Re: [ccp4bb] Apple Mac M1 chip machines and compatibility with structural biology software?

[Jurgen Bosch]

Only issue is that the MacBook Air has a 13” display but I didn’t want to wait 
for a 16” MacBook Pro with Apple Silicon. I’m waiting for the adapter to hook 
up my Cinema Display from 2010 (?) and I hope that it will also work for the 
Zalman for 3D visualization.

Another issue is I run out of steam before the battery runs out of steam.

The M1 MacBook Air is impressive, it smokes my Late October 2019 MacBook Pro 15”

I have yet to discover a problem with what I use on a regular basis.

Jürgen 

> On Jan 23, 2021, at 7:41 PM, Amit Singh  wrote:
> 
> Dear Prof Jon,
> 
> I haven't faced any problems while installing and using a couple of them like 
> CCP4 (including coot), pymol and Xquartz. 
> 
> On Sat, 23 Jan, 2021, 4:27 pm Jon Sayers,  > wrote:
> Dear All,
> Slightly off-topic. The new Apple  M1 chip machines have been out for a 
> while. Is anyone using them for the typical range of software structural 
> biology/docking software? Any obvious issues or no-goes?
> 
> CCP4, Pymol, Autodoc, Xquartz, iBabel, etc
> 
> BW 
> Jon
> Prof. Jon R Sayers  FRSB
> Florey Institute,
> Dept. of Infection, Immunity and Cardiovascular Disease
> University of Sheffield Medical School
> Beech Hill Rd
> Sheffield S10 2RX
> United Kingdom, 
> 
> Tel +44 114 215 9552
> Email  j.r.say...@shef.ac.uk 
> http://www.sheffield.ac.uk/iicd/profiles/sayers 
> 
> 
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Re: [ccp4bb] Apple Mac M1 chip machines and compatibility with structural biology software?

[Amit Singh]

Dear Prof Jon,

I haven't faced any problems while installing and using a couple of them
like CCP4 (including coot), pymol and Xquartz.

On Sat, 23 Jan, 2021, 4:27 pm Jon Sayers, 
wrote:

> Dear All,
> Slightly off-topic. The new Apple  M1 chip machines have been out for a
> while. Is anyone using them for the typical range of software structural
> biology/docking software? Any obvious issues or no-goes?
>
> CCP4, Pymol, Autodoc, Xquartz, iBabel, etc
>
> BW
> Jon
> Prof. Jon R Sayers  FRSB
> Florey Institute,
> Dept. of Infection, Immunity and Cardiovascular Disease
> University of Sheffield Medical School
> Beech Hill Rd
> Sheffield S10 2RX
> United Kingdom,
>
> Tel +44 114 215 9552
> Email  j.r.say...@shef.ac.uk 
> http://www.sheffield.ac.uk/iicd/profiles/sayers
>
>
> --
>
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>



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Re: [ccp4bb] The weekly nonsense

[Bernhard Rupp]

I am not sure how the relevance of the subject obviates the need to read 

at least the abstract of your references.

 

I actually stumbled upon this because I am receiving more and more citation
alerts from 

papers in those odd journals in the 'pay to play' category which have little
connection 

to what they cite. 'Cite by Google'  is almost certainly on the rise..and
that it happens to

AI researchers I find particularly ironic.

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Frank Von
Delft
Sent: Friday, January 22, 2021 23:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The weekly nonsense

 

It's certainly a real problem they're writing about. Or at least, one that
some people say we should be worrying about.

 

Sent from tiny silly touch screen

  _  

From: Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk
 >
Sent: Saturday, 23 January 2021 02:40
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] The weekly nonsense

 

Take care ;-

https://www.wicys.org/

Seems genuine enough group & everything to me. The referees should have
spotted that one ;-0

Sent from ProtonMail mobile



 Original Message 
On 22 Jan 2021, 23:03, Bernhard Rupp < hofkristall...@gmail.com
 > wrote: 

 

Dear CCP4 Fellows, 

 

for the subscribers of my immensely popular show "The weekly nonsense" I
recommend

https://arxiv.org/pdf/2101.06308.pdf

particularly reference [27] and its contextual environs.

 

Am I alone suspecting that this is some AI generated auto-paper-mill
product?

 

Cheers, BR

 

--

Bernhard Rupp

The Amt

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

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[ccp4bb] Apple Mac M1 chip machines and compatibility with structural biology software?

[Jon Sayers]

Dear All,
Slightly off-topic. The new Apple  M1 chip machines have been out for a while. 
Is anyone using them for the typical range of software structural 
biology/docking software? Any obvious issues or no-goes?

CCP4, Pymol, Autodoc, Xquartz, iBabel, etc

BW 
Jon
Prof. Jon R Sayers  FRSB
Florey Institute,
Dept. of Infection, Immunity and Cardiovascular Disease
University of Sheffield Medical School
Beech Hill Rd
Sheffield S10 2RX
United Kingdom, 

Tel +44 114 215 9552
Email  j.r.say...@shef.ac.uk
http://www.sheffield.ac.uk/iicd/profiles/sayers




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Re: [ccp4bb] Question about tncs and SAD phasing

[Eleanor Dodson]

Well - I would start with a self rotation analysis. That non-cryst twofold
and three folds would suggest something with 3-2 symmetry. I vaguely
remember an insulin structure with the hexamer 3-fold in similar
orientation..

And  this paterson peak "one major off origin peak at 0.5 0.5 0.173" might
help.
What about trying to reindex to halve the A B axes,   (reindex h/2,k/2,l
will work and wont change the spacegroup.)
You say 22 molecules but I would guess there is really 24, so reduce the
volume to a quarter and you want 6 ..
Check the self rotation for the smaller cell and see if there are still 3
folds and 2 folds, then solve it in the reduced cell and extend the model
later

Is that as clear as mud??
Eleanor



On Sat, 23 Jan 2021 at 11:45, Andrew Lovering  wrote:

> Dear All,
>
>
> Having some fun with a marginal SAD S phasing case that you may be able to
> help me on.
>
> My primary question is "does strong tNCS artefactually inflate FOM
> scores"? I have a solution with FOM 0.48 to 3.5Ang or so and the map isn't
> as good as I'd expect (in either hand).
>
>
> -more detail if this helps:
>
> We have collected 3 sweeps at 1.77A wavelength, Rpim is good 2% or less,
> xtriage Z-score is 2, aimless suggests anom signal to 3.9A, as does shelxc,
> no signs of radiation damage, anom multiplicity is 40, cc anom 0.4 overall
>
>
> Cell is P41212/P43212, 146.9 146.9 335.1 diffracts to 2Ang or so which
> suggests 50% solvent = 22 copies in asu!
>
>
> each copy should have 2 disulphides and 6 extra S in Met. I am using dsul
> keyword in shelxd. I ask for a variety of sites, usually gets 240+, there
> is also 300mM Mg and 20mM As in conditions (site completion in phaser  with
> Mg or As doesnt really help)
>
>
> When we look at native patterson we see one major off origin peak at 0.5
> 0.5 0.173 fractional, 25% height of origin
>
> -and a smaller peak at 0.35 0.35 0.5 10% of origin
>
>
> I have tried everything. Changing phasing limits, programme, cutting back
> data range, number of sites. But I can get a decent sites pdb from
> shelx/crank2 which popped into phenix autosol gives stats that wrongly make
> me think I am close (fom 0.4-0.5, score 30+, skew 0.1+). My model has no
> molrep possibilities and likely no alpha helical content
>
>
> If I run the substructure sites through profess, I get two nice operators:
>
> -(op1) polar 90 -44 179.9 trans -72 -73 -444.6 rotation order 8, N atoms
> paired 74 from 16 of input atoms
>
> -(op2) polar 90 -87 180 trans -147 -9 -863 rotation order 2 paired 8 atoms
> from 8 of input
>
> (profess notes these two sit 43 degrees apart)
>
>
> I can see that op1 has a translational component that is my tNCS vector
> (-0.5 -0.5 and 0.17 away from 0.5)and that likely I have 4 fold
> operator that sits over my crystallographic 2-fold, which is 45 degree from
> another 2 fold (self rotation function attached..). I would welcome a
> better description of this 
>
> Using these operators (or indeed a pure tNCS only operator) in dm gives
> good correlation but again no map improvement. Is it worth playing with
> nmol?
>
>
> Any suggestions welcome, before we hit this with some higher electron
> derivatives!
>
>
> Thanks
>
> Andy
>
>
>
>
>
>
> --
> *From:* >
> *Sent:* January 23, 2021 11:08 AM
> *To:* Andrew Lovering (Biosciences)
> *Subject:* Srf
>
>
> --
>
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