Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Huw Jenkins]

Hi Gerard,

> On 22 Feb 2021, at 19:38, Gerard Bricogne  wrote:
> 
> Did you perhaps deposit only part of the data you collected for the
> remote wavelength? For example, only one of several orientations that you
> might have collected in order to try and fill the cusp? 

data_r2xgfsf in the 2xgf-sf.cif file from the PDB contains 47650 reflections of 
which 6932 have:

I, sigI of 0., 0.
I(+), sigI(+) listed as missing (? ?) 
I(-), sigI(-) recorded.

47650 - 6932 = 40718 which is the number of reflections listed as the overall 
total Nref(obs) in the first table in the STARANISO logfile. 47650/47737 (the 
total for Nref(all) in the same table) is 99.8% complete.

Is it possible the count of Nref(obs) does not include these 6932 reflections 
where only I(-) was recorded?

Best regards,


Huw


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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Mark J van Raaij]

Hi Gerard,

fortunately I still have the data for this structure on my computer - and not 
on tape or somesuch.
Below is the summary of the SCALA logfile, from which the statistics were 
quoted. Collection was a single sweep of 180 degrees. I'll send you privately 
the complete log file and the output mtz (happy to share with other people 
also, but don't want to post big files to people to the BB in general).
Cell parameters are exactly the same, so I don't think we've submitted the 
wrong mtz to the PDB by mistake.


Summary data for   Project: D9-25 Crystal: nat Dataset: rm

   Overall  InnerShell  OuterShell
  Low resolution limit   22.00 22.00  2.32
  High resolution limit   2.20  6.96  2.20

  Rmerge 0.132 0.034 0.440
  Rmerge in top intensity bin0.052- -
  Rmeas (within I+/I-)   0.182 0.048 0.606
  Rmeas (all I+ & I-)0.177 0.048 0.598
  Rpim (within I+/I-)0.125 0.034 0.414
  Rpim (all I+ & I-) 0.090 0.025 0.305
  Fractional partial bias   -0.030-0.046-0.056
  Total number of observations  179203  5537 26037
  Total number unique47653  1546  6906
  Mean((I)/sd(I))  7.3  15.3   2.8
  Completeness99.9  96.8  99.9
  Multiplicity 3.8   3.6   3.8

  Anomalous completeness  84.5  92.1  80.0
  Anomalous multiplicity   2.0   2.0   2.0
  DelAnom correlation between half-sets -0.090-0.032-0.015
  Mid-Slope of Anom Normal Probability   0.911   - -

Outlier rejection and statistics assume that there is anomalous scattering, ie 
I+ differs from I-

Average unit cell:   157.34   53.98  112.75   90.00  100.43   90.00

Space group: C2

Average mosaicity: 0.68

Minimum and maximum SD correction factors: Fulls   1.04   6.74  Partials   1.63 
 13.05

Dataset: D9-25/nat/rm
 written as averaged data to output file /tmp/mark/D9-25_14_2_mtz.tmp

  Maximum resolution: 2.20A




Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 22 Feb 2021, at 20:38, Gerard Bricogne  wrote:
> 
> Dear Patrick, Mark and colleagues,
> 
> Examining the data associated to PDB entry 2XGF using the PDBpeep
> server, i.e. at 
> 
>  http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=2xgf
> 
> shows a large region (marked up in dark blue) of missing measurements where
> the analysis of the trends in the distribution of the local average I/sig(I)
> would have led to expect statistically significant intensities. Such
> systematic patterns of missing data are never good news when it comes to
> maps.
> 
> This raises a couple of questions for you, Mark:
> 
> 1. this is not the shape of a standard cusp, so would there have been
> features of the crystal morphology that made some regions of reciprocal
> space hard to reach in an experiment, apart from the usual cusp caused by
> the 2-fold axis being too close to the rotation axis? 
> 
> 2. this pattern of missing data makes it rather surprising that the 
> completeness reported in the paper is about 99%, all the way out to the
> outer resolution limit; the STARANISO logfile, accessible at  
> 
>  http://staraniso.globalphasing.org/PDB/2xgf.log
> 
> shows significantly lower values, even for the ellipsoidal completeness, of
> about 0.7 at the highest resolution, for the deposited data.
> 
> Did you perhaps deposit only part of the data you collected for the
> remote wavelength? For example, only one of several orientations that you
> might have collected in order to try and fill the cusp? 
> 
> This may seem a digression from the original question about negative
> difference density, but clearly any systematically missing data can create
> additional artefacts in maps and difference maps, besides those originating
> from chemical or radiation damage related causes.
> 
> 
> With best wishes,
> 
> Claus and Gerard.
> 
> --
> On Mon, Feb 22, 2021 at 07:51:11PM +0100, Mark J van Raaij wrote:
>> Hi Patrick,
>> couldn't see any text in you email, just the subject and the picture, but 
>> 2XGF is our T4 long tail fibre tail tip structure from 2010. 
>> (2XGF stands for "2nd eXtraordinary Great Fibre", at least that's what I 
>> *modestly* imagine..).
>> I think it's probably one or more of: 
>> - noise (was this contoured at 3sigma? or at a specific e/Å3 level? at the 
>> end of refinements 3sigma 

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Gerard Bricogne]

Dear Patrick, Mark and colleagues,

 Examining the data associated to PDB entry 2XGF using the PDBpeep
server, i.e. at 

  http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=2xgf

shows a large region (marked up in dark blue) of missing measurements where
the analysis of the trends in the distribution of the local average I/sig(I)
would have led to expect statistically significant intensities. Such
systematic patterns of missing data are never good news when it comes to
maps.

 This raises a couple of questions for you, Mark:

 1. this is not the shape of a standard cusp, so would there have been
features of the crystal morphology that made some regions of reciprocal
space hard to reach in an experiment, apart from the usual cusp caused by
the 2-fold axis being too close to the rotation axis? 

 2. this pattern of missing data makes it rather surprising that the 
completeness reported in the paper is about 99%, all the way out to the
outer resolution limit; the STARANISO logfile, accessible at  

  http://staraniso.globalphasing.org/PDB/2xgf.log

shows significantly lower values, even for the ellipsoidal completeness, of
about 0.7 at the highest resolution, for the deposited data.

 Did you perhaps deposit only part of the data you collected for the
remote wavelength? For example, only one of several orientations that you
might have collected in order to try and fill the cusp? 

 This may seem a digression from the original question about negative
difference density, but clearly any systematically missing data can create
additional artefacts in maps and difference maps, besides those originating
from chemical or radiation damage related causes.


 With best wishes,

 Claus and Gerard.

--
On Mon, Feb 22, 2021 at 07:51:11PM +0100, Mark J van Raaij wrote:
> Hi Patrick,
> couldn't see any text in you email, just the subject and the picture, but 
> 2XGF is our T4 long tail fibre tail tip structure from 2010. 
> (2XGF stands for "2nd eXtraordinary Great Fibre", at least that's what I 
> *modestly* imagine..).
> I think it's probably one or more of: 
> - noise (was this contoured at 3sigma? or at a specific e/Å3 level? at the 
> end of refinements 3sigma corresponds to less e/Å3 than at the start, or at 
> least it should).
> - perhaps a small percentage of another metal than iron in the site (Co, Ni, 
> Cu, Zn?), it's quite clear most of it was iron though from the X-ray 
> fluorescence spectrum and the fact that the MAD phasing worked
> - perhaps some radiation damage
> - ripple effects around the heavy atom sites
> Resolution was 2.2Å and data was 99.9% complete, multiplicity 3.8, more 
> statistics here: https://www.pnas.org/content/107/47/20287/tab-figures-data 
>  (paper 
> https://www.pnas.org/content/107/47/20287). 
> We didn't consider lowering the occupancy of the irons, or changing from Fe2+ 
> to Fe3+, because that would have meant less electrons, not more as suggested 
> by the positive density.
> In any case, happy that this thread serves to learn something more from the 
> comments by the experts.
> Mark
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
> 
> 
> > On 22 Feb 2021, at 16:16, Patrick Needham  wrote:
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
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> >  > Shot 2021-02-22 at 10.08.36 AM.png>
> 
> 
> 
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[ccp4bb] Celebrate PDB50 at the Inaugural May 4-5 Event (register by March 15)

[Christine Zardecki]

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB 
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We have a 3 year postdoc position available in the group studying structural 
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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Mark J van Raaij]

Hi Patrick,
couldn't see any text in you email, just the subject and the picture, but 2XGF 
is our T4 long tail fibre tail tip structure from 2010. 
(2XGF stands for "2nd eXtraordinary Great Fibre", at least that's what I 
*modestly* imagine..).
I think it's probably one or more of: 
- noise (was this contoured at 3sigma? or at a specific e/Å3 level? at the end 
of refinements 3sigma corresponds to less e/Å3 than at the start, or at least 
it should).
- perhaps a small percentage of another metal than iron in the site (Co, Ni, 
Cu, Zn?), it's quite clear most of it was iron though from the X-ray 
fluorescence spectrum and the fact that the MAD phasing worked
- perhaps some radiation damage
- ripple effects around the heavy atom sites
Resolution was 2.2Å and data was 99.9% complete, multiplicity 3.8, more 
statistics here: https://www.pnas.org/content/107/47/20287/tab-figures-data 
 (paper 
https://www.pnas.org/content/107/47/20287). 
We didn't consider lowering the occupancy of the irons, or changing from Fe2+ 
to Fe3+, because that would have meant less electrons, not more as suggested by 
the positive density.
In any case, happy that this thread serves to learn something more from the 
comments by the experts.
Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 22 Feb 2021, at 16:16, Patrick Needham  wrote:
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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>  Shot 2021-02-22 at 10.08.36 AM.png>




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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Diana Tomchick]

Depending upon the amount of radiation exposure, the iron might be reduced (or 
more likely, in a mixed oxidation state) by the X-ray beam.


Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
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diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of Nukri Sanishvili 

Sent: Monday, February 22, 2021 12:33 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Student Question--Negative Difference Density in some 
Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model 
Structure


EXTERNAL MAIL

Sorry, in my previous email I was oblivious to the fact that there was Fe. Iron 
is almost certainly oxidized. So, if you started collecting data with reduced 
iron, but it got oxidized during data collection, you are probably using the 
parametrization for the reduced rather than oxidized one in the refinement. I 
wonder if it is so and if going to the reduced state would make a difference.
Best,
N.

On Mon, Feb 22, 2021 at 12:23 PM Pavel Afonine 
mailto:pafon...@gmail.com>> wrote:
Hi,

as others pointed out electron rich elements tend to amplify imperfections 
visible in Fo-Fc maps. Consider:
- refining occupancy of Fe, the site may be partially occupied;
- refining f' and f'' if data are anomalous;
- surrounding histidines may 'see' this Fe as a nonbonded interaction and thus 
repulsion terms may kick in and push Fe from its position. Try defining weak 
coordination bonds between Fe and respective nitrogens;
- refining anisotropic ADP of Fe only.

Good luck!
Pavel

On Mon, Feb 22, 2021 at 7:27 AM Patrick Needham 
mailto:needh...@miamioh.edu>> wrote:



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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Nukri Sanishvili]

Sorry, in my previous email I was oblivious to the fact that there was Fe.
Iron is almost certainly oxidized. So, if you started collecting data with
reduced iron, but it got oxidized during data collection, you are probably
using the parametrization for the reduced rather than oxidized one in the
refinement. I wonder if it is so and if going to the reduced state would
make a difference.
Best,
N.

On Mon, Feb 22, 2021 at 12:23 PM Pavel Afonine  wrote:

> Hi,
>
> as others pointed out electron rich elements tend to amplify imperfections
> visible in Fo-Fc maps. Consider:
> - refining occupancy of Fe, the site may be partially occupied;
> - refining f' and f'' if data are anomalous;
> - surrounding histidines may 'see' this Fe as a nonbonded interaction and
> thus repulsion terms may kick in and push Fe from its position. Try
> defining weak coordination bonds between Fe and respective nitrogens;
> - refining anisotropic ADP of Fe only.
>
> Good luck!
> Pavel
>
> On Mon, Feb 22, 2021 at 7:27 AM Patrick Needham 
> wrote:
>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>
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>
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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Nukri Sanishvili]

Is the oxidation state of the coordinated atom, or the identity of that
atom correct?
If there was a very slightly bigger atom, it would take care of the
positive residual density and would push out the His side chains a little
bit, which in turn could take care of the negative ones.
Or, the same effect could be achieved if the coordination distances end up
being slightly longer by identifying the "correct" atom or oxidation state.
Good luck!
Nukri

On Mon, Feb 22, 2021 at 12:22 PM Patrick Needham 
wrote:

>
> --
>
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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Pavel Afonine]

Hi,

as others pointed out electron rich elements tend to amplify imperfections
visible in Fo-Fc maps. Consider:
- refining occupancy of Fe, the site may be partially occupied;
- refining f' and f'' if data are anomalous;
- surrounding histidines may 'see' this Fe as a nonbonded interaction and
thus repulsion terms may kick in and push Fe from its position. Try
defining weak coordination bonds between Fe and respective nitrogens;
- refining anisotropic ADP of Fe only.

Good luck!
Pavel

On Mon, Feb 22, 2021 at 7:27 AM Patrick Needham 
wrote:

>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Jon Cooper]

Hello, there usually is noise in the difference map near electron-dense 
elements. Maybe refining against I(+) and I(-) might help, as someone suggested 
a few months ago or perhaps you have already done that. It would be interesting 
to know if it helps. Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 22 Feb 2021, 15:16, Patrick Needham wrote:

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[ccp4bb] Virtual Annual CCP4/APS Crystallographic School (2021) in the US

[Xu, Qingping]

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 
14-25, 2021 at the Advanced Photon Source (APS), Argonne National Laboratory 
(ANL), near Chicago, Illinois, USA. All details can be found at the school 
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Dates: June 14 through 25, 2021 (with a weekend break on June 19 and 20th)

Location: Virtual/Remote

The school comprises two parts: remote data collection workshop and virtual 
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data collection, only the participants' crystals will be used. Crystallographic 
computation workshop will feature many modern crystallographic software 
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http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, 
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crystals so the problems can be addressed during data collection and/or 
computation workshops.

Application: Application deadline is April 1st, 2021. To apply, visit 
https://www.ccp4.ac.uk/schools/APS-2021/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, Garib and Qingping




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Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

[Eleanor Dodson]

Well - that doesnt look too bad - it is hard to see in a screenshot but
presumably the N & C in the ring are correctly placed?
Why is there positive density over the Fe?  Are there other similar
features elsewhere in the map which can be assigned to noise?
Eleanor

On Mon, 22 Feb 2021 at 15:27, Patrick Needham  wrote:

>
> --
>
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[ccp4bb] synthetic protein materials postdoc position available - deadline 2 March

[James MacDonald]

Dear all,

We have a postdoc position available to work on a synthetic protein
materials project in collaboration with Prof. Milo Shaffer (Dept of
Materials) and industrial partners.

https://www.imperial.ac.uk/jobs/description/MED02267/research-associate-synthetic-protein-materials

https://www.jobs.ac.uk/job/CEF626/research-associate-in-synthetic-protein-materials

This project uses computationally designed synthetic proteins to create
novel tough fibres. The project is an exciting opportunity to accelerate
the development of new materials using methods drawn from synthetic biology
– and to accelerate the development of a new manufacturing technology.

Please get in contact with any questions.

best wishes,
James.



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[ccp4bb] Post-Doctoral position in Porto, Portugal

[Pedro Pereira]

We are looking for a highly motivated post-doc to join the 
Macromolecular Structure group of i3S - Instituto de Investigação e 
Inovação em Saúde (https://www.i3s.up.pt/research-group?x=113) in Porto, 
Portugal. The position, funded for 3 years, is expected to start in 
April 2021.


Building on our recent work (1-5), the project aims to develop direct 
anticoagulants against alternative targets in the blood coagulation 
cascade that have not been clinically exploited to date or represent a 
completely unexplored mechanism of intervention. The successful 
candidate will investigate the inhibition potency and anticoagulant 
activities /in vitro/ of potential inhibitors screened by Random 
nonstandard Peptide Integrated Discovery (RaPID). The candidate will 
also study the molecular determinants of inhibition, using X-ray 
crystallography, and perform SAR studies. Finally, the efficacy of lead 
compounds will be investigated /in vivo/.


The ideal candidate should hold a PhD in Biochemistry, Structural 
Biology or in a related field, with a good publication record (at least 
2 publications as first author in peer-reviewed journals).


Informal enquiries can be addressed to Jorge Ripoll-Rozada 
(jorge.roz...@ibmc.up.pt ) or Pedro J.B. 
Pereira (ppere...@ibmc.up.pt) .


Please note that applications will be considered ONLY if submitted 
(together with all accompanying documentation) before 2021/03/07, using 
the online tool at https://www.i3s.up.pt/job-opportunities.php#positions 
(Position reference: Researcher/FCT_PROJ2020/i3S/1202/2021).


Direct application link: 
https://dozer.i3s.up.pt/applicationmanagement/#/addapplications/ResearcherFCT_PROJ2020i3S12022021


Further information: 
https://dozer.i3s.up.pt:8443/fileupload/downloadfile/viewpdfnewtab/50f244dcc6f8b1ecb55beb7ceff2a57 
(in Portuguese) or 
https://dozer.i3s.up.pt:8443/fileupload/downloadfile/viewpdfnewtab/33258f72eae84e385ca4ea1abeb764 
(in English).


1- Thompson, R.E.; Liu, X.; Ripoll-Rozada, J.; Alonso-García, N.; 
Parker, B.L.; Pereira, P.J.B.; Payne, R.J. (2017) Tyrosine sulfation 
modulates activity of tick-derived thrombin inhibitors. /Nature 
Chemistry/ *9*, 909-917. DOI: 10.1038/nchem.2744


2 - Watson, E.; Liu, X.; Thompson, R.; Ripoll-Rozada, J.; Wu, M.; Alwis, 
I.; Gori, A.; Loh, C.-T.; Parker, B.; Otting, G.; Jackson, S.; Pereira, 
P.J.B.; Payne, R. (2018) Mosquito-derived anophelin sulfoproteins are 
potent anti-thrombotics. /ACS Central Science/ *4*, 468-476. DOI: 
10.1021/acscentsci.7b00612


3 - Watson, E.E.; Ripoll-Rozada, J.; Lee, A.C.; Wu. M.C.L.; Franck, C.; 
Pasch, T.; Premdjee, B.; Sayers, J.; Pinto, M.F.; Martins, P.M.; 
Jackson, S.P.; Pereira, P.J.B.; Payne, R.J. (2019) Rapid Assembly and 
Profiling of an Anticoagulant Sulfoprotein Library. /Proceedings of the 
National Academy of Sciences of the USA/ *116*, 13873-13878. DOI: 
10.1073/pnas.1905177116


4 - Calisto, B.M.; Ripoll-Rozada, J.; Dowman, L.J.; Franck, C.; Agten, 
S.M.; Parker, B.L.; Veloso, R.C.; Vale, N.; Gomes, P.; de Sanctis, D.; 
Payne, R.J.; Pereira, P.J.B. (2021) Sulfotyrosine-Mediated Recognition 
of Human Thrombin by a Tsetse Fly Anticoagulant Mimics Physiological 
Substrates. /Cell Chemical Biology/ *28*, 26-33. DOI: 
10.1016/j.chembiol.2020.10.002


5 - Agten, S.M.; Watson, E.E.; Ripoll-Rozada, J.; Dowman, L.J.; Wu, M.; 
Alwis, I.; Jackson, S.; Pereira, P.J.B.; Payne, R.J. (2021) Potent 
trivalent inhibitors of thrombin through hybridization of salivary 
sulfopeptides from hematophagous arthropods. /Angewandte Chemie 
International Edition/, in press. DOI: 10.1002/anie.202015127


--
Pedro J. B. Pereira, PhD
IBMC - Biomolecular Structure Group
i3S - Macromolecular Structure Group
Rua Alfredo Allen 208
4200-135 Porto
Portugal
Tel.  +351 226 074 954
E-mail:ppere...@ibmc.up.pt

--
Pedro J. B. Pereira, PhD
IBMC - Biomolecular Structure Group
i3S - Macromolecular Structure Group
Rua Alfredo Allen 208
4200-135 Porto
Portugal
Tel.  +351 226 074 954
E-mail: ppere...@ibmc.up.pt




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Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

[Eugene Osipov]

Dear Tom,
I updated the workstation with Ubuntu 16.04->20.04  This update broke 3d
vision and I am thinking about moving back to Ubuntu 16.04. Other programs
work well.




вс, 21 февр. 2021 г. в 10:59, Folmer Fredslund :

> Dear Tom
>
> Be aware that python2 is currently not supported.  It is end-of-life since
> 1/1-2020 and is not part of Ubuntu 20.04
>
> This might not be a big concern, bit depends on which software you use.
>
>
> Best regards
> Folmer
>
>
>
> lør. 20. feb. 2021 21.50 skrev Peat, Tom (Manufacturing, Parkville)
> :
>
>> Speaking of Linux, but somewhat tangential to the thread:
>> Ubuntu has recently released their newest version 20.04 (Focal Fossa).
>> Has anyone implemented this and is there anything that doesn't work? Any
>> gotchas that one might want to be aware of?
>>
>> Cheers, tom
>>
>> Tom Peat, PhD
>> Proteins Group
>> Biomedical Program, CSIRO
>> 343 Royal Parade
>> Parkville, VIC, 3052
>> +613 9662 7304
>> +614 57 539 419
>> tom.p...@csiro.au
>>
>> --
>> *From:* CCP4 bulletin board on behalf of Tim Gruene
>> *Sent:* Sunday, February 21, 2021 2:35 AM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] Linux Distro for setting up workstations - Is
>> CentOS still a good choice?
>>
>> Hi Matthias,
>>
>> I have been using Debian for more than a decade. Every stable release
>> is supported for at least 5 years.
>> Many crystallographic libraries and some programs are part of the
>> standard repository, like raster3d, pymol, shelxle, libccp4,
>> libclipper, ...
>>
>> Debian is particularly stable, and requires little maintenance.
>>
>> Cheers,
>> Tim
>>
>> On Fri, 19 Feb 2021 21:35:46 +0100
>> Matthias Zeug  wrote:
>>
>> > Hi all,
>> >
>> >
>> >
>> > I just came across the (already quite old) news that Red-Hat switches
>> > their support-policy for CentOS to a rolling preview model (replacing
>> > CentOS Linux by CentOS Stream):
>> >
>> >
>> https://www.zdnet.com/article/why-red-hat-dumped-centos-for-centos-stream/
>> >
>> >
>> https://www.enterpriseai.news/2021/01/22/red-hats-disruption-of-centos-unlea
>> > shes-storm-of-dissent/
>> >
>> >
>> >
>> > I wondered if that has any implications for the community, as
>> > scientific programs - maybe except the big ones like coot, Phenix,
>> > and ccp4 - are often not *that* well maintained for an extended
>> > period. I had the impression CentOS was liked especially for its
>> > "unbreakability,"  and it seems to be the main developing platform
>> > for some widely used smaller programs (e.g., adxv).
>> >
>> >
>> >
>> > Do you think it would be advisable to switch to a Ubuntu-distro when
>> > setting up new workstations in the future, or is it safe to stick to
>> > CentOS?
>> >
>> >
>> >
>> > Please let me know what you think :-)
>> >
>> >
>> >
>> > Best,
>> >
>> >
>> >
>> > Matthias
>> >
>> >
>> >
>> >
>> >
>> > Matthias Zeug
>> >
>> > Buchmann Institute of Molecular Life Sciences
>> >
>> > Goethe University Frankfurt
>> >
>> >
>> >
>> >
>> > 
>> >
>> > 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/
>>
>>
>>
>> --
>> --
>> 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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>>
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-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O



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