Just to make sure: was your initial attempt File->Get Monomer entered GOL and got an error message?
Tim On Tue, Sep 28, 2010 at 12:30:43PM +0100, David Briggs wrote: > Bernard, > > Libcheck seems to run fine from command line, and when called from the > ccp4i gui. > > Curious. > > Dave > ============================ > David C. Briggs PhD > Father, Structural Biologist and Sceptic > ============================ > University of Manchester E-mail: > david.c.bri...@manchester.ac.uk > ============================ > http://manchester.academia.edu/DavidBriggs (v.sensible) > http://xtaldave.wordpress.com/ (sensible) > http://xtaldave.posterous.com/ (less sensible) > Twitter: @xtaldave > Skype: DocDCB > ============================ > > > > On 28 September 2010 12:20, Bernhard Lohkamp <bernhard.lohk...@ki.se> wrote: > > > > Dave, > > > > you certainly got the right end of the stick. > > > > With respect to the error messages, I am not an expert on OSX, but it looks > > to me that libcheck is not running properly (nothing to do with Coot ;-) ) > > possibly because library paths (e.g. DYLD_LIBRARY_PATH) are not set > > properly. Does libcheck outside of Coot run as expected? > > > > B > > > >> Thanks - "Extension->Modelling->Add Other Solvent Molecule" looks to > >> be *exactly* what I am looking for - apart from the fact that I still > >> cannot get it to generate the co-ordinates for GOL - which is what I > >> assumed it would do. > >> > >> If I centre the crosshairs on a GOL shaped blob, and do > >> "Extension->Modelling->Add Other Solvent Molecule... [GOL]" I was > >> expecting a GOL to appear at the crosshairs, like when I add a water, > >> etc.? Have I got the wrong end of the stick? > >> > >> This is what the console says: > >> > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] > >> [1m(monomer-molecule-from-3-let-code "GOL" "") [0m > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] > >> /Applications/ccp4-6.1.13/bin/libcheck > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] > >> /Applications/ccp4-6.1.13/bin/libcheck > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] dyld: Symbol > >> not found: ___intel_cpu_indicator > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] Referenced > >> from: /Applications/ccp4-6.1.13/bin/libcheck > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] Expected in: > >> /Applications/coot.app/Contents/Resources/../coot/lib/libmmdb.dylib > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] > >> [1m(get-monomer "GOL") [0m > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] > >> [1m(get-monomer "GOL") [0m > >> 28/09/2010 11:26:10 [0x0-0x44a44a].com.ccp4.coot[36589] > >> [1m(get-monomer "GOL") [0m > >> > >> Cheers, > >> > >> Dave > >> > >> ============================ > >> David C. Briggs PhD > >> Father, Structural Biologist and Sceptic > >> ============================ > >> University of Manchester E-mail: > >> david.c.bri...@manchester.ac.uk > >> ============================ > >> http://manchester.academia.edu/DavidBriggs (v.sensible) > >> http://xtaldave.wordpress.com/ (sensible) > >> http://xtaldave.posterous.com/ (less sensible) > >> Twitter: @xtaldave > >> Skype: DocDCB > >> ============================ > >> > >> > >> > >> On 28 September 2010 09:50, Bernhard Lohkamp<bernhard.lohk...@ki.se> > >> wrote: > >>> > >>> Hi Dave, > >>> > >>> I am slightly confused what you are actually doing. What do you mean by > >>> 'go > >>> to Libcheck to import a GOL'? The error message you get comes when you > >>> open > >>> the 'Find Ligand' dialog and a map, protein, and/or ligand is missing. > >>> There > >>> should be a more detailed message in the console output (not just the > >>> statusbar) and actually a warning dialog if the ligand is missing (maybe > >>> hidden somewhere). Anyway before you can let Coot find a ligand you need > >>> to > >>> import it (use e.g. 'Get Monomer' or for solvent molecules > >>> Extension->Modelling->Add Other Solvent Molecule). > >>> > >>> Hope this helps you a bit further, > >>> > >>> B > >>> > >>>> I'm running the version of coot as obtained from the ccp4.ac.uk > >>>> website last week, using OSX 10.5.8 > >>>> > >>>> My problem is this - I have what appear to be bound, ordered glycerols > >>>> in my maps - I want to import "GOL" and use the Ligand fitting > >>>> routines to help with this. I know I could do this "by hand" - but > >>>> COOT looks like it has some rather nice features to do what I want > >>>> with minimal fuss. > >>>> > >>>> I have added the fix to the COOT script in the launcher (getting it to > >>>> source the ccp4.setup file) and COOT reports it can now find libcheck > >>>> in the "get monomer" window. > >>>> > >>>> However, when I go to Libcheck to import a GOL, I get "problem finding > >>>> maps, coords or ligands" reported in the message bar, and nothing > >>>> happens. > >>>> > >>>> Help! > >>>> > >>>> Dave > >>>> > >>>> ============================ > >>>> David C. Briggs PhD > >>>> Father, Structural Biologist and Sceptic > >>>> ============================ > >>>> University of Manchester E-mail: > >>>> david.c.bri...@manchester.ac.uk > >>>> ============================ > >>>> http://manchester.academia.edu/DavidBriggs (v.sensible) > >>>> http://xtaldave.wordpress.com/ (sensible) > >>>> http://xtaldave.posterous.com/ (less sensible) > >>>> Twitter: @xtaldave > >>>> Skype: DocDCB > >>>> ============================ > >>> > >>> > >>> -- > >>> *************************************************** > >>> > >>> Dr. Bernhard Lohkamp > >>> Assistant Professor > >>> Div. Molecular Structural Biology > >>> Dept. of Medical Biochemistry and Biophysics (MBB) > >>> Karolinska Institutet > >>> S-17177 Stockholm > >>> Sweden > >>> > >>> phone: (+46) 08-52487651 > >>> fax: (+46) 08-327626 > >>> email: bernhard.lohk...@ki.se > >>> > > > > > > -- > > *************************************************** > > > > Dr. Bernhard Lohkamp > > Assistant Professor > > Div. Molecular Structural Biology > > Dept. of Medical Biochemistry and Biophysics (MBB) > > Karolinska Institutet > > S-17177 Stockholm > > Sweden > > > > phone: (+46) 08-52487651 > > fax: (+46) 08-327626 > > email: bernhard.lohk...@ki.se > > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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