Re: [ccp4bb] Mac OSX 10.7 Lion

[Jacques-Philippe Colletier]

Hi,

Overall, the transition from 10.6 is seemingless, crystallographically-wise.

Of course you need to have the new XCode 4.1 installed, and you should also 
download new, 10.7-dedicated 64bits gcc/gfortran/g77 bundles from 
http://hpc.sourceforge.net/
And then, CNS, Phenix, CCP4, etc... will just run perfect.
I had to reinstall Coot -- but that's minor.
(Mac)Pymol also works fine, yet (for some reason) uses a lot of resources even 
when idle.
As per the Upsalla Soft. Factory programs, you'll have to recompile then using 
the above mentioned bundles, or get already compiled binaries from Mark Harris.
You'll also need to recompile Gromacs (and fftw3) if you're using it -- but it 
then works great.

I agree with W. Scott on the fact that the new OS is really greedy in terms of 
resources.
I surely wont upgrade my other, older mac computers that run just fine on 10.6.
But if you have a new Mac, Lion is is really neat.

Best
Jacques


Le Sep 10, 2011 à 2:09 AM, William Scott a écrit :

> Hi Phil:
> 
> I've found few, if any advantages.  I fear for the future.
> 
> I've had problems getting coot to run stereo due to the X11 implementation in 
> 10.7.  Apart from that, no major problems with crystallographic software.
> 
> Lion greedily uses memory, and any computer I have with less than 4 gig of 
> memory has become extremely sluggish as a consequence of the "upgrade."  
> Ideally, you need 8 gig.
> 
> Even with that, on my 2010 mini that I use for music playback, I regressed to 
> 10.6.8, because of the audio interface. (It seems less robust, more prone to 
> dropouts and now lacks integer mode output).
> 
> Sara has been screaming at me for the last two weeks (nothing us usual in of 
> itself) because Apple decided to get rid of "Save As".
> 
> Xcode and the compiler set is free again on 10.7.
> 
> I've put some suggestions here for how to get rid of the most annoying new 
> features:
> http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes
> 
> All the best,
> 
> Bill
> 
> 
> 
> 
> 
> 
> On Sep 9, 2011, at 1:28 AM, Phil Evans wrote:
> 
>> Is there any opinion or experience about whether Lion is ready for 
>> crystallographic use? Should I "upgrade"?
>> 
>> Phil
> 
> William G. Scott
> 
> Contact info:
> http://chemistry.ucsc.edu/~wgscott/

Re: [ccp4bb] drops swelling

[anita p]

Thanks a lot for your suggestions.
Would it be worth while to try and remove glycerol at the last step which is
gel filtration and then set trays in my case?
I have never tried without glycerol.
reg.
Anita


On Fri, Sep 9, 2011 at 7:54 PM, Enrico Stura  wrote:

> Anita,
>
> see the message I posted yesterday on the CCP4bb:
> http://www.mail-archive.com/**ccp4bb@jiscmail.ac.uk/**msg22638.html
>
> or google "stura glycerol"
> Re: [ccp4bb] How to help crystal grow bigger
>
> In your case the sentence you need is:
> "You need to have a higher (double) glycerol concentration in the reservoir
> else you will risk finding that your drops will get biggger and not smaller.
> This note of caution applies to vapour diffusion set ups as equilibration
> can be tricky in such context: Vera,L., Czarny, B., Georgiadis, D., Dive,
> V., Stura, E.A. (2011) Practical Use of Glycerol in Protein Crystallization.
> Cryst. Growth & Des. 11 :2755–2762. "
>
> http://pubs.acs.org/doi/abs/**10.1021/cg101364m
>
> Enrico.
>
>
>
> On Fri, 09 Sep 2011 13:22:53 +0200, anita p  wrote:
>
>  Dear Crystallographers,
>> I have set hanging drop trays with 2ul of protein and 2 ul of resorvior
>> solution. I have seen in some cases the drops are swelling. My protein
>> buffer has 15% glycerol in it.
>> This is happening mainly when I have peg 400 or peg MME or MPD or
>> Jeffamine
>> in the buffer condition.
>> Could any one suggest a remedy for this.
>>
>> with regards
>> Anita
>>
>
>
> --
> Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office
> Room 19, Bat.152,   Tel: 33 (0)1 69 08 9449Lab
> LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette,   FRANCE
> http://www-dsv.cea.fr/en/**institutes/institute-of-**
> biology-and-technology-saclay-**ibitec-s/unites-de-recherche/**
> department-of-molecular-**engineering-of-proteins-**
> simopro/molecular-toxinology-**and-biotechnology-laboratory-**
> ltmb/crystallogenesis-e.-stura
> http://www.chem.gla.ac.uk/**protein/mirror/stura/index2.**html
> e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
>

[ccp4bb] PhD position at Imperial College London

[Ebbels, Timothy M D]

EPSRC 3-year PhD Studentship
Department of Surgery and Cancer
Imperial College London

Overcoming the Protein Crystallization Bottleneck by Machine Learning


Applications are invited for a 3-year PhD studentship funded by the Engineering 
and Physical Sciences Research Council commencing 2011 under the joint 
supervision of Prof. Naomi Chayen and Dr Tim Ebbels in the field of 
computational protein crystallization.

The Project
Protein crystallography plays a major role in modern biomedicine because 
proteins, being the major machinery of life, are often the targets of drugs. 
Protein functions are determined by their three-dimensional structure, hence 
detailed understanding of protein structure is essential for rational design of 
therapeutic treatments. The most powerful method for determining the structure 
of proteins is X-ray crystallography which is totally reliant on the 
availability of high quality crystals. However, producing useful crystals has 
always been the bottleneck to structure determination. With the advent of 
genomics/proteomics and hence the exponentially increasing number of potential 
drug target proteins, this problem is becoming increasingly acute. While 
conventional techniques effectively rely on trial and error to find the optimal 
crystallization conditions, statistical and machine learning approaches have 
the potential to significantly increase the efficiency and accuracy of the 
process. In this project we will explore the ability of such computational 
tools to improve the protein crystallization process. Specifically, the student 
will:


1. Apply a multivariate Design of Experiments approach to optimise 
crystallisation conditions using fewer experiments than conventional methods.

2. Investigate existing databases of crystallisation conditions and 
associated outcomes (crystal quality) to derive multivariate models able to 
predict crystallisation from a set of input conditions.

The project will investigate the use of a diverse array of machine learning 
tools such as genetic algorithms, partial least squares regression and kernel 
density approaches. While the project will be primarily computational in 
nature, the student will also have the opportunity to gain experience in the 
experimental side of protein crystallization. The final result will be a more 
efficient methodology for conducting crystallisation experiments and an in 
silico approach to prediction of crystallizability.

Studentship Details
Applicants should hold (or obtain soon) a masters degree (or equivalent 
overseas qualification) in a physical science, bioinformatics or otherwise 
numerate field. Outstanding candidates possessing an appropriate bachelors 
degree may also be considered. The studentship is ONLY open to students who 
hold settled status in the UK and have been ‘ordinarily resident’ in the UK for 
three years. Further eligibility details can be found at:
http://www.epsrc.ac.uk/funding/students/Pages/eligibility.aspx.

For informal enquiries and application please contact Prof. Naomi Chayen 
(n.cha...@imperial.ac.uk) or Dr Tim Ebbels 
(t.ebb...@imperial.ac.uk). Pleaase send a full 
CV, stating your nationality, and the full contact details of two academic 
referees.

Re: [ccp4bb] Mac OSX 10.7 Lion

[harry powell]

Hi

My two ha'porth.

If you are thinking of "upgrading" your sole Mac software development  
box to Lion I'd say "don't do it unless you like a lot of pain".  
Anything built on Snow Leopard should run okay on Lion (my Tiger  
builds seem okay on 10.4, 10.5, 10.6...), so unless you really have  
an over-riding need to move to 10.7, I'd hang fire.


If you're only running applications and not developing, you can  
always shout at the developers if things go wrong.


My plan is to install Lion on a spare bootable disk and see what  
happens - if all else fails, at least I can ignore the upgrade until  
Apple release 10.7.1, 10.7.2, etc and fix most of their screw-ups.


On 10 Sep 2011, at 08:03, Jacques-Philippe Colletier wrote:


Hi,

Overall, the transition from 10.6 is seemingless,  
crystallographically-wise.


Of course you need to have the new XCode 4.1 installed, and you  
should also download new, 10.7-dedicated 64bits gcc/gfortran/g77  
bundles from http://hpc.sourceforge.net/

And then, CNS, Phenix, CCP4, etc... will just run perfect.
I had to reinstall Coot -- but that's minor.
(Mac)Pymol also works fine, yet (for some reason) uses a lot of  
resources even when idle.
As per the Upsalla Soft. Factory programs, you'll have to recompile  
then using the above mentioned bundles, or get already compiled  
binaries from Mark Harris.
You'll also need to recompile Gromacs (and fftw3) if you're using  
it -- but it then works great.


I agree with W. Scott on the fact that the new OS is really greedy  
in terms of resources.
I surely wont upgrade my other, older mac computers that run just  
fine on 10.6.

But if you have a new Mac, Lion is is really neat.

Best
Jacques


Le Sep 10, 2011 à 2:09 AM, William Scott a écrit :


Hi Phil:

I've found few, if any advantages.  I fear for the future.

I've had problems getting coot to run stereo due to the X11  
implementation in 10.7.  Apart from that, no major problems with  
crystallographic software.


Lion greedily uses memory, and any computer I have with less than  
4 gig of memory has become extremely sluggish as a consequence of  
the "upgrade."  Ideally, you need 8 gig.


Even with that, on my 2010 mini that I use for music playback, I  
regressed to 10.6.8, because of the audio interface. (It seems  
less robust, more prone to dropouts and now lacks integer mode  
output).


Sara has been screaming at me for the last two weeks (nothing us  
usual in of itself) because Apple decided to get rid of "Save As".


Xcode and the compiler set is free again on 10.7.

I've put some suggestions here for how to get rid of the most  
annoying new features:

http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes

All the best,

Bill






On Sep 9, 2011, at 1:28 AM, Phil Evans wrote:

Is there any opinion or experience about whether Lion is ready  
for crystallographic use? Should I "upgrade"?


Phil


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/


Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH

Re: [ccp4bb] Mac OSX 10.7 Lion

[Jürgen Bosch]

One really nice feature though comes with what Bill's wife hates. No worries 
about saving an edited file in many programs. The background versioning is 
great no more needs of having my_manuscript_###1.doc :-) one file to handle 
them all. And you can go back to older versions of course. The only disturbing 
feature about this integrated auto backup is sometimes your Mac goes idle 
before you can typebecause it is saving another version. This is particularly 
annoying when you edit large Keynote files.

Jürgen 
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

On Sep 10, 2011, at 5:26, harry powell  wrote:

> Hi
> 
> My two ha'porth.
> 
> If you are thinking of "upgrading" your sole Mac software development  
> box to Lion I'd say "don't do it unless you like a lot of pain".  
> Anything built on Snow Leopard should run okay on Lion (my Tiger  
> builds seem okay on 10.4, 10.5, 10.6...), so unless you really have  
> an over-riding need to move to 10.7, I'd hang fire.
> 
> If you're only running applications and not developing, you can  
> always shout at the developers if things go wrong.
> 
> My plan is to install Lion on a spare bootable disk and see what  
> happens - if all else fails, at least I can ignore the upgrade until  
> Apple release 10.7.1, 10.7.2, etc and fix most of their screw-ups.
> 
> On 10 Sep 2011, at 08:03, Jacques-Philippe Colletier wrote:
> 
>> Hi,
>> 
>> Overall, the transition from 10.6 is seemingless,  
>> crystallographically-wise.
>> 
>> Of course you need to have the new XCode 4.1 installed, and you  
>> should also download new, 10.7-dedicated 64bits gcc/gfortran/g77  
>> bundles from http://hpc.sourceforge.net/
>> And then, CNS, Phenix, CCP4, etc... will just run perfect.
>> I had to reinstall Coot -- but that's minor.
>> (Mac)Pymol also works fine, yet (for some reason) uses a lot of  
>> resources even when idle.
>> As per the Upsalla Soft. Factory programs, you'll have to recompile  
>> then using the above mentioned bundles, or get already compiled  
>> binaries from Mark Harris.
>> You'll also need to recompile Gromacs (and fftw3) if you're using  
>> it -- but it then works great.
>> 
>> I agree with W. Scott on the fact that the new OS is really greedy  
>> in terms of resources.
>> I surely wont upgrade my other, older mac computers that run just  
>> fine on 10.6.
>> But if you have a new Mac, Lion is is really neat.
>> 
>> Best
>> Jacques
>> 
>> 
>> Le Sep 10, 2011 à 2:09 AM, William Scott a écrit :
>> 
>>> Hi Phil:
>>> 
>>> I've found few, if any advantages.  I fear for the future.
>>> 
>>> I've had problems getting coot to run stereo due to the X11  
>>> implementation in 10.7.  Apart from that, no major problems with  
>>> crystallographic software.
>>> 
>>> Lion greedily uses memory, and any computer I have with less than  
>>> 4 gig of memory has become extremely sluggish as a consequence of  
>>> the "upgrade."  Ideally, you need 8 gig.
>>> 
>>> Even with that, on my 2010 mini that I use for music playback, I  
>>> regressed to 10.6.8, because of the audio interface. (It seems  
>>> less robust, more prone to dropouts and now lacks integer mode  
>>> output).
>>> 
>>> Sara has been screaming at me for the last two weeks (nothing us  
>>> usual in of itself) because Apple decided to get rid of "Save As".
>>> 
>>> Xcode and the compiler set is free again on 10.7.
>>> 
>>> I've put some suggestions here for how to get rid of the most  
>>> annoying new features:
>>> http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes
>>> 
>>> All the best,
>>> 
>>> Bill
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Sep 9, 2011, at 1:28 AM, Phil Evans wrote:
>>> 
 Is there any opinion or experience about whether Lion is ready  
 for crystallographic use? Should I "upgrade"?
 
 Phil
>>> 
>>> William G. Scott
>>> 
>>> Contact info:
>>> http://chemistry.ucsc.edu/~wgscott/
> 
> Harry
> --
> Dr Harry Powell,
> MRC Laboratory of Molecular Biology,
> Hills Road,
> Cambridge,
> CB2 0QH

Re: [ccp4bb] drops swelling

[Ed Pozharski]

On Sat, 2011-09-10 at 15:00 +0800, anita p wrote:
> Would it be worth while to try and remove glycerol at the last step
> which is gel filtration and then set trays in my case? 

Sure, assuming that your protein does not become unstable without
glycerol (protein solubility is likely to decrease too).  On a general
note, protein crystallization is the (dark) art of trying as many things
as you possibly can (including the crazy stuff).  Quoting the great
Bruce Foxman, you need to use the crystallization method number eight,
which is the one that works :)

-- 
Hurry up, before we all come back to our senses!
  Julian, King of Lemurs

Re: [ccp4bb] Crystypos [WAS: [ccp4bb] Mac OSX 10.7 Lion]

[Ed Pozharski]

The best X-ray related typo I ever seen was the "Small angel scattering"
- poor little things!

On Fri, 2011-09-09 at 18:23 -0400, Patrick Loll wrote:
> Still doesn't beat my all-time favorite, an early Microsoft spell-checker 
> that changed "diffract" to "defrocked."
> 
> > 
> > I forgot to mention how delightful the spelling auto-"correction"  feature 
> > can be.  (It should have read "nothing unusual in and of itself").
> > 
> > That, at least, can be turned off.

Re: [ccp4bb] refmac and DNA

[Ed Pozharski]

On Sat, 2011-09-10 at 08:21 +0200, Miguel Ortiz Lombardía wrote:
> A, C and G are RNA nucleotides. T is (mostly) not, its RNA-equivalent
> is
> uridine phosphate, U.
> 
> 

Right, that was my suspicion.  But I thought that RNA bases would be Xr,
not Xd.  Plus, refmac does not complain about missing oxygens.  Anyway,
the latest coot rocks, as usual, now if I only can figure out who is
Linda...

Cheers,

Ed.



-- 
Coot verendus est

Re: [ccp4bb] Mac OSX 10.7 Lion

[Herbert J. Bernstein]

Dear Colleagues,

  Lion is an reality all developers have to live with.  While I
agree that it would be a bad idea to update one's primary
development environment to Lion, it does seem a good idea to have
at least one system with sufficient memory, disk and good enough
graphics and the new UI (user interface) to be able to wring out
problems, especially on the UI side.

  So the question is:  Is a new MacBook Pro or new MacBook Air
sufficient for such testing, or is something heftier with a
studio display necessary?

  Regards,
Herbert



At 10:26 AM +0100 9/10/11, harry powell wrote:

Hi

My two ha'porth.

If you are thinking of "upgrading" your sole Mac software 
development box to Lion I'd say "don't do it unless you like a lot 
of pain". Anything built on Snow Leopard should run okay on Lion (my 
Tiger builds seem okay on 10.4, 10.5, 10.6...), so unless you really 
have an over-riding need to move to 10.7, I'd hang fire.


If you're only running applications and not developing, you can 
always shout at the developers if things go wrong.


My plan is to install Lion on a spare bootable disk and see what 
happens - if all else fails, at least I can ignore the upgrade until 
Apple release 10.7.1, 10.7.2, etc and fix most of their screw-ups.


On 10 Sep 2011, at 08:03, Jacques-Philippe Colletier wrote:


Hi,

Overall, the transition from 10.6 is seemingless, crystallographically-wise.

Of course you need to have the new XCode 4.1 installed, and you 
should also download new, 10.7-dedicated 64bits gcc/gfortran/g77 
bundles from http://hpc.sourceforge.net/

And then, CNS, Phenix, CCP4, etc... will just run perfect.
I had to reinstall Coot -- but that's minor.
(Mac)Pymol also works fine, yet (for some reason) uses a lot of 
resources even when idle.
As per the Upsalla Soft. Factory programs, you'll have to recompile 
then using the above mentioned bundles, or get already compiled 
binaries from Mark Harris.
You'll also need to recompile Gromacs (and fftw3) if you're using 
it -- but it then works great.


I agree with W. Scott on the fact that the new OS is really greedy 
in terms of resources.
I surely wont upgrade my other, older mac computers that run just 
fine on 10.6.

But if you have a new Mac, Lion is is really neat.

Best
Jacques


Le Sep 10, 2011 à 2:09 AM, William Scott a écrit :


Hi Phil:

I've found few, if any advantages.  I fear for the future.

I've had problems getting coot to run stereo due to the X11 
implementation in 10.7.  Apart from that, no major problems with 
crystallographic software.


Lion greedily uses memory, and any computer I have with less than 
4 gig of memory has become extremely sluggish as a consequence of 
the "upgrade."  Ideally, you need 8 gig.


Even with that, on my 2010 mini that I use for music playback, I 
regressed to 10.6.8, because of the audio interface. (It seems 
less robust, more prone to dropouts and now lacks integer mode 
output).


Sara has been screaming at me for the last two weeks (nothing us 
usual in of itself) because Apple decided to get rid of "Save As".


Xcode and the compiler set is free again on 10.7.

I've put some suggestions here for how to get rid of the most 
annoying new features:

http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes

All the best,

Bill






On Sep 9, 2011, at 1:28 AM, Phil Evans wrote:

Is there any opinion or experience about whether Lion is ready 
for crystallographic use? Should I "upgrade"?


Phil


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/


Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH



--
=
 Herbert J. Bernstein, Professor of Computer Science
   Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769

 +1-631-244-3035
 y...@dowling.edu
=

Re: [ccp4bb] Crystypos [WAS: [ccp4bb] Mac OSX 10.7 Lion]

[Vellieux Frederic]

Well in fact, it all depends on the type of detector these small angels 
end up on and on the speed of this "godly" radiation. Only once you have 
considered both these elements can you say "poor little things".


My 2p worth.

Fred.

Ed Pozharski wrote:

The best X-ray related typo I ever seen was the "Small angel scattering"
- poor little things!

On Fri, 2011-09-09 at 18:23 -0400, Patrick Loll wrote:
  

Still doesn't beat my all-time favorite, an early Microsoft spell-checker that changed 
"diffract" to "defrocked."



I forgot to mention how delightful the spelling auto-"correction"  feature can be.  (It 
should have read "nothing unusual in and of itself").

That, at least, can be turned off.