Dear William, Problem solved!! After installing the coot you suggested me I've tried to auto open the MTZ file both in a new account and in the mine old one. I've noticed that in the new one coot was running without problem while in mine was stuck after opening the MTZ files (but it was no longer giving the following error: coot-real(244,0xa0b1c540) malloc: *** mmap(size=1140850688) failed (error code=12)). Looking in Edit->Map parameter->Map radius I've noticed that in the new account the default parameter was 10 Å while in the old one was 100 Å. The huge map dimension was the reason why coot was stuck. Changing this parameter back to 10 Å coot allowed coot to work smoothy. I cannot understand though why coot has such a different default parameter in the two accounts. Thank you very much for your help, I really appreciate. Best regards.
Stefano On 5 Aug 2012, at 13:07, William G. Scott wrote: > Dear Stefano: > > I just tried this: > > http://scottlab.ucsc.edu/~wgscott/coot/Coot-0.7-pre-1-4307_64bit_10.6.8.pkg.zip > > It works on my wife's 10.8 computer. > > Install it, and invoke it with > > /Library/Coot/bin/coot > > and then perform the same test. > > If that doesn't work, try creating a new account. If coot now works, that > tells us that it is something in your own directory. Otherwise it must be a > system problem. > > I don't have any experience with the ccp4 version that installs in > /Applications, so I can't help with that one. I can at least try with this > one. > > Bill > > > > > On Aug 5, 2012, at 12:48 AM, "Pernigo, Stefano" <stefano.1.pern...@kcl.ac.uk> > wrote: > >> Dear William, >> >> I have the same problem earlier reported. Coot unfortunately crashed again >> giving the following error message: >> >> Map mean: ........ -0.00510334 >> Map sigma: ....... 0.331845 >> Map maximum: ..... 4.98866 >> Map minimum: ..... -1.43613 >> coot-real(244,0xa0b1c540) malloc: *** mmap(size=1140850688) failed (error >> code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> terminate called after throwing an instance of 'std::bad_alloc' >> what(): std::bad_alloc >> /Applications/coot.app/Contents/coot/bin/coot: line 251: 244 Abort trap >> $coot_real $@ >> coot-exe: "/Applications/coot.app/Contents/coot/bin/coot-real" >> coot-version: >> /Applications/coot.app/Contents/coot/bin/coot-real >> platform: >> /usr/bin/uname >> core: #f >> >> Best regards >> >> Stefano >> ________________________________________ >> From: William G. Scott [wgsc...@ucsc.edu] >> Sent: Friday, August 03, 2012 9:59 PM >> To: Pernigo, Stefano >> Cc: COOT@JISCMAIL.AC.UK >> Subject: Re: [COOT] problem with "Auto open MTZ" in coot >> >> What happens if you try to display a pdb and map downloaded from the EDS? I >> believe that uses the same auto-open sequence, and it would help in figuring >> out whether the problem is with a refmac incompatibility or something else… >> >> On Aug 2, 2012, at 8:13 AM, "Pernigo, Stefano" <stefano.1.pern...@kcl.ac.uk> >> wrote: >> >>> Dear coot users, >>> >>> I've tried to auto-open several MTZ files without success. >> >> >> > >
