[ccp4bb] PDRA position in antiviral drug discovery at Diamond Light Source

[Fearon, Daren (DLSLtd,RAL,LSCI)]

Dear all,

We are currently recruiting for a Post-Doctoral Research Associate within the 
XChem/I04-1 team at Diamond Light Source to drive high-throughput fragment 
screening experiments and structural biology support for hit-to-lead 
development as part of our NIH-funded Anti-Viral Drug Discovery Center - the 
AI-driven, Structure-enabled Antiviral Platform (ASAP). The position is 
available for the duration of the grant; in the first instance until May 2025.

Applications should be submitted by the 10th of March and more details on how 
to apply can be found on the link below:
https://vacancies.diamond.ac.uk/vacancy/postdoctoral-research-associate-antiviral-xchem-551007.html

Please feel free to contact me with any informal enquiries.

Cheers, Daren

Dr Daren Fearon (he/him)
Senior Beamline Scientist (XChem)
Diamond Light Source Ltd
Harwell Science & Innovation Campus
Didcot Oxfordshire OX11 0DE

Tel: 01235 778936
Mobile: 07425638147
Email: daren.fea...@diamond.ac.uk
Web: 
www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html




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Re: [ccp4bb] i2run crank2 problem

[zx2...@connect.hku.hk]

Dear Stuart,

Thank you very much for your prompt and helpful response. I apologize for my 
delayed reply. Your guidance offered a solid foundation, enabling me to 
successfully implement the procedures you suggested. However, I've encountered 
additional challenges that were not resolved. Specifically, I need to run the 
process with the --noDb feature, which operates outside an existing project and 
generates all output files in the current directory. This requirement continues 
to pose a problem.

I am unsure of the correct way to specify the mtz file and sequence file. 
Despite following the formats suggested in the 
Documentation, my attempts 
have been unsuccessful, and I noticed there are no examples for Crank2 in this 
documentation.

Nonetheless, I am grateful for your assistance.

Best regards,
Xin

From: CCP4 bulletin board  on behalf of Stuart 
McNicholas <19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>
Sent: 20 February 2024 23:01
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] i2run crank2 problem

I got i2run to work with this data by:

* Importing the data with "Import merged"
* Importing the 2 sequences one at a time with 2 import sequence jobs
* Running a 'Define AU contents' job with both sequences added to the contents.
* Creating a Crank2 job, then clicking the "Show i2 run command" to produce 
script.
* I tweaked the i2run script to put double quotes around strings with brackets 
"()<>"

I have attached my script.

On Tue, 20 Feb 2024 at 12:05, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hmm - I can't help with the scripting question, but it solved easily from the 
I2 interface?

This is run on a Mac.

CRANK2 called SHELX - found SE with weak signal..
Some difference between hand
It traced ALA - R factor 41%

Then BUCCANEER or MODELFIR quickly built and sequenced the rest..
Eleanor


On Thu, 15 Feb 2024 at 09:07, 
zx2...@connect.hku.hk 
mailto:zx2...@connect.hku.hk>> wrote:
Dear Colleagues,

I hope this message finds you well. I am reaching out to inquire if anyone has 
experience with running Crank2 using the CCP4i2 i2run command. Unfortunately, 
I've encountered some difficulties and would greatly appreciate any guidance or 
advice.

For context, I've attached the script and files utilized in my attempts. 
Specifically, I'm interested in understanding how to address the errors I've 
encountered and would like to know the minimum input requirements for 
successfully running this script.

Below are the errors I've received:


Error in wrapper crank2 0.02: -ERROR- crank2:0 Error in wrapper crank2 0.02::
Anomalous scattering coeficients could not be determined.  Please input them or 
the wavelength.

Traceback (most recent call last):
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
 line 41, in CallCrankFromCCP4i2
raise
RuntimeError: No active exception to reraise

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/script/crank2_script.py",
 line 466, in process
crank2 = ccp4i2crank.CallCrankFromCCP4i2(self, inpfile=inpfile, 
defaults=defaults, rvapi_style=rvapi_style)
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
 line 43, in CallCrankFromCCP4i2
raise error
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
 line 29, in CallCrankFromCCP4i2
crank = parser.ParseAndRun(ccp4i2crank,defaults,rvapi_style=rvapi_style)
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/parse.py",
 line 58, in ParseAndRun
crank_prep.Run()
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/process.py",
 line 1017, in Run

self.RunPreprocess(rundir=rundir,clear_out=clearout,save=restore,*args,**kwargs)
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/manager.py",
 line 107, in RunPreprocess
self.GetAnomScatCoefs()
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/manager.py",
 line 327, in GetAnomScatCoefs
common.Error('Anomalous scattering coeficients could not be determined.  
Please input them or the wavelength.')
  File 
"/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/common.py",
 line 34, in Error
raise CrankError(message)
common.CrankError: Anomalous scattering coeficients could not be determined.  
Please input them or the wavelength.

I would be grateful for any insights or suggestions you might have regarding 
this issue. Thank 

Re: [ccp4bb] mixture

[Tim Gruene]

Dear Marius,

it looks like you didn't receive an answer, yet. It would be easy in
SHELXL. You may convert the PDB file to the starting instruction
filewith PDB2INS.

Fixing any parameter is done by adding 10 to it, i.e. you can simply
run awk on the ins-file to fix x,y,z and Uiso for structure 1, and
leave structure 2 to be refined. Actually you would want to add 20 to
Uiso and -20 to Uiso for structure 2 in order to refine the fraction of
1:2.

Best,
Tim

On Wed, 28 Feb 2024 16:43:14 + Marius Schmidt 
wrote:

> Dear All,
> can someone quickly update me with a
> way to refine a mixture of structures in
> refmac or phenix.
> For example, the mixture consists of
> 80 % structure 1 and 20 % structure 2.
> It is important that structure 1 is kept
> fixed (is not refined) and only structure
> 2 is varied.
> 
> Best
> Marius
> 
> 
> Marius Schmidt, Dr. rer. Nat. (habil.)
> Professor
> University of Wisconsin-Milwaukee
> Kenwood Interdisciplinary Research Complex
> Physics Department, Room 3087
> 3135 North Maryland Avenue
> Milwaukee, Wi 53211
> phone (office): 1-414-229-4338
> phone (lab): 414-229-3946
> email: smar...@uwm.edu
> https://uwm.edu/physics/people/schmidt-marius/
> https://sites.uwm.edu/smarius/
> https://www.bioxfel.org/
> Nature News and Views:
> https://www.nature.com/articles/d41586-023-00504-4
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgpR0vQOyi6A6.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] Rwork and Rfree the same?

[Gerard Bricogne]

Dear Justin,

 Would it be possible for you to send off-list the report_staraniso.pdf
file created by your autoPROC job (or the job number of your STARANISO
submission if you used the server) so that we can examine the pattern of
data incompleteness indicated by the plots? 

 This would be a great help in deciding whether this incompleteness is
caused by a missing angular range or purely by anisotropy in the diffraction
limits. We would then know what kind of in-filling with Fcalc would occur
with what refinement program(s), with what consequences on the maps.

 Please send this file to "proc-deve...@globalphasing.com" . Thank you!


 With best wishes,

  Gerard.

--
On Wed, Feb 28, 2024 at 11:21:26AM -0500, Justin Cruite wrote:
> Thanks everyone,
> 
> I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset.
> The data was processed using autoProc and the staranisano mtz was used for
> MR. The completeness is only 38%. It could be that the Rfree and Rwork
> reflection sets are small because of this? What is the best way to check
> the number of reflections used for Rwork and Rfree? Is this dataset usable
> at all?
> 
> Thanks!
> 
> Justin
> 
> On Wed, Feb 28, 2024 at 10:21 AM nicfoos  wrote:
> 
> > Hello Justin,
> >
> > There is something weird in your results. You mention Rwork/Rfree of
> > 0.1837.
> > This means a pretty good refinement and also is very unusual to be
> > obtain for a resolution of 3.37.
> > Additionally you should not have Rfree = Rwork.
> > I suspect something wrong with you Rfree reflections sets. What size is
> > it ? Is your dataset complet ?
> > How did you cut the res. ?
> >
> > I hope this may help you.
> >
> > Nicolas
> >
> >
> >
> > On 2024-02-28 16:10, Justin Cruite wrote:
> > > Hi everyone,
> > >
> > > What does it mean if your Rwork and Rfree are exactly the same?
> > >
> > > I solved a 3.37 Å structure with Phaser-MR and immediately ran 10
> > > cycles of refinement with wxc = 0.1. Everything else at default. The
> > > Rwork and Rfree are both 0.1837. Is this bad?
> > >
> > > Thank you!
> > >
> > > Justin
> > >
> > > -
> > >
> > > 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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> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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Re: [ccp4bb] RES: [ccp4bb] Rwork and Rfree the same?

[Eleanor Dodson]

That is extremely likely! - certainly REFMAC will do that..
If 5% missing using DFcalc is a good thing - if 35% is missing not wise..
Eleanor

On Mon, 4 Mar 2024 at 07:53, Ben Bax  wrote:

>
> Fcalc maps look fantastic. Are you sure they were not using an Fcalc for
> the missing 35% of the data?
>   Ben
>
>
> On 29 Feb 2024, at 21:33, Rafael Marques 
> wrote:
>
> Sorry for jumping into the post, but I would like the community’s opinion
> about completeness, once this topic was raised here. What could be
> considered reasonable? Recently I have seen a 65% completeness Crystal
> structure and, surprisingly, the electron density map was not that bad for
> a > 3.2 A structure. How such a nice map could have been calculated with
> such poor parameters? I could only think of anisotropy.
>
> Best
>
>
> Rafael Marques da Silva
> PhD Student – Structural Biology
> University of Leicester
>
> Mestre em Física Biomolecular
> Universidade de São Paulo
>
> Bacharel em Ciências Biológicas
> Universidade Federal de São Carlos
>
> phone: +55 16 99766-0021
>
> *   "A sorte acompanha uma mente bem treinada"*
> **
>
> --
> *De:* CCP4 bulletin board  em nome de Paul Adams <
> pdad...@lbl.gov>
> *Enviado:* Wednesday, February 28, 2024 2:58:16 PM
> *Para:* CCP4BB@JISCMAIL.AC.UK 
> *Assunto:* Re: [ccp4bb] Rwork and Rfree the same?
>
>
> By setting wxc (weight of the X-ray term) to 0.1 there is good chance that
> the refinement is dominated by the geometry term and the model isn’t really
> seeing the effect of the X-ray data. I suspect this would result in
> R-factors that are similar. Why they are so low is less clear, but as
> others have pointed out 38% completeness is a problem. It would be good to
> check if that is 38% overall, or just very incomplete in the higher
> resolution shells. If it is complete at lower resolution you might be able
> to do something with the dataset, but not using the default
> parameterization in refinement programs - you’ll need to apply constraints
> and additional restraints if you can, and look at the weighting (by
> modifying wxc_scale, not wxc).
>
> There is a Phenix mailing list you might want to use as well (I assume you
> are using phenix.refine):
> https://phenix-online.org/mailman/listinfo/phenixbb
>
> On Feb 28, 2024, at 8:21 AM, Justin Cruite 
> wrote:
>
> Thanks everyone,
>
> I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset.
> The data was processed using autoProc and the staranisano mtz was used for
> MR. The completeness is only 38%. It could be that the Rfree and Rwork
> reflection sets are small because of this? What is the best way to check
> the number of reflections used for Rwork and Rfree? Is this dataset usable
> at all?
>
> Thanks!
>
> Justin
>
> On Wed, Feb 28, 2024 at 10:21 AM nicfoos  wrote:
>
> Hello Justin,
>
> There is something weird in your results. You mention Rwork/Rfree of
> 0.1837.
> This means a pretty good refinement and also is very unusual to be
> obtain for a resolution of 3.37.
> Additionally you should not have Rfree = Rwork.
> I suspect something wrong with you Rfree reflections sets. What size is
> it ? Is your dataset complet ?
> How did you cut the res. ?
>
> I hope this may help you.
>
> Nicolas
>
>
>
> On 2024-02-28 16:10, Justin Cruite wrote:
> > Hi everyone,
> >
> > What does it mean if your Rwork and Rfree are exactly the same?
> >
> > I solved a 3.37 Å structure with Phaser-MR and immediately ran 10
> > cycles of refinement with wxc = 0.1. Everything else at default. The
> > Rwork and Rfree are both 0.1837. Is this bad?
> >
> > Thank you!
> >
> > Justin
> >
> > -
> >
> > 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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>
>
> --
> 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 [