Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

[Tim Grüne]

Hi Mark,
responsible people are resigning from X.
Cheers,
Tim

Am 01.12.2023 23:24, schrieb Mark J. van Raaij:

just came across this critique of that paper on Twitter:

This exciting paper shows AI design of materials, robotic synthesis.
10s of new compounds in 17 days. But did they? This paper has very
serious problems in materials characterisation. In my view it should
never have got near publication. Hold on tight let's take a look 

 [1]

Robert Palgrave (@Robert_Palgrave) on X [1]
twitter.com [1]

but I'm not enough of an expert to judge - perhaps some
characterizations were wrong and a lot of the paper does stand.


On 1 Dec 2023, at 20:51, Bryan Lepore  wrote:

Adding to that literature list a bit outside :

Merchant, A., Batzner, S., Schoenholz, S.S. _et al._

Quote:

"... we show that graph networks trained at scale can reach
unprecedented levels of generalization, improving the efficiency of
materials discovery by an order of magnitude. "

Scaling deep learning for materials discovery.

_Nature_ (2023), November

https://doi.org/10.1038/s41586-023-06735-9





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Links:
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Re: [ccp4bb] PDB redo R free

[Tim Grüne]

Dear Qixu Cai,
the sets do not have to be identical, as long as refinement reaches a 
steady state.

Best regards,
Tim

Am 28.04.2023 04:51, schrieb Qixu Cai:

Dear all,

I'm using the PDB-REDO server to refine my structure. I found that
PDB-REDO said that 5% R-free set is too small and it created a new
R-free set.

Is possible for the PDB-REDO server to keep the original R-free set to
make final Rfree value comparable?

Best regards,

Qixu Cai
Email: caiq...@gmail.com

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Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

[Tim Grüne]

Dear Andre,

easiest would be to select the FP and FC_ALL with sftools, write out the 
values to a text file and calculate the R-value with a scripting 
language like awk.


Best,
Tim

Am 01.07.2019 15:02, schrieb Andre LB Ambrosio:

Dear colleagues,

Can a CCP4 program calculate r_work and r_free directly from a .mtz
file containing FP and FC_ALL (from PDB_REDO)? this without inputing
the matching .pdb file and ideally using a commando line.

Many thanks in advance,

--

Andre LB Ambrosio

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Re: [ccp4bb] [phenixbb] Copying mtz file

[Tim Grüne]

Dear Mirek,

it is a stubborn myth the Free-R flags need to be conserved. You can 
simply regenerate a new set of flags. This does not compromise the free 
F-value. This is based on what I would call Tickle's conjecture, even 
though with one of his latest emails on the ccp4bb, where he explained 
this in an extremely beautiful manner, it is not a conjecture anymore, 
rather a corollary.


It is sad that even some well established crystallographers stick to 
said myth.


Best regards,
Tim

cc ccp4bb for information

Am 25.06.2019 04:09, schrieb Cygler, Miroslaw:

Hi Phenixers,
I have copied mtz file to a new file with a lower resolution limit
using the "Reflection file editor” tool. I copied all arrays to the
output file. When I attempted to continue refinement with the new mtz
file, a message appears saying that there are no R-free flags in the
mtz file. Yet, the new file contains the R-free-flags column but the
values are inverted, 1 is changed to 0 and 0 is changed to 1. In the
output option dialog the box “Preserve original flag values” was
checked.
How to fix this?
Thanks,

Mirek
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Re: [ccp4bb] Phenix / Coot neutron queries.

[Tim Grüne]

Dear Jonathan,

since structure for neutron data are usually pre-refined and you are 
only interested in the small print, you can also use SHELXL for 
refinement (https://doi.org/10.1107/S1600576713027659). That gives you 
full control over what you want to achieve.


With PDB2INS (https://doi.org/10.1107/S1600576719005478) it is very 
simple to get the starting ins-file from a PDB entry (it may even take 
care of the NEUT command).


Coot works pretty well with SHELXL files, too.

Best,
Tim

Am 21.06.2019 00:44, schrieb Jonathan Cooper:

I am trying to refine a neutron structure for someone and I have come
across a couple of things which I need help with.

I am struggling to get the occupancy refinement of the
hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some
of them get deleted by readyset but the trick seems to be to call them
hydrogen in the atom name field yet say they are D in the element
symbol field. Is that the best way?  Also, readyset seems to delete
the D's in D2O?

I would appreciate any tips on what is the best 'strategy' for
refining with neutron data i.e. reciprocal- versus real-space or both,
etc, because my R-free just seems to go up.

Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it
stretches the O-D bond length from around 1 to 1.3 Angstrom and the
bond angle from ~110 to about 120 degrees so it seems to be picking-up
wrong geometry info from somewhere.

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Re: [ccp4bb] Mandatory mmCIF format for crystallographic depositions to the PDB

[Tim Grüne]

Dear John, dear CCP4,
Is there a converter from CIF to mmCIF?
Some structures are refined with Shelxl,   which can output CIF.
A converter would be very useful, even if they  make only a small fraction of 
the PDB.
Best regards,
Tim


On February 20, 2019 9:06:22 AM GMT+01:00, John Berrisford  
wrote:
>From July 1st 2019 onward, mmCIF format files will become mandatory for
>crystallographic depositions to the Protein Data Bank. PDB format files
>will
>no longer be accepted for deposition of structures solved by these
>techniques.
>
>PDBx/mmCIF will be the only format accepted for deposition of PDB
>structures
>resulting from macromolecular crystallography (MX), including X-ray,
>neutron, fiber, and electron diffraction methods via OneDep starting
>July
>1st 2019. The deposition of PDBx/mmCIF format files will improve the
>efficiency of the deposition process and enhance validation through
>capture
>of the more extensive experimental metadata supported by PDBx/mmCIF,
>compared to the legacy PDB format.
>
>For information about these changes, please visit the
>
>wwPDB
>news page. If you have any queries or comments regarding these changes,
>please contact the wwPDB consortium via
> deposit-h...@mail.wwpdb.org.
>
>The wwPDB consortium
>
> 
>
> 
>
> 
>
>--
>
>John Berrisford
>
>PDBe
>
>European Bioinformatics Institute (EMBL-EBI)
>
>European Molecular Biology Laboratory
>
>Wellcome Trust Genome Campus
>
>Hinxton
>
>Cambridge CB10 1SD UK
>
>Tel: +44 1223 492529
>
> 
>
>  http://www.pdbe.org
>
> 
>http://www.facebook.com/proteindatabank
>
>  http://twitter.com/PDBeurope
>
> 
>
>
>
>
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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Tim Grüne]

Hi Jacob,
The idea of a scientific service being restricted by nationality is so strange 
to me that this possibility for misunderstanding did not occur to me.
Best,
Tim

On November 29, 2018 10:24:49 PM GMT+01:00, "Keller, Jacob" 
 wrote:
>I saw explicitly that it is not limited to EU.
>
>JPK
>
>+
>Jacob Pearson Keller
>Research Scientist / Looger Lab
>HHMI Janelia Research Campus
>19700 Helix Dr, Ashburn, VA 20147
>Desk: (571)209-4000 x3159
>Cell: (301)592-7004
>+
>
>The content of this email is confidential and intended for the
>recipient specified in message only. It is strictly forbidden to share
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>consent of the sender. If you received this message by mistake, please
>reply to this message and follow with its deletion, so that we can
>ensure such a mistake does not occur in the future.
>
>-Original Message-
>From: CCP4 bulletin board  On Behalf Of
>graeme.win...@diamond.ac.uk
>Sent: Thursday, November 29, 2018 4:22 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] Long term storage for raw images/
>crystallographic data sets
>
>Dear Tim,
>
>I do not think Zenodo is limited to Europeans - at least I could not
>find this on their policy page:
>
>http://about.zenodo.org/policies/
>
>I know of plenty of uploads from Japan for example
>
>Best wishes Graeme
>
>On 29 Nov 2018, at 21:16, Tim Gruene
>mailto:tim.gru...@psi.ch>> wrote:
>
>Dear Raquel,
>
>when they are associated with a publication, you can publish them on
>data.sbgrid.org in the US or at
>zenodo.org in Europe.
>
>Best regards,
>Tim
>
>On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L
>wrote:
>Dear All,
>
>How do your labs handle long-term raw data backups? My lab is maxing
>out our 6TB RAID backup (with two off-site mirrors) so I am
>investigating our next long term solution. The vast majority of the
>data sets are published structures (i.e. processed data deposited in
>PDB) or redundant/unusable so immediate access is not anticipated, but
>the size of data sets is increasing quickly with time, so I am looking
>for a scalable-yet-affordable solution.
>
>Would be grateful for input into various options, e.g. bigger HD/RAIDs,
>cloud backup, tape, anything else.
>
>I will compile.
>
>Thank you,
>
>Raquel
>--
>Raquel L. Lieberman, Ph.D.
>Professor
>School of Chemistry and Biochemistry
>Georgia Institute of Technology
>
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

[Tim Grüne]

Hi Graeme,
I meant to say that the zenodo server sits in Europe, and the sbgrif server in 
the us. It was not meant to indicate any restrictions. 
Best,
Tim


On November 29, 2018 10:21:36 PM GMT+01:00, "graeme.win...@diamond.ac.uk" 
 wrote:
>Dear Tim,
>
>I do not think Zenodo is limited to Europeans - at least I could not
>find this on their policy page:
>
>http://about.zenodo.org/policies/
>
>I know of plenty of uploads from Japan for example
>
>Best wishes Graeme
>
>On 29 Nov 2018, at 21:16, Tim Gruene
>mailto:tim.gru...@psi.ch>> wrote:
>
>Dear Raquel,
>
>when they are associated with a publication, you can publish them on
>data.sbgrid.org in the US or at
>zenodo.org in Europe.
>
>Best regards,
>Tim
>
>On Thursday, November 29, 2018 9:54:02 PM CET Lieberman, Raquel L
>wrote:
>Dear All,
>
>How do your labs handle long-term raw data backups? My lab is maxing
>out our
>6TB RAID backup (with two off-site mirrors) so I am investigating our
>next
>long term solution. The vast majority of the data sets are published
>structures (i.e. processed data deposited in PDB) or redundant/unusable
>so
>immediate access is not anticipated, but the size of data sets is
>increasing quickly with time, so I am looking for a
>scalable-yet-affordable
>solution.
>
>Would be grateful for input into various options, e.g. bigger HD/RAIDs,
>cloud backup, tape, anything else.
>
>I will compile.
>
>Thank you,
>
>Raquel
>--
>Raquel L. Lieberman, Ph.D.
>Professor
>School of Chemistry and Biochemistry
>Georgia Institute of Technology
>
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>--
>--
>Paul Scherrer Institut
>Tim Gruene
>- persoenlich -
>OSUA/204
>Forschungsstrasse 111
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>
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>Diamond Light Source Ltd. cannot guarantee that this e-mail or any
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>may be transmitted in or with the message.
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[ccp4bb]

[Tim Grüne]

Dear Daniel,
Did you solve the structure of a small molecule, or do you have a small 
molecule ligand as part of  a protein/ macromolecular complex? In the latter 
case you don't need checkCIF.
Best,
Tim 

On September 14, 2018 5:43:48 PM GMT+02:00, "Moss, Daniel L" 
 wrote:
>They say for small molecules they want IUCr's CheckCIF validation
>report. I think you're on to something and that I may be mistaken. This
>is probably not for protein structures and the PDB validation report is
>likely enough. I think I will email the journal and confirm. Thanks for
>the help!
>
>Daniel Moss
>
>-Original Message-
>From: Paul Emsley  
>Sent: Friday, September 14, 2018 10:23 AM
>To: Moss, Daniel L ; CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb]
>
>On 14/09/2018 15:50, Moss, Daniel L wrote:
>> 
>> I am trying to generate a checkCIF report for a publication
>submission and I am not having any luck. 
>
>That's the wrong sort of cif check :-/
>
> > The journal I'm submitting to requires a checkCIF report.
>
>If so, they are wrong to do so - or you might be trying to submit to
>the wrong journal.  To be clear, do they need checkCIF or cif
>validation?
>
>Paul.
>
>
>
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