Thanks for the suggestion Paul - apols for my less than clear top post. I am at home now and have tried to reproduce the error on my laptop - but everything seems to work fine - I.e Get monomer > [GOL] produces co-ordinates for GOL at the pointer.
The only obvious difference is that I am running OSX 10.6 on my laptop, and 10.5.8 on my work machine. I will try adding your fix tomorrow. 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 21:18, Paul Emsley <paul.ems...@bioch.ox.ac.uk> wrote: > That (Tim's suggestion (wretched top posting)) will fail too I believe. > > I also believe that Bernhard is right and the fix is to set > DYLD_LIBRARY_PATH to include (at a guess) /Applications/ccp4-6.1.13/lib in > the environment that invokes coot. > > Alternatively, you could try > > (let ((e "DYLD_LIBRARY_PATH")) (putenv (string-append e "=" (getenv e) ":" > "/Applications/ccp4-6.1.13/lib"))) > > (Do that before starting libcheck). > > Paul. > > On 28/09/10 12:49, Tim Gruene wrote: >> >> 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. >>>>>>> >>>>>>> >
