be able to provide evidence of expertise in protein purification, 
structural biology, and preferably X-ray crystallography. Excellent computing 
skills and a track record of high-quality published research would be an 
advantage. Self-motivation, an ability to work as part of a team and excellent 
research management and presentation skills are essential.

The start date is July 2023 or as soon as possible thereafter. The post is 
full-time and available for 2 years. The salary is in the range of £36,411 - 
£43,592 per annum and is inclusive of London allowance.

Informal enquiries should be addressed to Prof Richard Pickersgill via 
r.w.pickersg...@qmul.ac.uk

The closing date for applications is 14th June 2023.

Further details on the post and application process can be accessed using the 
link:  https://www.jobs.ac.uk/job/CZW464/postdoctoral-research-assistant

Best Regards,
Vidya



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[ccp4bb] Post-doc opportunity in integrative structural biology

[John Kirkpatrick]

Dear All,


Please see the link below for details about a post-doc (Research Fellow) position available in the field of integrative 
structural biology, based in the group of Prof. Teresa Carlomagno at the University of Birmingham.


Research Fellow in Integrative Structural Biology (Institute of Cancer & Genomic Sciences) 



Please send any enquiries by email to: t.carloma...@bham.ac.uk

And for more information on the group, please visit our website: carlomagno-group.org 



Apologies for any cross-posting.

Best wishes,

John



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[ccp4bb] Research Scientist Position - Flaherty Lab Purdue University

[Flaherty, Daniel P]

Hello All,

My lab in the Department of Medicinal Chemistry and Molecular Pharmacology at 
Purdue University is seeking qualified candidates at the level of Research 
Scientist in the field of Structural Biology for the pursuit of the first 
structures for a high-impact malaria drug target. Please see the position link 
below for details.

https://careers.purdue.edu/job/West-Lafayette-Research-Associate-Life-and-Physical-Sciences-IN-47906/1033137000/

Thanks!
Dan


--
Daniel P. Flaherty, PhD
Associate Professor of Medicinal Chemistry
Department of Medicinal Chemistry and Molecular Pharmacology
College of Pharmacy
Purdue University
575 Stadium Mall Dr.
West Lafayette, IN 47907

Email: dfla...@purdue.edu
Phone: 765-494-4761
Lab Website: www.flahertylab.com
Twitter: @FlahertyLab







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[ccp4bb] New release of PISA-lite software for calculating macromolecular interaction data

[Deborah Harrus]

**

*Dear all,*

*

We are excited to announce the release of the new version of the PISA 
software, developed at PDBe, based on the jsPISA implementation from 
CCP4. This new version, PISA-lite, developed in collaboration with the 
CCP4 core team, enables the calculation of macromolecular interaction 
data for every assembly in the PDB.



PISA-lite generates new and enhanced PISA interaction data based on all 
the annotated assemblies in the PDB archive and is available in JSON 
format from the PDBe API. It is designed to reduce the computational 
overhead of the software by working only on known assemblies in PDB 
entries and calculating interactions.



By focusing on known assemblies, PISA-lite enables the weekly 
calculation of macromolecular interactions for each assembly in the PDB, 
providing up-to-date information on protein structures and their 
interactions. These pre-calculated annotations can then be provided for 
every PDB entry to support researchers in structural biology, 
bioinformatics, and related fields.



To find out more about the PISA-lite implementation and how to access 
the data, 
visit:https://www.ebi.ac.uk/pdbe/news/improved-macromolecular-interactions-data-pisa-lite 




Kind Regards,

*Deborah Harrus

PDBe

--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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Re: [ccp4bb] Issues with viewing images with dials

[Winter, Graeme (DLSLtd,RAL,LSCI)]

HI Zoe

If, from a terminal with CCP4 configured, you type

dials.image_viewer (path-to-hdf5-master-file)

Where (path-to-hdf5-master-file) is your file location, does it work?

All the i2 message says is “something went wrong” which is not super helpful

As a general rule, I also usually recommend pulling a DIALS release from


Installation — DIALS documentation
dials.github.io
[favicon.ico]


since sometimes the CCP4 version is lagging some

All the best Graeme

On 26 May 2023, at 10:11, Zoe Markham-Lee 
 wrote:

Hi everyone,

I am currently trying to view images with dials through CCP4i2 (on mac)
I have so far tried using the DUI but when importing files, nothing seems to 
happen… there are no error codes appearing as such but no images/experimental 
data is imported. I have tried this on both .cbf and .h5 file types but with no 
success on either.
I also then tried downloading a json file type to use the image viewer option 
found in ccp4i2 and received this error code

-ERROR- CTaskDials_image:9 Error in wrapper dials_image 1.0:: Failed starting 
external process - this can be due to a number of things, butusually is due to 
the command used by subprocess/QProcess not working for some reason. Missing 
inputfiles, bad commands, non-functional programs etc. Check log files and 
stdout.
Process: dials.image_viewer

 -ERROR- CTaskDials_image:47 Error in wrapper dials_image 
1.0:: Error in checking external process after completion
exit status and  code: 1 1

If anyone could advise me on what might be causing these issues I would be very 
grateful (as a side note I can view these .cbf images imosflm so I’m assuming 
the files are okay and hence the issue is something dials related?)

BW,
Zoe

--
Zoe Markham-Lee
PhD Student
Biodiscovery Institute (Phase1/2)
School of Pharmacy,
University of Nottingham,
University Park,
Nottingham.
NG72RD
--


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[ccp4bb] Issues with viewing images with dials

[Zoe Markham-Lee]

Hi everyone,

I am currently trying to view images with dials through CCP4i2 (on mac)
I have so far tried using the DUI but when importing files, nothing seems to 
happen… there are no error codes appearing as such but no images/experimental 
data is imported. I have tried this on both .cbf and .h5 file types but with no 
success on either.
I also then tried downloading a json file type to use the image viewer option 
found in ccp4i2 and received this error code

-ERROR- CTaskDials_image:9 Error in wrapper dials_image 1.0:: Failed starting 
external process - this can be due to a number of things, butusually is due to 
the command used by subprocess/QProcess not working for some reason. Missing 
inputfiles, bad commands, non-functional programs etc. Check log files and 
stdout.
Process: dials.image_viewer

 -ERROR- CTaskDials_image:47 Error in wrapper dials_image 
1.0:: Error in checking external process after completion
exit status and  code: 1 1

If anyone could advise me on what might be causing these issues I would be very 
grateful (as a side note I can view these .cbf images imosflm so I’m assuming 
the files are okay and hence the issue is something dials related?)

BW,
Zoe

--
Zoe Markham-Lee
PhD Student
Biodiscovery Institute (Phase1/2)
School of Pharmacy,
University of Nottingham,
University Park,
Nottingham.
NG72RD
--




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Re: [ccp4bb] Render artifacts with CCP4MG

[Stuart McNicholas]

Dear Matt,
  What version of CCP4MG are you using? I thought I had fixed this in the
version that is in recent CCP4 8.0, but apologies if this is still causing
problems.

Best wishes,
Stuart


On Thu, 25 May 2023 at 21:54, Matt McLeod  wrote:

> Hi all,
>
> I am having a weird issue where the CCP4MG render.  I am wondering if
> others have had this problem or have a potential solution?  I am wondering
> if my GPU isnt working correctly.
>
> Thanks,
> Mattt
>
> 
>
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Re: [ccp4bb] British X-ray Crystallographers

[Eleanor Dodson]

Very interesting one from Katherine Lonsdale- thank you

On Thu, 25 May 2023 at 21:21, CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> I found these audio clips on the BBC website - might be of interest -
>
> https://www.bbc.co.uk/archive/dame_kathleen_lonsdale/z6v8kmn
>
> https://www.bbc.co.uk/archive/dorothy_hodgkin/zdhgbdm
>
>
> Harry
>
> On 24 May 2023, at 14:33, Frances C. Bernstein 
> wrote:
>
> Many years ago Shoshona Wodak told me that Word kept changing her name to
> Shoeshine Kodak!  At least Garmin is less typing to fix.
>
>   Frances
>
> On 2023-05-24 06:14, Elspeth Garman wrote:
>
> Thanks a lot Harry! Unfortunately there is only one of me so it should
> indeed be ‘man’ not ‘men’, although in these days of political correctness
> it should really be ‘Garperson’!
>
> Also Microsoft often changes it to ‘ Garmin’.
>
> Best wishes
>
> Elspeth
>
> Sent from my iPhone
>
> On 24 May 2023, at 10:56, Randy John Read  wrote:
>
> So have I! They’ll learn not to disrespect one of our favourite people.
>
> Randy
>
> On 24 May 2023, at 10:44, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi Gerard
>
> I’ve mentioned it to the organiser - we shall see how long the Garmen will
> be there!
>
> Harry
>
> On 24 May 2023, at 10:27, Gerard Bricogne  wrote:
>
> Dear Jon,
>
>  Quite a line-up indeed.
>
>  Might someone at the RSC correct the typo in Elspeth's surname (in two
>
> places)? Or is it a plural form ;-) ?
>
>  With best wishes,
>
>   Gerard
>
> --
>
> On Tue, May 23, 2023 at 10:16:54PM +, Jon Cooper wrote:
>
> I am biased, but this looks like an interesting meeting:
>
> https://www.rsc.org/events/detail/76719/british-x-ray-crystallographers
>
> Best wishes, Jon Cooper.
>
> jon.b.coo...@protonmail.com
>
> Sent with [Proton Mail](https://proton.me/) secure email.
>
> 
>
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> -
>
> Randy J. Read
>
> Department of Haematology, University of Cambridge
>
> Cambridge Institute for Medical Research Tel: +44 1223 336500
>
> The Keith Peters Building
>
> Hills Road   E-mail:
> rj...@cam.ac.uk
>
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> 
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