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

2011-09-11 Thread 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.
  



  


Re: [ccp4bb] refmac and DNA

2011-09-11 Thread Miguel Ortiz Lombardia
Le 11/09/2011 00:23, Ed Pozharski a écrit :
 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.  

My understanding is that the Xr/Xd scheme has been dropped from the
latest refmac5/coot to comply with the X/DX (and OP1, OP2, prime signs
instead of asterisks...) standard from the PDB/NDB.

Cheers,


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I  II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia


Re: [ccp4bb] Mac OSX 10.7 Lion

2011-09-11 Thread Bosch, Juergen
Regarding MBP versus MBA, one of my graduate students just got a new MBA and 
her machine is much faster than my MBP 2.8 GHz Intel Core 2 Duo with 4 GB RAM. 
Both machines are running Lion.

The new MBA is hot, only disadvantage you can't lock it down, there's no option 
for it.

Jürgen

On Sep 10, 2011, at 8:39 PM, Herbert J. Bernstein wrote:

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.edumailto:y...@dowling.edu
=

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/







Re: [ccp4bb] Mac OSX 10.7 Lion

2011-09-11 Thread Sean Seaver
Dear Herbert,

I've come across quite a few people that are using mac books as their main 
development computer.  This site ( http://usesthis.com/ ) can be an good way to 
learn about various setups.  A popular trend seems to be using a mac book along 
with the apple thunderbolt display for more screen real estate.

Take Care,

Sean Seaver

P212121
http://store.p212121.com/


[ccp4bb] COOT on CentOS 6 (x86_64)

2011-09-11 Thread Yuri Pompeu
Hello everyone,
Could anyone tell me (or point me to) how to get COOT running on CentOS6 64-bit?
It doesnt launch due to failed dependencies, it requires packages that CentOS6 
has replaced...
At least that is what it looks like to me...
Cheers,


Re: [ccp4bb] COOT on CentOS 6 (x86_64)

2011-09-11 Thread Paul Emsley

On 12/09/11 00:05, Yuri Pompeu wrote:

Hello everyone,
Could anyone tell me (or point me to) how to get COOT running on CentOS6 64-bit?
It doesnt launch due to failed dependencies, it requires packages that CentOS6 
has replaced...



I would try the centos5 binaries - if that didn't work, I'd try to 
compile it myself (build-it-gtk2-simple).  You can try to fiddle it by 
linking the new library so files with the old names in coot's lib 
directory - but that doesn't seem like the best solution to me.


Paul.