[COOT] fink coot : unstable branch
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Coot_on_OS_X "Be sure to use the so-called "unstable" branch of fink to get the latest pre-releases of coot" do i read this correctly : it means ONLY pre-releases, right? and then : "`fink -y install coot` [...] whenever you require the latest version. " means precisely that - the latest version, NOT a pre-release, so that the unstable branch does not need activation. -bryan
[COOT] Coot crashes during DNA refinement
All, I am running coot-0.6-pre-1-revision-2481 on Mac OS 10.6.1. Whenever I try to regularize or refine more than 1 DNA base at a time, the program crashes. This does not happen at all with protein and does not happen with a single base, just when I try it with more than 1 base at a time. I've tested this with files from various refinement programs, and I know these files work just fine in coot on another older mac in the lab. It crashes with this message: click on 2 atoms (in the same molecule) (3) P /1/chainid="A"/-3/Gd, A occ: 1 with B-factor: 114.63 element: P at (- 1.43,17.115,42.479) : 0.125923 (3) P /1/chainid="A"/-2/Td, A occ: 1 with B-factor: 127.8 element: P at (- 1.164,11.699,46.9) : 0.112732 regularize: molecule 3 atom index 3012 to 3034 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 4 residues selected for refined and flanking residues created 45 bond restraints created 65 angle restraints created 2 plane restraints created 6 chiral vol restraints created 118 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues -3 and -2 of chain A /usr/local/xtal/coot/bin/coot: line 7: 74779 Bus error /usr/local/xtal/coot/bin/coot-real "$@" Any ideas? I suspect it is a problem with the OS but not sure how to fix it. Thanks, Jill
Re: [COOT] NCS ghosts leaking memory?
Johan Hattne wrote: Dear all; My coot, 0.6-pre-1-revision-2312 running on Gentoo, seems to be leaking memory when switching the NCS master. Anybody else notice leaks here or while doing superpositions (which I guess is the underlying cause)? OK, thanks for the info. Yes, there could well be leak there - NCS ghosts code is complex and has many pointers. I'll make a note to investigate (after 0.6 is released). Paul.
Re: [COOT] Disulfides across a crystallographic symmetry
Mark Nance wrote: Hi Cooters, I have a pair of disulfide bonds which link two monomers in separate asymmetric units. There is a single monomer in the asymmetric unit, and two monomers come together to form disulfides between Cys 26-Cys45, and Cys45-Cys26. For the record, you can't refine symmetry-related disulfides in Coot (yet). Paul.
[COOT] NCS ghosts leaking memory?
Dear all; My coot, 0.6-pre-1-revision-2312 running on Gentoo, seems to be leaking memory when switching the NCS master. Anybody else notice leaks here or while doing superpositions (which I guess is the underlying cause)? // Cheers; Johan
