Hi Bernard, 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 >
