Re: [ccp4bb] Automated refinement convergence

[Nigel Moriarty]

I, too, love the smell of cooking (or cooked?) jobs in the morning.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : nwmoria...@lbl.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Thu, Jan 18, 2024 at 1:16 PM James Holton  wrote:

> Hey there Robert,
>
> Refmac has a keyword called "kill" that I think is what you are looking
> for.  It is documented here:
>
> https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html
>
>You can specify a conditional exit based on R factor, etc. Or you can
> just create a specified file containing "stop Y" from an external
> process.  I use it when running refmac on a cluster that has run time
> limits but difficult-to-predict CPU speeds.
>
> Phenix, I don't think has a checkpointing feature. Not that I know of.
>
> Amber does support checkpointing and now counts as a refinement program
> since support for structure factor restraints was added in 22.
>
> Personally, when I do refinements I do dozens to hundreds of
> macro-macro-cycles. As in, take the pdb file output by one run and feed
> it into another run. There is an instantiation overhead to doing this,
> as you note, but I like my models to be super converged. I define
> convergence as the x,y,z,B and occ values in the pdb file are not
> changed by the refinement program. This does not happen quickly, but it
> does eventually happen. Yes, you can get oscillations, but one way to
> deal with those is to add a bit more damping, or to adjust the x-ray
> weight down and then up and then back to auto again. This "weight snap"
> tends to take things that were dangling from a cliff in the energy
> landscape and knock them to the ground. After that, the oscillations are
> less common.
>
>   And like an equilibrated chromatography column, an xyz-converged model
> is the best way to know that when you edit and re-refine, everything you
> see is due to the edit, and not some other process that just wasn't
> finished yet.
>
> That's what I do. Maybe I just want to feel like I've got something
> cooking while I sleep...
>
> Cheers,
>
> -James Holton
> MAD Scientist
>
> On 1/18/2024 3:04 AM, Robert Oeffner wrote:
> > Hi,
> >
> > I am wondering if authors of refinement programs would like to consider
> putting on their users wish list the ability of refinement programs to
> automatically terminate once the refinement has reached convergence.
> Various refinement metrics such as R factors, CC or RMS values typically
> will reach a plateau once the refinement of a macromolecular structure with
> X-ray or EM-data has converged and further macro-cycles of refinement will
> no longer improve the structure. The default number of macro-cycles in
> programs such as Phenix-refine and Refmac are probably sensible for most
> cases but in some cases it would be nice if the programs automatically
> extended the number of macro-cycles as needed (or decreased the number).
> >
> > The user can of course examine log files from refinement themselves and
> decide whether to continue refinement. But since starting a new session of
> refinement appears to always create an initial fluctuation in the
> refinement metrics before they align with the values of the last
> macro-cycles in the previous refinement session, the user is compelled to
> do at least, say 3 or more macrocycles in addition to whatever may be
> needed for reaching convergence. I guess it would therefore be more
> efficient if this was implemented directly in the refinement programs and
> presented as an option for the user to choose.
> >
> > There could be cases where alternate conformations of a structure will
> repeatedly be oscillating in and out of density thus causing the refinement
> metrics also to oscillate. Hopefully such cases could be covered by gauging
> the level of fluctuations of the refinement metrics and terminate the
> refinement accordingly.
> >
> > Many thanks,
> >
> > Robert
> >
> > 
> >
> > 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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>
> 
>
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[ccp4bb] Introducing the UNTANGLE Challenge

[James Holton]

Greetings Everybody,

I present to you a Challenge.

Structural biology would be far more powerful if we can get our models 
out of local minima, and together, I believe we can find a way to escape 
them.


tldr: I dare any one of you to build a model that scores better than my 
"best.pdb" model below. That is probably impossible, so I also dare you 
to approach or even match "best.pdb" by doing something more clever than 
just copying it. Difficulty levels range from 0 to 11. First one to 
match the best.pdb energy score an Rfree wins the challenge, and I'd 
like you to be on my paper. You have nine months.


Details of the challenge, scoring system, test data, and available 
starting points can be found here:

https://bl831.als.lbl.gov/~jamesh/challenge/twoconf/

Why am I doing this?
We all know that macromolecules adopt multiple conformations. That is 
how they function. And yet, ensemble refinement still has a hard time 
competing with conventional single-conformer-with-a-few-split-side-chain 
models when it comes to revealing correlated motions, or even just 
simultaneously satisfying density data and chemical restraints. That is, 
ensembles still suffer from the battle between R factors and geometry 
restraints. This is because the ensemble member chains cannot pass 
through each other, and get tangled. The tangling comes from the 
density, not the chemistry. Refinement in refmac, shelxl, phenix, 
simulated annealing, qFit, and even coot cannot untangle them.


The good news is: knowledge of chemistry, combined with R factors, 
appears to be a powerful indicator of how near a model is to being 
untangled. What is really exciting is that the genuine, underlying 
ensemble cannot be tangled. The true ensemble _defines_ the density; it 
is not being fit to it. The more untangled a model gets the closer it 
comes to the true ensemble, with deviations from reasonable chemistry 
becoming easier and easier to detect. In the end, when all alternative 
hypotheses have been eliminated, the model must match the truth.


Why can't we do this with real data? Because all ensemble models are 
tangled. Let's get to untangling them, shall we?


To demonstrate, I have created a series of examples that are 
progressively more difficult to solve, but the ground truth model and 
density is the same in all cases. Build the right model, and it will not 
only explain the data to within experimental error, and have the best 
possible validation stats, but it will reveal the true, underlying 
cooperative motion of the protein as well.


Unless, of course, you can prove me wrong?

-James Holton
MAD Scientist



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[ccp4bb] Crystal imagers?

[Olga Moroz]

Dear All,

Does anyone use Jansci PS256 imager? And if yes, what do you think about
it? Is it reliable, easy to use, or has some problems? We are thinking of
buying it to replace our Rigaku Minstrel, which has been out of action for
more than a year...

Thanks a lot!

Olga


Dr Olga Moroz
York Structural Biology Laboratory
University of York,
Heslington,
York, UK
YO10 5DD



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Re: [ccp4bb] Automated refinement convergence

[James Holton]

Hey there Robert,

Refmac has a keyword called "kill" that I think is what you are looking 
for.  It is documented here:

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html

  You can specify a conditional exit based on R factor, etc. Or you can 
just create a specified file containing "stop Y" from an external 
process.  I use it when running refmac on a cluster that has run time 
limits but difficult-to-predict CPU speeds.


Phenix, I don't think has a checkpointing feature. Not that I know of.

Amber does support checkpointing and now counts as a refinement program 
since support for structure factor restraints was added in 22.


Personally, when I do refinements I do dozens to hundreds of 
macro-macro-cycles. As in, take the pdb file output by one run and feed 
it into another run. There is an instantiation overhead to doing this, 
as you note, but I like my models to be super converged. I define 
convergence as the x,y,z,B and occ values in the pdb file are not 
changed by the refinement program. This does not happen quickly, but it 
does eventually happen. Yes, you can get oscillations, but one way to 
deal with those is to add a bit more damping, or to adjust the x-ray 
weight down and then up and then back to auto again. This "weight snap" 
tends to take things that were dangling from a cliff in the energy 
landscape and knock them to the ground. After that, the oscillations are 
less common.


 And like an equilibrated chromatography column, an xyz-converged model 
is the best way to know that when you edit and re-refine, everything you 
see is due to the edit, and not some other process that just wasn't 
finished yet.


That's what I do. Maybe I just want to feel like I've got something 
cooking while I sleep...


Cheers,

-James Holton
MAD Scientist

On 1/18/2024 3:04 AM, Robert Oeffner wrote:

Hi,

I am wondering if authors of refinement programs would like to consider putting 
on their users wish list the ability of refinement programs to automatically 
terminate once the refinement has reached convergence. Various refinement 
metrics such as R factors, CC or RMS values typically will reach a plateau once 
the refinement of a macromolecular structure with X-ray or EM-data has 
converged and further macro-cycles of refinement will no longer improve the 
structure. The default number of macro-cycles in programs such as Phenix-refine 
and Refmac are probably sensible for most cases but in some cases it would be 
nice if the programs automatically extended the number of macro-cycles as 
needed (or decreased the number).

The user can of course examine log files from refinement themselves and decide 
whether to continue refinement. But since starting a new session of refinement 
appears to always create an initial fluctuation in the refinement metrics 
before they align with the values of the last macro-cycles in the previous 
refinement session, the user is compelled to do at least, say 3 or more 
macrocycles in addition to whatever may be needed for reaching convergence. I 
guess it would therefore be more efficient if this was implemented directly in 
the refinement programs and presented as an option for the user to choose.

There could be cases where alternate conformations of a structure will 
repeatedly be oscillating in and out of density thus causing the refinement 
metrics also to oscillate. Hopefully such cases could be covered by gauging the 
level of fluctuations of the refinement metrics and terminate the refinement 
accordingly.

Many thanks,

Robert



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[ccp4bb] Updated links - Phenix version 1.21 released

[Paul Adams]

The Phenix developers are pleased to announce that version 1.21 of Phenix is 
now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and 
Windows (under Windows Subsystem for Linux), and the source installer, are 
available at the download site:

http://phenix-online.org/download

Highlights for the 1.21 version of Phenix include:

- Likelihood-based docking of models into cryo-EM maps.
   • Full support for structure determination with AlphaFold models.
   • New joint X-ray and neutron refinement algorithm.
   • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ.

Detailed changes are:

- Full support for structure determination with AlphaFold models in Phenix GUI
 - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences
 - Phenix AlphaFold server
 - Video tutorials for prediction, X-ray structure solution and Cryo-EM map 
interpretation
- Cryo-EM tools support ChimeraX visualization
- Cryo-EM density modification and anisotropic scaling display local resolution
- Tutorials available for automated structure determination with PredictAndBuild
- New em_placement and emplace_local tools
 - likelihood-based docking of models into cryo-EM maps
- MOPAC v22 is now distributed with Phenix
- Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ
 - Available in phenix.refine and separate command-line tool, 
mmtbx.quantum_interface
 - Defaults to MOPAC's PM6-D3H4
 - Higher level QM available via 3rd-party Orca package
- Restraints
 - Approximately 27k of 37k restraints (QM calculated and validated) deployed 
in the GeoStd
- Automated tests for programs in the Phenix GUI
- ERRASER no longer supported and removed from installation
- Remove rebuild_predicted_model (duplicated by predict_and_build)
- JSON output added to MolProbity structure validation scripts

Please note that this publication should be used to cite the use of Phenix:

Macromolecular structure determination using X-rays, neutrons and electrons: 
recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, 
Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner 
RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, 
Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams 
CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. 
https://doi.org/10.1107/S2059798319011471

Full documentation is available here:

http://www.phenix-online.org/documentation

There is a Phenix bulletin board:

http://www.phenix-online.org/mailman/listinfo/phenixbb

Please consult the installer README file or online documentation for 
installation instructions.

Direct questions and problem reports to the bulletin board or:

h...@phenix-online.org and b...@phenix-online.org

Commercial users interested in obtaining access to Phenix should visit the 
Phenix website for information about the Phenix Industrial Consortium.

The development of Phenix is funded by the National Institute of General 
Medical Sciences (NIH) under grant P01-GM063210. The maintenance and 
distribution of Phenix is funded by the National Institute of General Medical 
Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous 
support of the members of the Phenix Industrial Consortium.

--
Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences, LBL 
(https://biosciences.lbl.gov) 
Principal Investigator, Computational Crystallography Initiative, LBL 
(http://cci.lbl.gov) 
Vice President for Technology, the Joint BioEnergy Institute 
(http://www.jbei.org) 
Principal Investigator, ALS-ENABLE, Advanced Light Source 
(http://als-enable.lbl.gov) 
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) 
Adjunct Professor, Department of Bioengineering, UC Berkeley 
(http://bioeng.berkeley.edu) 
Member of the Graduate Group in Comparative Biochemistry, UC Berkeley 
(http://compbiochem.berkeley.edu) 

Building 91, Room 410
Building 978, Room 4126
Tel: 1-510-486-4225
http://cci.lbl.gov/paul 
ORCID: -0001-9333-8219

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 91R0183
Berkeley, CA 94720, USA.

Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ]
--



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[ccp4bb] Postdoctoral position in Structural Biology at the University of Toronto

[Jeffrey Lee]

Postdoctoral position in Structural Biology at the University of Toronto

We are seeking an enthusiastic and self-motivated Postdoctoral Fellow to study 
the mechanisms of fertilization in the Lee Lab at the University of Toronto, 
Department of Laboratory Medicine and Pathobiology. The Postdoctoral Fellow 
will lead research efforts on a Bill and Melinda Gates Foundation funded 
project to develop non-hormonal contraceptives targeting essential membrane 
glycoproteins involved in human sperm and egg attachment. The research will 
entail protein-protein interaction studies, crystallography, and protein 
engineering.

Qualifications:
*PhD in Biochemistry, Structural Biology, Biophysics, or a related field
*Experience with cloning, protein expression, and protein purification methods
*Experience with insect or mammalian cell culture is a benefit
*Solid practical and theoretical understanding in X-ray crystallography
*Strong publication record (candidates must have first authored publications)
*Fluent in English (written and oral)
*Strong scientific writing skills
*Excellent problem solving, interpersonal, communication and presentation skills

The position is available immediately. University of Toronto is well equipped 
with state-of-the-art equipment for molecular biology, protein expression and 
purification, biophysics and structural biology (crystallography, NMR and 
cryo-EM). Please visit the Lee Lab website (https://www.leelab-utoronto.com) 
for more information.

Interested candidates are invited to send your CV, a brief description of 
research interest and experience, names of three references by email to: Prof. 
Jeff Lee
jeff@utoronto.ca

All qualified candidates are encouraged to apply by Feb 15, 2024, but the 
position will remain open until filled

. We thank all applicants for their interest, however only those shortlisted 
for interviews will be contacted.




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Re: [ccp4bb] Automated refinement convergence

[Robbie Joosten]

Hi Robert,

I see your point but extending the number of cycles to reach convergence has a 
big risk of going into infinite loops (which you point out). In the case of 
Refmac stopping early is not really needed as it is very fast anyway; a few 
unnecessary cycles won't take that long. Generally it is better to err in the 
direction of having too many cycles than too few, especially in your 'final' 
refinement. This is also the logic applied to pdb-redo, it does 20 cycles by 
default (more than the typical number for Refmac) and then extends the number 
of cycles when it uses options that slow down convergence (jelly body, 
anisotropic B-factors, new data from paired refinement). This (almost) always 
leads to something that we can call "convergence", at least for models that 
were at the final stages of model building.

That said, I have only really achieved convergence in Refmac (i.e. gradients 
are '0') once in twenty years and that was after more than 500 cycles of jelly 
body refinement.* Apparently, there is a large step between "things don't 
change a lot anymore" and real convergence.   

Cheers,
Robbie

* Refmac crashed at that point. A division by zero if I remembered correctly.

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Robert
> Oeffner
> Sent: Thursday, January 18, 2024 12:05
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Automated refinement convergence
> 
> Hi,
> 
> I am wondering if authors of refinement programs would like to consider
> putting on their users wish list the ability of refinement programs to
> automatically terminate once the refinement has reached convergence. Various
> refinement metrics such as R factors, CC or RMS values typically will reach a
> plateau once the refinement of a macromolecular structure with X-ray or EM-
> data has converged and further macro-cycles of refinement will no longer
> improve the structure. The default number of macro-cycles in programs such as
> Phenix-refine and Refmac are probably sensible for most cases but in some
> cases it would be nice if the programs automatically extended the number of
> macro-cycles as needed (or decreased the number).
> 
> The user can of course examine log files from refinement themselves and
> decide whether to continue refinement. But since starting a new session of
> refinement appears to always create an initial fluctuation in the refinement
> metrics before they align with the values of the last macro-cycles in the
> previous refinement session, the user is compelled to do at least, say 3 or 
> more
> macrocycles in addition to whatever may be needed for reaching convergence. I
> guess it would therefore be more efficient if this was implemented directly in
> the refinement programs and presented as an option for the user to choose.
> 
> There could be cases where alternate conformations of a structure will
> repeatedly be oscillating in and out of density thus causing the refinement
> metrics also to oscillate. Hopefully such cases could be covered by gauging 
> the
> level of fluctuations of the refinement metrics and terminate the refinement
> accordingly.
> 
> Many thanks,
> 
> Robert
> 
> ###
> #
> 
> 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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[ccp4bb] Automated refinement convergence

[Robert Oeffner]

Hi,

I am wondering if authors of refinement programs would like to consider putting 
on their users wish list the ability of refinement programs to automatically 
terminate once the refinement has reached convergence. Various refinement 
metrics such as R factors, CC or RMS values typically will reach a plateau once 
the refinement of a macromolecular structure with X-ray or EM-data has 
converged and further macro-cycles of refinement will no longer improve the 
structure. The default number of macro-cycles in programs such as Phenix-refine 
and Refmac are probably sensible for most cases but in some cases it would be 
nice if the programs automatically extended the number of macro-cycles as 
needed (or decreased the number). 

The user can of course examine log files from refinement themselves and decide 
whether to continue refinement. But since starting a new session of refinement 
appears to always create an initial fluctuation in the refinement metrics 
before they align with the values of the last macro-cycles in the previous 
refinement session, the user is compelled to do at least, say 3 or more 
macrocycles in addition to whatever may be needed for reaching convergence. I 
guess it would therefore be more efficient if this was implemented directly in 
the refinement programs and presented as an option for the user to choose.

There could be cases where alternate conformations of a structure will 
repeatedly be oscillating in and out of density thus causing the refinement 
metrics also to oscillate. Hopefully such cases could be covered by gauging the 
level of fluctuations of the refinement metrics and terminate the refinement 
accordingly.

Many thanks,

Robert



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Re: [ccp4bb] Phenix version 1.21 released

[Randy John Read]

For anyone who is confused:

Unfortunately, the link given here (https://phenix-online.org/download/) says 
that the latest release is 1.19.2-4158! That’s very odd because the same URL 
without the trailing slash (https://phenix-online.org/download) gets to a 
different page with the right information! Must be something relatively obscure 
about how URLs are interpreted. I’m using Safari in case other people are 
having a different experience...

Best wishes,

Randy Read

> On 17 Jan 2024, at 19:12, Paul Adams  wrote:
>
> The Phenix developers are pleased to announce that version 1.21 of Phenix is 
> now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and 
> Windows (under Windows Subsystem for Linux), and the source installer, are 
> available at the download site:
>
> http://phenix-online.org/download/
>
> Highlights for the 1.21 version of Phenix include:
>
> - Likelihood-based docking of models into cryo-EM maps.
>• Full support for structure determination with AlphaFold models.
>• New joint X-ray and neutron refinement algorithm.
>• Quantum Mechanical Restraints (QMR) to calculate ligand restraints in 
> situ.
>
> Detailed changes are:
>
> - Full support for structure determination with AlphaFold models in Phenix GUI
>  - PredictAndBuild X-ray and Cryo-EM structure solution from data and 
> sequences
>  - Phenix AlphaFold server
>  - Video tutorials for prediction, X-ray structure solution and Cryo-EM map 
> interpretation
> - Cryo-EM tools support ChimeraX visualization
> - Cryo-EM density modification and anisotropic scaling display local 
> resolution
> - Tutorials available for automated structure determination with 
> PredictAndBuild
> - New em_placement and emplace_local tools
>  - likelihood-based docking of models into cryo-EM maps
> - MOPAC v22 is now distributed with Phenix
> - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ
>  - Available in phenix.refine and separate command-line tool, 
> mmtbx.quantum_interface
>  - Defaults to MOPAC's PM6-D3H4
>  - Higher level QM available via 3rd-party Orca package
> - Restraints
>  - Approximately 27k of 37k restraints (QM calculated and validated) deployed 
> in the GeoStd
> - Automated tests for programs in the Phenix GUI
> - ERRASER no longer supported and removed from installation
> - Remove rebuild_predicted_model (duplicated by predict_and_build)
> - JSON output added to MolProbity structure validation scripts
>
> Please note that this publication should be used to cite the use of Phenix:
>
> Macromolecular structure determination using X-rays, neutrons and electrons: 
> recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi 
> G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, 
> Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, 
> Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau 
> LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. 
> https://doi.org/10.1107/S2059798319011471
>
> Full documentation is available here:
>
> http://www.phenix-online.org/documentation/
>
> There is a Phenix bulletin board:
>
> http://www.phenix-online.org/mailman/listinfo/phenixbb/
>
> Please consult the installer README file or online documentation for 
> installation instructions.
>
> Direct questions and problem reports to the bulletin board or:
>
> h...@phenix-online.org and b...@phenix-online.org
>
> Commercial users interested in obtaining access to Phenix should visit the 
> Phenix website for information about the Phenix Industrial Consortium.
>
> The development of Phenix is funded by the National Institute of General 
> Medical Sciences (NIH) under grant P01-GM063210. The maintenance and 
> distribution of Phenix is funded by the National Institute of General Medical 
> Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous 
> support of the members of the Phenix Industrial Consortium.
>
> --
> Paul Adams (he/him/his)
> Associate Laboratory Director for Biosciences, LBL 
> (https://biosciences.lbl.gov/)
> Principal Investigator, Computational Crystallography Initiative, LBL 
> (http://cci.lbl.gov/)
> Vice President for Technology, the Joint BioEnergy Institute 
> (http://www.jbei.org/)
> Principal Investigator, ALS-ENABLE, Advanced Light Source 
> (http://als-enable.lbl.gov/)
> Laboratory Research Manager, ENIGMA Science Focus Area 
> (http://enigma.lbl.gov/)
> Adjunct Professor, Department of Bioengineering, UC Berkeley 
> (http://bioeng.berkeley.edu/)
> Member of the Graduate Group in Comparative Biochemistry, UC Berkeley 
> (http://compbiochem.berkeley.edu/)
>
> Building 91, Room 410
> Building 978, Room 4126
> Tel: 1-510-486-4225
> http://cci.lbl.gov/paul
> ORCID: -0001-9333-8219
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 91R0183
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ]
> Phenix