Thanks for everyone's help! I got the refinement working in version 1.4-125 and am all set. -Sam On Tue, Aug 25, 2009 at 4:19 PM, Ben Eisenbraun wrote:

There's version 1.4-125 in the SBGrid software tree. Did you try it? Is that version too old?

You should ask Katya to update her user list. You're not in our database.

-ben

On Tue, Aug 25, 2009 at 04:13:44PM -0400, Sam Stampfer wrote:

...

I couldn't get the source code to compile- the final message was: "error: configuration step incomplete, exiting". Any ideas? Thanks, -Sam

[A copy of my problem is pasted here]:

I'm running the latest complete version of phenix (version 1.4-147, on Linux 2.6-x86 64). When I run my .csh file I get the following error (with the 4 previous lines included):

/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd)

...

[0x446bdd]

/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python

...

[0x4396e4]

/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python

...

[0x4470a9] /lib64/libc.so.6 [0x30fca322a0] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical.

When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my .csh file, it runs for a slightly longer period of time before ending with a different error:

311240e000-3112410000 rw-p 0000e000 fd:00 14237822 /lib64/libbz2.so.1.0.4 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920

/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so

...

2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920

/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so

...

2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920

/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so

...

2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941

/usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so

...

2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort

However, the file ran fine and successfully output an improved .pdb file without any BOOST-related problems on my PI's Mac- she is running version 95 of Phenix (which I was unable to obtain for linux- is it available somewhere?)

Can you help me with this?

Thanks!

-Sam

On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve wrote:

...

Could you try with a source installation?

https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show_source=1

...

I recommend you rm -rf the binary installation before ./install from sources. Add --nproc=N to the ./install command to use all N cpus in your machine for the installation.

Let me know if the problem persists.

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

...

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-- | Ben Eisenbraun | Tools Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |