Re: [phenixbb] phenixbb Digest, Vol 56, Issue 30
Message: 4 Date: Tue, 27 Jul 2010 08:39:17 -0700 From: Nathaniel Echols
To: PHENIX user mailing list Subject: Re: [phenixbb] 32-bit binaries for version 1.6.3-473 Message-ID: Content-Type: text/plain; charset="iso-8859-1" On Tue, Jul 27, 2010 at 8:15 AM, Leonid Flaks
wrote: I am running phenix 1.6.2-432 on a set of systems running 32-bit version of fedora-12. The latest version of phenix (1.6.3-473) has binaries mostly for 64-bit OS. The only 32-bit OS I see is fedora-3. I would be happy to switch to 64-bit OS one day, but HKL2000 that runs on the same computers has a big warning about instability of it on the 64-bit (it is dated back to 2005!) Coot is also crashing on the the 64-bit test system, so I have to stay with 32-bit for now. Does anybody know if fc-3 version would run on f-12?
I suspect it will be okay, but I haven't tested it. It partly depends on which features will be used - the GUI is twitchier about system libraries on Linux. Fortunately, we also distribute all of the source code for Phenix, so if the binary installer doesn't work, I'd recommend switching to the source installer. Are these the same machines (and OS) that were used for RapiData?
Yes, same 'cafe' systems. They all run f-12-32bit.
Would it be possible to have 32-bit version built for f-12 or f-13?
Possibly - we are probably going to pull some machines from our queueing system because they have only 8 cores, and some of these will become build machines for additional platforms (64-bit Ubuntu and CentOS are candidates). Also, we now build a CentOS 5 (similar to FC6) installer - it didn't work properly for 1.6.3, but I think I've fixed it now, and we're going to push out a 1.6.4 very soon because of some unrelated problems in 1.6.3.
-Nat
And on top of that, I don't see coot with python binary available for f-12 anymore. I will be testing fc-3 version then. Leon
i have one data of 3 A of a unknown protein don't have sequence homlogous
pdb known . but showing highly coserved fold.
space group is p622 and showing hexamer in assymmetric unit . in molecuar replacement with a single monomer when i m searching 6 copies lots of clashes are coming. with single copy serach i m getting fully fit template in density but unable to search density for others ensembles. how should i proceed for this
regards vandana kukshal
What about trying heavy atom phasing? Like introducing Se-Mets in your protein for MAD data collection. Sometimes you can waste plenty of time trying molecular replacement and the solution never comes out. particularly when you have no sequence homology... Fred. shuchi moni wrote:
i have one data of 3 A of a unknown protein don't have sequence homlogous pdb known . but showing highly coserved fold.
space group is p622 and showing hexamer in assymmetric unit . in molecuar replacement with a single monomer when i m searching 6 copies lots of clashes are coming. with single copy serach i m getting fully fit template in density but unable to search density for others ensembles. how should i proceed for this
regards vandana kukshal ------------------------------------------------------------------------
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participants (3)
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Leonid Flaks
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shuchi moni
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Vellieux Frederic