Re: [phenixbb] Problem with version 1.7.1-743 on OSX

Hi Nat, I'm using the command-line installer for Mac, as I have always done. I typically run it with: sudo ./install.sh --no-apps --prefix=/some/where It is not a problem with the pdb file or with the mtz: 1/ the same pdb and mtz files work perfectly in the same Mac computer providede I run phenix.refine from the command line 2/ they also work fine if I run phenix.refine in a linux computer (in this case they work from both GUI and command line) 3/ Any file downloaded from the PDB gives the same negative result So, it is clearly a GUI problem on the Macs, which is not the same than saying that the problem is *in* the Phenix GUI: it could be yet another side-effect of an Apple software update... To be complete, for a typical Mac here:

uname -a Darwin think.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:16:10 PST 2011; root:xnu-1504.9.37~1/RELEASE_X86_64 x86_64

xcodebuild -version Xcode 3.2.6 Component versions: DevToolsCore-1809.0; DevToolsSupport-1806.0 BuildVersion: 10M2518

Best, Miguel Le 02/05/11 16:45, Nathaniel Echols a écrit :

By the way, are you using the graphical or command-line installer for Mac?

thanks, Nat

On Mon, May 2, 2011 at 7:41 AM, Nathaniel Echols wrote:

...

2011/5/2 Miguel Ortiz Lombardía :

...

Last Friday (April 29) we upgraded phenix to its most recent version (1.7.1-743). Installation went smoothly on both Mac (10.6.7 64-bit) and Linux (Ubuntu 10.10 64-bit) machines. However, we observe that we cannot use phenix.refine (I don't know for the rest of the applications) from the GUI on the Macs. phenix.refine does work from the command line, though.

So, whenever we try to add a pdb in the GUI, we get this error message:

This application does not support the file type for /path/to/the/file.pdb (format: txt)

I just tried about a dozen different PDB files and a few MTZs and I couldn't reproduce this. However, I only have the 32-bit version installed on this computer; I will try the 64-bit version when I arrive at the lab (although I'm pretty certain I tried loading PDB files in the installed version sometime last week without issues). The error you're seeing usually indicates some kind of formatting problem with the PDB file that caused the PDB parser to fail (it will default to reading it as a text file instead - not very helpful, I know). Could you please send me the file that is having this problem?

I'm not sure what the MTZ-related error means - it looks like the CCP4 library is choking on the CCP4 symop.lib, which is bizarre. Those extra spaces certainly shouldn't be there in the original file. Could you please also send me the file $PHENIX/ccp4io/lib/data/symop.lib?

thanks, Nat

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-- 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:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.