[ccp4bb] Regarding RNA AMBER OL3 Force field

[Abhilasha Thakur]

Hello!!

If anyone is using the AMBER OL3 force field kindly send it to me. I am
working on RNA str prediction. It would be a great help if you can send me
this.

Thank you
Sincerely



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[ccp4bb] Forthcoming RSC meeting

[Jon Cooper]

A reminder that the registration deadline for the free one-day RSC meeting on 
British X-ray Crystallographers is fast approaching. More details can be found 
here:

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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Re: [ccp4bb] Outlawed PDB files, what should a muggle do

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

Thanks David (and others who replied the same off list)

Yes, this is exactly what I wanted thank you

Agree that dimple should probably accept mmCIF, but for the moment I have the 
capacity to compute maps so jobsagoodun

All the best Graeme

From: David Waterman 
Sent: 20 September 2023 16:35
To: Winter, Graeme (DLSLtd,RAL,LSCI) 
Cc: CCP4BB@jiscmail.ac.uk 
Subject: Re: [ccp4bb] Outlawed PDB files, what should a muggle do

gemmi convert --shorten 7qgf.cif foo.pdb

?
-- David


On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) 
<6a19cead4548-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Looks like PDB files have been outlawed because mmCIF

But dimple needs PDB files

cif2pdb says nope

Grey-Area work :( $ cif2pdb --help

 * ERROR *
  No cif file read on input

Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif

 * ERROR *
  No cif file read on input


Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif

 * ERROR *
  No cif file read on input



For someone who only used PDB files to get F^2 to validate processing, how best 
to get one *from the command line* ?

Thanks Graeme


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Re: [ccp4bb] Outlawed PDB files, what should a muggle do

[David Waterman]

Of course the proper answer should be to fix dimple to read mmCIF (for
which I would also recommend gemmi)

-- David


On Wed, 20 Sept 2023 at 16:35, David Waterman  wrote:

> gemmi convert --shorten 7qgf.cif foo.pdb
>
> ?
> -- David
>
>
> On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) <
> 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Looks like PDB files have been outlawed because mmCIF
>>
>> But dimple needs PDB files
>>
>> cif2pdb says nope
>>
>> Grey-Area work :( $ cif2pdb --help
>>
>>  * ERROR *
>>   No cif file read on input
>>
>> Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif
>>
>>  * ERROR *
>>   No cif file read on input
>>
>>
>> Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif
>>
>>  * ERROR *
>>   No cif file read on input
>>
>>
>>
>> For someone who only used PDB files to get F^2 to validate processing,
>> how best to get one *from the command line* ?
>>
>> Thanks Graeme
>>
>>
>> --
>> This e-mail and any attachments may contain confidential, copyright and
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>> use, copy, retain, distribute or disclose the information in or attached to
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>> Any opinions expressed within this e-mail are those of the individual and
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>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
>> attachments are free from viruses and we cannot accept liability for any
>> damage which you may sustain as a result of software viruses which may be
>> transmitted in or with the message.
>> Diamond Light Source Limited (company no. 4375679). Registered in England
>> and Wales with its registered office at Diamond House, Harwell Science and
>> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>>
>> 
>>
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Re: [ccp4bb] Outlawed PDB files, what should a muggle do

[David Waterman]

gemmi convert --shorten 7qgf.cif foo.pdb

?
-- David


On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) <
6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:

> Looks like PDB files have been outlawed because mmCIF
>
> But dimple needs PDB files
>
> cif2pdb says nope
>
> Grey-Area work :( $ cif2pdb --help
>
>  * ERROR *
>   No cif file read on input
>
> Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif
>
>  * ERROR *
>   No cif file read on input
>
>
> Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif
>
>  * ERROR *
>   No cif file read on input
>
>
>
> For someone who only used PDB files to get F^2 to validate processing, how
> best to get one *from the command line* ?
>
> Thanks Graeme
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
> 
>
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Re: [ccp4bb] wwPDB NEWS - Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

[Marcin Wojdyr]

I'm using a similar scheme for converting mmCIF to PDB with 'gemmi convert'.
1. Long CCD codes are replaced with 3-character codes
   that end with a tilde (ABCDE -> AB~)
2. The HETNAM record is used to store the original CCD codes (in columns 72-79).
HETNAM AB~ ABCDE


On Wed, Sep 20, 2023 at 4:53 PM Putnam, Christopher
 wrote:
>
> Would it be reasonable to reserve one of the remaining three-character CCD ID 
> for use in PDB files that means “this component cannot be represented using a 
> three character ID code”?
>
>
>
> A translation for each ambiguous residue in the PDB file to the correct code 
> could be provided in the REMARKs.
>
>
>
> This way you can still provide files in the legacy PDB format, even if the 
> file can’t be directly used for refinement.
>
>
>
> Thanks.
>
>
>
> Chris Putnam



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[ccp4bb] Outlawed PDB files, what should a muggle do

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

Looks like PDB files have been outlawed because mmCIF

But dimple needs PDB files

cif2pdb says nope

Grey-Area work :( $ cif2pdb --help

 * ERROR *
  No cif file read on input 

Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif 

 * ERROR *
  No cif file read on input 

 
Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif 

 * ERROR *
  No cif file read on input 



For someone who only used PDB files to get F^2 to validate processing, how best 
to get one *from the command line* ?

Thanks Graeme


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This e-mail and any attachments may contain confidential, copyright and or 
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please notify us of receipt by returning the e-mail and do not use, copy, 
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Any opinions expressed within this e-mail are those of the individual and not 
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the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
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[ccp4bb] 3 Year Structural Biologist Position in Australia

[Wai-Hong Tham]

An opportunity exists for Postdoctoral Fellow (Structural Biologist) to join 
the research laboratory of Professor Wai-Hong Tham in the Department of 
Biomedical Sciences and Biochemistry, Research School of Biology at the 
Australian National University.
 
The Tham Laboratory works on infectious diseases, with an emphasis on 
understanding how pathogens infect their hosts. In particular, we focus on 
development of human antibodies and nanobodies that prevent pathogens from 
infecting and transmitting within their hosts.
 
We are looking for a postdoc with expertise in structural biology and 
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desirable.
 
AUD $78,940 - $99,083 per annum, Full Time, Fixed Term (up 36 months) , Closing 
date: Oct 1st
 
More details here: 
https://jobs.anu.edu.au/jobs/postdoctoral-fellow-tham-canberra-act-act-australia
 



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Re: [ccp4bb] the structures of Nucleic acid

[Harry Powell]

Hi

I am also reminded that I was involved in the data collection but not structure 
solution of a DNA cyclic octamer from a single wavelength dataset collected to 
atomic resolution (on image plate…), which was solved after locating a Ba 
(which turned out to be one of several with partial occupancy); the structure 
solution was actually carried out in the laboratory of one G.M. Sheldrick, 
using software that I think may have never been released to the public.

See 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20809/

for details...

Harry

> On 19 Sep 2023, at 20:53, Diana Tomchick  
> wrote:
> 
> I have also found that there is significant anomalous signal from strontium 
> near the Se K-edge, which is useful if one uses strontium chloride instead of 
> potassium chloride (or in addition to KCl) during crystal growth.
> 
> Diana
> 
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> 
> 
> 
>> On Sep 19, 2023, at 1:32 PM, Wagner, Armin (DLSLtd,RAL,LSCI) 
>>  wrote:
>> 
>> 
>> EXTERNAL MAIL
>> 
>> Dear Fu Xingke,
>>  
>> Indeed P-SAD is quite attractive but requires high resolution as the number 
>> of anomalous scatterers (1 P per nucleotide) is rather large, but the unit 
>> cells are typically quite small, resulting in a rather small number of 
>> anomalous differences per scatterer. Based on the very nice publication from 
>> Tom Terwilliger et al. ( https://doi.org/10.1107/S2059798315019269) we wrote 
>> a little web app to predict the success for S-SAD phasing at the 
>> long-wavelength beamline I23 at Diamond. 
>> https://www.diamond.ac.uk/Instruments/Mx/I23/resolution-requirement-phasing-app.html
>> While the predictions are pretty reliable for S-SAD, there is a (not heavily 
>> tested) option to also submit DNA or RNA sequences, which can give you a 
>> hint on what you are against, or what resolution you should aim for. 
>> Unfortunately, we have not had many successful examples to far, but 
>> basically all the P-SAD projects which were predicted not to work at the 
>> resolutions the crystals diffracted to didn’t solve, so we are very 
>> interested in projects which are predicted to work to fine tune this also 
>> for P-SAD as there will be continuous need for experimental phasing in 
>> particular for non-canonical RNA/DNA structures.
>>  
>> 5-Br-U is a good alternative and works well, but we have also managed to 
>> solve RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439) and 
>> Ca could be attractive as a potential anomalous scatter as well.
>>  
>> Best regards,
>>  
>> Armin
>>  
>>  
>>  
>>  
>> From: CCP4 bulletin board  on behalf of Mark J. van 
>> Raaij 
>> Date: Tuesday, 19 September 2023 at 12:31
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] the structures of Nucleic acid
>> 
>> This just appeared and may be relevant:
>> https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628
>>  
>> Critical Reviews and Perspectives
>> When will RNA get its AlphaFold moment? 
>> Mark van Raaij
>> Dpto de Estructura de Macromoleculas, lab 20B
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. +34 91 585 4616 (internal 432092)
>> 
>> 
>> 
>> On 18 Sep 2023, at 18:07, William G. Scott 
>> <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:
>>  
>> The phosphorus absorption edge is about 5.8Å.
>> 
>> I've had much better luck with 5-Br-U for anomalous phasing.
>> 
>> Molecular replacement with sub-structural fragments can also work:
>> 
>> 
>> 
>> Yours sincerely,
>> 
>> William G. Scott
>> Professor, Department of Chemistry and Biochemistry
>> and The Center for the Molecular Biology of RNA
>> University of California at Santa Cruz
>> Santa Cruz, California 95064  
>> USA
>> 
>> 
>> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
>> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> I am afraid most scientists will use the most straightforward technique! 
>> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
>> signal to allow SAD to work, and you get an unambiguous answer to whether it 
>> is A-DNA or B or Z...
>> MR will usually work of course as well
>> Eleanor
>> 
>> 
>> On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  
>> wrote:
>> Dear Fu Xingke,
>> 
>> Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
>> can expect some sequence to tertiary structure correspondence so you might 
>> be able to try more MR as compared to DNA.   DNA may have double helical 
>> architecture but less sequence to tertiary structure correspondence, and 
>> hence DNA is less likely to hav

Re: [ccp4bb] the structures of Nucleic acid

[Harry Powell]

Hi folks

just my two ha’porth.

Back in the mid 1990s, when MAD was becoming common and tunable beamlines were 
being installed at every synchrotron you could shake a stick at, I was involved 
in several successful projects involving 5-Br-U in oligo-DNA crystallography. 
In my (very, very) naïve hands at the time it worked like magic (I remember my 
shock at seeing the base stacking in the first map I calculated for one of the 
structures) - and this was using data collected on image plates with each image 
spanning rather more than 1 degree - so not how it would be done now.

Since just about everything to do with data collection and processing and 
structure solution has improved by leaps and bounds since then, I would back 
Br-SAD to yield a structure.

If anyone’s interested, they can see my contribution regarding this at the 1997 
CCP4 Study Weekend proceedings (this was prior to them appearing in Acta D), 
available at - 

https://legacy.ccp4.ac.uk/courses/proceedings/1997/h_powell/main.html

Contributions at the same meeting by others whose names will be instantly 
recognizable may well be more use than mine…

Best wishes

Harry

> On 19 Sep 2023, at 19:32, Wagner, Armin (DLSLtd,RAL,LSCI) 
>  wrote:
> 
> 5-Br-U is a good alternative and works well, but we have also managed to 
> solve RNA/DNA by K-SAD or Co-SAD (https://doi.org/10.1093/nar/gkaa439) and Ca 
> could be attractive as a potential anomalous scatter as well.
>  
> Best regards,
>  
> Armin
>  
>  
>  
>  
> From: CCP4 bulletin board  on behalf of Mark J. van 
> Raaij 
> Date: Tuesday, 19 September 2023 at 12:31
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] the structures of Nucleic acid
> 
> This just appeared and may be relevant:
> https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad726/7272628
>  
> Critical Reviews and Perspectives
> When will RNA get its AlphaFold moment? 
> Mark van Raaij
> Dpto de Estructura de Macromoleculas, lab 20B
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. +34 91 585 4616 (internal 432092)
> 
> 
> 
> On 18 Sep 2023, at 18:07, William G. Scott 
> <2844d921eb97-dmarc-requ...@jiscmail.ac.uk> wrote:
>  
> The phosphorus absorption edge is about 5.8Å.
> 
> I've had much better luck with 5-Br-U for anomalous phasing.
> 
> Molecular replacement with sub-structural fragments can also work:
> 
> 
> 
> Yours sincerely,
> 
> William G. Scott
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064  
> USA
> 
> 
> On Sep 18, 2023, at 2:43 AM, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> I am afraid most scientists will use the most straightforward technique! 
> If SAD is available the PHOSPHATE backbone of DNA will provide sufficient 
> signal to allow SAD to work, and you get an unambiguous answer to whether it 
> is A-DNA or B or Z...
> MR will usually work of course as well
> Eleanor
> 
> 
> On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan  
> wrote:
> Dear Fu Xingke,
> 
> Depends on what Nucleic Acid you are talking of.  If it is RNA, you 
> can expect some sequence to tertiary structure correspondence so you might be 
> able to try more MR as compared to DNA.   DNA may have double helical 
> architecture but less sequence to tertiary structure correspondence, and 
> hence DNA is less likely to have a 3D structure like RNA specific structure 
> for a sequence.
> 
> SAD has become a straight forward method to avoid all these problems 
> to get ab-initio structure.  So many go for it directly.
> 
> Hope that helps.
> Best wishes,
> Natesh
> 
> On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:
> Dear Colleagues,
> 
> Reacently, I find the structures of Nucleic acid are solved by 
> single-wavelength anomalous diffraction(SAD). So, why molecular replacement 
> (MR) not?
> 
> Regards
> 
> 
> 
> Best wishes,
> 
> Fu Xingke
> 
> Institute of Physics CAS
> 
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> 
> 
> 
> -- 
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> 
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Associate Professor, 
> School of Biology and Center for High-Performance Computing (CHPC),
> Founding and Current President of Cryo Electron Microscopy and 3 Dimensional 
> Image Processing Society of India (CEM3DIPSI),
> Indian Institute of Science Education and Research Thiruvananthapuram 
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, Indi