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.
