phenix-installer-1.4-55-intel-linux-2.6-x86_64.tar I downloaded the newest nightly build per Nathaniel Echols' instructions. I was trying to fix the following error: A Python error was detected. This is almost certainly a bug; please send an email containing this message to [email protected] so we can fix it. Thanks! IndexError : string index out of range Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/ phenix/wxGUI2/Refine.py", line 259, in OnExcept raise event.data IndexError: string index out of range phenix.refine_gui and phenix.refine were working perfectly well and then all of the sudden between 2 saves, something went wrong. My first PDB (refine_001-coot-2.pdb) is normal, but then refine_001-coot-3.pdb and onward are missing ALL of the REMARK cards. It starts with the CRYST card followed by the coordinates. Could this be a coot problem? Can I cut and paste the REMARKs from refine_001-coot-2.pdb into the top of refine_001-coot-5.pdb? Thanks! On Mon, May 4, 2009 at 12:06 PM, Ralf W. Grosse-Kunstleve wrote:

Possible quick fix: yum install lapack

However, we don't really want to depend on a system lapack. I'd like to track down why we have that dependency. Could you send me the file name of the tar file you downloaded?

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

ERROR: Reading package lists... Done Building dependency tree Reading state information... Done E: Couldn't find package lapack3 Thanks for your help. I've tried installing lapack and/or lapack3 through apt-get and synaptic... and I can't find it. I'll continue looking and potentially ask the Ubuntu people since this is not a Phenix problem. Thanks again, Leigh On Mon, May 4, 2009 at 1:00 PM, Nathaniel Echols wrote:

On May 4, 2009, at 8:56 AM, Leigh Allen wrote:

...

How do I fix this? You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below.

As Ralf said, the quick solution is to install lapack - it's usually there already, but some systems don't include it by default. On Ubuntu, "apt-get install lapack3" will take care of it. I will see if I can add it to the installer - this will probably not happen until next week, though. For now, I've fixed the code so it will fail more gracefully if plotting is disabled - that will be in 1.4-56 (tomorrow morning).

thanks, Nat

------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]

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On May 4, 2009, at 10:14 AM, Leigh Allen wrote:

ERROR:

Reading package lists... Done Building dependency tree Reading state information... Done E: Couldn't find package lapack3

Thanks for your help. I've tried installing lapack and/or lapack3 through apt-get and synaptic... and I can't find it. I'll continue looking and potentially ask the Ubuntu people since this is not a Phenix problem.

Well, we try to distribute packages that will work without any extra tinkering or compilation. . . which is sometimes difficult on Linux, but the lapack3 error should be avoidable (we don't actually need to link to it, it's just difficult to disable this behavior if it's present on the build system). To access lapack3 in Ubuntu, you need to have enabled the "universe" repositories. I think I did this manually by editing /etc/apt/ sources.list, but in Synaptic, you can do it via the menu item Settings-->Repositories. Searching for "lapack" then finds it - it will probably also come up with the BLAS libraries, which I recommend installing just to be safe. -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]