Re: [ccp4bb] Virtual Annual CCP4/APS Crystallographic School (2022) in the US

[Qingping Xu]

Dear Colleagues,

Just a friendly reminder that the registration of the upcoming CCP4/APS 
virtual school is open. If you plan to attend the school, please submit 
your application before the Apr 15th, 2022 deadline, preferably sooner.


The school schedule is available on the CCP4 school website 
(https://www.ccp4.ac.uk/schools/APS-2022/index.php).


Charles, Andrey, Garib and Qingping


On 1/24/22 10:07, Qingping Xu wrote:


Dear Colleagues,

We are pleased to announce the virtual annual CCP4/APS 
crystallographic school “From data collection to structure refinement 
and beyond” will be held on June 13-24, 2022 at the Advanced Photon 
Source (APS), Argonne National Laboratory (ANL), near Chicago, 
Illinois, USA. All details can be found at the school website: 
http://www.ccp4.ac.uk/schools/APS-2022/index.php.


Dates: June 6 (Bioinformatics & setup) and June 13 through 24, 2022 
(with a weekend break on June 18 and 19th)


Location: Virtual/Remote

The school comprises two parts: remote data collection workshop and 
virtual crystallographic computing workshop. Data collection workshop 
includes beamline training, data collection on GM/CA at APS beamlines 
23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors 
respectively, and data processing. For data collection, only the 
participants’ crystals will be used. Crystallographic computation 
workshop will feature many modern crystallographic software packages 
taught by authors and other experts. The daily schedule will be 
organized in three sections – lectures, tutorials, and hands-on 
(interactive troubleshooting of the technical difficulties the 
participants face in their projects). We have had considerable success 
resolving these problems in past years, attested by resulting 
publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft of 
the program, contact info and other details can be found at the School 
website. Note that for the virtual school, an additional day (June 
6th, 2022) was scheduled to prepare for the main event, with lectures 
on generating AlphaFold models to use in later part of the school.


Applicants: Graduate students, postdoctoral researchers and 
early-career faculty, along with commercial/industrial researchers are 
encouraged to apply. Only about 20 applicants will be selected for 
participation. Participants of the workshop are strongly encouraged to 
bring their own problem data sets or crystals so the problems can be 
addressed during data collection and/or computation workshops.


Application: Application deadline is April 15th, 2022. To apply, visit 
https://www.ccp4.ac.uk/schools/APS-2022/application.php.


Fees: There is no fee for attending the virtual school for the chosen 
applicants.


We hope to see you at the school.

Charles, Andrey, Garib and Qingping





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Re: [ccp4bb] Unable to reduce the values of R-work and R-free

[Jon Cooper]

One practical point: I had the same experience recently with a structure that 
had been worked on by others previously. Refmac was automatically picking up a 
data column from some earlier work, unknown to me, rather than the observed 
data from XDS and the R-factors were sticking at the values you have. So, 
stating the very obvious, sorry, it would be worth double-checking which data 
are being used as the refinement target.

Sent from ProtonMail mobile

 Original Message 
On 7 Mar 2022, 08:39, Mudassar Ali Khan wrote:

> Dear all,
>
> I am trying to solve an x-ray structure of a protein for which the structure 
> is not available. I have performed data reduction using XDS followed by 
> Aimless (output file attached herewith). Molecular replacement was performed 
> using Phaser MR (CCP4i) with modelled structure followed by rigid body and 
> restrained refinement. In coot, the electron density is fitting well with the 
> structure, however, I am not able to reduce the R-work and R-free beyond 0.43 
> and 0.46 respectively.
>
> I have also tried the same with Phenix, but the R-work and R-free were almost 
> the same as obtained from ccp4i.
> Any suggestion to reduce R-work and R-free will be greatly appreciated.
>
> Thanks!
>
> Regards,
> Mudassar Ali Khan
> Graduate student
> KS-101, Varma Lab
> Advanced Centre for Treatment Education and Research in Cancer (ACTREC)
> Navi-Mumbai, India
>
> ---
>
> 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] DMMULTI replacement in CCP4i2?

[Mydy, Lisa]

Hi all,

 I read that Parrot is a replacement for DM based on CCP4i2 documentation 
and am curious if Parrot has the same capabilities as DMMULTI for phase 
extension?


Is DMMULTI by command line only? I see DM in CCP4i GUI.


I'm trying to figure out best path forward with phase extension including 
2-fold averaging, solvent flattening, and extending phases from 4 A to 2.9 A 
for SeMet SAD.



Thank you kindly,

--Lisa Mydy



lm...@med.umich.edu

Postdoctoral Fellow

University of Michigan
**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 



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[ccp4bb] 2 opened positions at ZoBio, NL

[Inês Justo]

Hi everyone,

ZoBio (www.zobio.com) offers innovative research services 
in the field of small-molecule drug discovery to the pharmaceutical and biotech 
industries. Our international team of over 35 people covers four fields of 
expertise: Protein Engineering and Production, Assay Development and Screening, 
Structural Biology and Medicinal Chemistry.

Currently we have 2 positions opened that might interest the CCP4BB community:


  *   Scientist in NMR-based RNA Drug Discovery (PhD), for a collaborative 
project involving ZoBio and Peter Güntert's and Roland Riek's groups at the ETH 
Zürich (job listing: 
https://zobio.com/careers/scientist-in-nmr-based-rna-drug-discovery-phd/)
  *   Senior Scientist Medicinal Chemistry (PhD) (job listing: 
https://zobio.com/careers/senior-scientist-medicinal-chemistry/)

If you or anyone in your circle would be interested in applying to either 
position, please send your application (CV, motivation letter and names of 
potential referees) to h...@zobio.com, clearly 
mentioning the job you're applying to in the subject line.

Best,
Inês Justo

Inês Justo
Researcher
T +31-71-2040580
ZoBio B.V. •
J.H. Oortweg 19
2333 CH
Leiden •
The Netherlands



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Re: [ccp4bb] ligand binds to one molecule

[Harry Powell - CCP4BB]

Hi folks

Just my two ha’porth; if you go back to one of the first two structures 
determined by protein crystallography, haemoglobin (horse?) has multiple oxygen 
binding sites) which are potentially different (the binding of oxygen ion one 
affects the binding in the other - “allostery”). I’m not sure if the two sites 
are distinguishable in any 3D structures, but the possiblility would be there. 
No doubt experts on this BB would be able to expand on this or tell me that I’m 
wrong…

My answer to the OP would be along the lines of “I wouldn’t be surprised by 
this at all”...

Harry

> On 6 Mar 2022, at 18:02, Dom Bellini - MRC LMB  
> wrote:
> 
> I dont think it is necessary to prove what others have said so far, but if 
> you would like some concrete evidence to support those statements:
> 
> we cocrystallized a protein together with a small peptide, producing a 
> crystal with for molecules in the AU but only one promoter showed clear 
> density for the bound peptide (crystal contacts played a part in this); then 
> the construct was shorten a bit and cocrystallized in a different space group 
> still, by chance, with 4 molecules in the AU, but this time we could clearly 
> see the peptide bound to all 4 copies. So indeed each protomer in the AU can 
> be affected differently in the way they bind a ligand, depending on all 
> causes (and perhaps even more) that people have already mentioned.
> 
> BW,
> 
> D
> 
> On 06/03/2022 12:38, David J. Schuller wrote:
>> I think it would be a mistake to generalize. 
>> I have seen a situation in which 1 of 4 sites was occupied, the ligand was 
>> not included in the crystallization solution(which means it must have been 
>> bound beforehand) and the site participated in crystal contacts. I do not 
>> doubt that examples of the opposite causality exist. And the data I used to 
>> make my conclusions in my own example came from outside the structure itself.
>> 
>> ===
>>  All Things Serve the Beam
>>  ===
>>  David J. Schuller
>>  modern man in a post-modern world
>>  MacCHESS, Cornell University
>>  schul...@cornell.edu
>> From: CCP4 bulletin board  on behalf of Palm, 
>> Gottfried 
>> Sent: Sunday, March 6, 2022 4:10 AM
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] ligand binds to one molecule
>>  
>> Dear all, 
>>   I don't think, there is much to add to the statement of Bernhard or James 
>> that different protomers in the asymmetric unit (must) have some difference 
>> in there contacts and therefore often in their conformation. What it doesn't 
>> answer is a chicken or the egg question: 
>> do the different environments in the crystal allow or force different 
>> conformations (e.g. open or closed loops) and/or different (active) site 
>> occupancies or
>> do different states in an oligomer allow or force crystallization only in a 
>> packing and space group with multiple states?
>> Latter could be due to an anti-cooperative binding to a dimer. We have seen 
>> this in the dimeric Tet repressor: wt binds the ligand (a tetracycline) in 
>> each monomer of the dimer with one chain in the asymmetric unit, but some of 
>> the mutants bind only one ligand per dimer (confirmed by ITC, Biochimica et 
>> Biophysica Acta, 2020). Despite the same packing, this forces reduction of 
>> space group symmetry from I422 to P422 (omitting screws). 
>> From the crystal structures alone, I think, one cannot prove what comes 
>> first. From my gut feeling, in most cases multiple states in solution force 
>> multiple states in the crystal - in other words - I tend to say, multiple 
>> states in the crystal are "real" in the sense they also occur in solution. 
>> Does somebody want to comment on this?
>> Greetings
>>   Gottfried
>> 
>> 
>> Am Sonntag, den 06-03-2022 um 00:40 schrieb Bernhard Rupp:
>> As you stated, you have multiple protomers in the asymmetric unit, where 
>> they are free from 
>> crystallographic symmetry constraints. Generally that means different local 
>> environment for
>> each protomer. Inspecting the sites in the different protomers (frequently 
>> related by various 
>> non-crystallographic symmetry operations) often can reveal plausible reasons 
>> for different occupancies. One hydrogen bond more or less for example can 
>> mean a 
>> difference of 4 orders of magnitude in Kd.
>> 
>> Best, BR
>> 
>> -Original Message-
>> From: CCP4 bulletin board  On Behalf Of 
>> Sent: Saturday, March 5, 2022 12:01
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] ligand binds to one molecule
>> 
>> Hello all,
>> 
>> In homo-dimeric or homo-oligomeric protein crystal structures, what would be 
>> the reason for having a ligand (chemical compound or fragment) binds to one 
>> molecule and 

Re: [ccp4bb] Unable to reduce the values of R-work and R-free

[Kay Diederichs]

Hello Mudassar ali Khan,

these R-values after refinement rather indicate a failure of Molecular 
Replacement.

Did you see in aimless.pdf:

"WARNING: the L-test suggests that the data may be twinned
   so the indicated Laue symmetry may be too high
   Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.215 +/- 
(0.013)
  Estimated twin fraction alpha from0.209
  Estimated twin fraction alpha from0.199"

In case of twinning, a subgroup of P63 could be the correct spacegroup. 
Subgroups of P63 are P3 and P21. 
I'd try Molecular Replacement in these two spacegroups, and twin refinement.

Best wishes,
Kay


On Mon, 7 Mar 2022 14:09:40 +0530, Mudassar Ali Khan  
wrote:

>Dear all,
>
>I am trying to solve an x-ray structure of a protein for which the
>structure is not available. I have performed data reduction using XDS
>followed by Aimless (output file attached herewith). Molecular replacement
>was performed using Phaser MR (CCP4i) with modelled structure followed by
>rigid body and restrained refinement. In coot, the electron density is
>fitting well with the structure, however, I am not able to reduce the
>R-work and R-free beyond 0.43 and 0.46 respectively.
>
>I have also tried the same with Phenix, but the R-work and R-free were
>almost the same as obtained from ccp4i.
>Any suggestion to reduce R-work and R-free will be greatly appreciated.
>
>Thanks!
>
>Regards,
>Mudassar Ali Khan
>Graduate student
>KS-101, Varma Lab
>Advanced Centre for Treatment Education and Research in Cancer (ACTREC)
>Navi-Mumbai, India
>
>
>
>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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>



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Re: [ccp4bb] Unable to reduce the values of R-work and R-free

[Wim Burmeister]

  
  
Hello,
the crystal is certainly twinned. Not sure that this explains
  completely the R-factor. Check https://www.ccp4.ac.uk/html/twinning.html.

Check the packing. Maybe you miss a molecule.
Are other spacegroups giving MR solutions ? The assignment of the
  spacegroup may still be wrong. Have a look at the systematic
  absences, whether the information is really sound.
Best wishes
Wim

Le 07/03/2022 à 09:39, Mudassar Ali
  Khan a écrit :


  
  
Dear all,


I am trying to solve an x-ray structure of a protein for
  which the structure is not available. I have performed data
  reduction using XDS followed by Aimless (output file attached
  herewith). Molecular replacement was performed using Phaser MR
  (CCP4i) with modelled structure followed by rigid body and
  restrained refinement. In coot, the electron density is
  fitting well with the structure, however, I am not able to
  reduce the R-work and R-free beyond 0.43 and 0.46
  respectively.


I have also tried the same with Phenix, but the R-work and
  R-free were almost the same as obtained from ccp4i. 

Any suggestion to reduce R-work and R-free will be greatly
  appreciated.


Thanks!


Regards,
Mudassar Ali Khan
Graduate student
KS-101, Varma Lab

Advanced Centre for Treatment Education and Research in
  Cancer (ACTREC)
Navi-Mumbai, India



  
  
  
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-- 
  
  
  Wim
Burmeister
  

  

  

  

  

  

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