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 >
