Hi Stefano,
Sorry for the delay, I was coming back from the ACA.
On 02/08/12 16:13, Pernigo, Stefano wrote:
I've tried to auto-open several MTZ files without success.
The MTZ files were produced using REFMAC5 (restrain refinement). After
loading the PDB file in coot (successfully) I tried to auto-open the
related MTZ file but coot crushed giving the following message:
coot crashes, I am crushed...
Number of OBSERVED reflections: 8194
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 120, 120, 56)
INFO:: 0.047 seconds to read MTZ file
INFO:: 0.033 seconds to initialize map
INFO:: 0.069 seconds for FFT
INFO:: 0.005 seconds for statistics
Map mean: ........ -1.00728e-05
Map sigma: ....... 0.41828
Map maximum: ..... 3.22839
Map minimum: ..... -1.11302
It seems that the map generation and calculation has gone OK...
What happens if you use CCP4's FFT to make the map, and read it in to Coot?
coot-real(1234,0xa0b1c540) malloc: *** mmap(size=1140850688) failed
(error code=12)
*** error: can't allocate region
I wonder what is going on here...
*** set a breakpoint in malloc_error_break to debug
that would indeed be a useful thing.
core: #f
No core file found. No debugging
This is not helpful.
Please turn on core dumps before sending a crash report.
This is a message to you, not to me.
This should not be a problem related to the coot version. I had the
same error message from coot using both the 0.7-pre version (installed
using fink) and the latest stable release (0.6.2 version, installed
using the pkg-coot installer, the dmg was downloaded from the ccp4 web
site). Moreover this is not a problem related to a particular MTZ
file: I had the same error message testing 3 different MTZ files from
3 independent projects.
OK, so my first guess was that you have a huge high resolution map and
that you were exceeding the indexing limits. That seems not to be the
case, give that it fails similarly for multiple MTZ files.
I'm using as operative system a Mac OS X 10.6.8 on a MacBook Pro.
My bet is that if you used WinCoot (0.6.2 or 0.7-pre) you would not get
the same crash. So my second guess is that you have an unpleasant tangle
of libraries - that is to say th e run-time linking is pulling in
non-approved shared libs. I don't know why that should be, I try to
guard against it - the devil's in the details and macintosh binaries are
somewhat out of my hands.
But as I say, I am simply trying psychic debugging without a core dump.
Regards,
Paul.
