Re: [phenixbb] Molecule and maps will not load into coot from Phenix 1.7.1-743

Dear Nat, Thank you for your help. Please see the attached output after running coot_test.py I will also try to install the coot version you send to me. Jobi COOT_PREFIX is /usr/local /usr/local/bin/coot-real --script coot_test.py Acquiring application resources from /usr/local/share/coot/cootrc INFO:: splash_screen_pixmap_dir /usr/local/share/coot/pixmaps ** (coot-real:15619): WARNING **: Couldn't find pixmap file: coot-0.6.2.png INFO:: Colours file: /usr/local/share/coot/colours.def loaded INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers/ There are 125 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//list/mon_lib_list.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//a/ALA.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//a/ASP.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//a/ASN.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//c/CYS.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//g/GLN.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//g/GLY.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//g/GLU.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//p/PHE.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//h/HIS.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//i/ILE.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//l/LYS.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//l/LEU.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//m/MET.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//m/MSE.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//p/PRO.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//a/ARG.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//s/SER.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//t/THR.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//v/VAL.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//t/TRP.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//t/TYR.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//p/PO4.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//s/SO4.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//g/GOL.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//e/ETH.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//c/CIT.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//a/AR.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//c/CR.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//c/CD.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//g/GD.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//t/TD.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//a/A.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//c/C.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//g/G.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//u/U.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//d/DA.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//d/DC.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//d/DG.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//d/DT.cif There are 2 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//h/HOH.cif There are 1 data in /usr/local/ccp4inew/ccp4-6.2.0/lib/data/monomers//ener_lib.cif sbase monomer dir: . sbase files not found in . Reading coordinate file: /usr/local/share/coot/standard-residues.pdb PDB file /usr/local/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) 'import site' failed; use -v for traceback (use-graphics-interface-state) DEBUG:: stating pydirectory /usr/local/share/coot/python INFO:: importing coot.py from /usr/local/share/coot/python/coot.py Importing python module coot using command from coot import * Traceback (most recent call last): File "<string>", line 1, in <module> File "/usr/local/share/coot/python/coot.py", line 8, in <module> import new ImportError: No module named new ERROR:: could not import coot.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /usr/local/share/coot/scheme load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "coot-gui.scm" Coot Scheme Scripting GUI code found and loaded. load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" load "local-code.scm" load "hello.scm" Good morning Jobi,,,,. Welcome to Coot 0.6.2 (revision 3562) [with guile 1.8.7 embedded] [with python 2.6.0 embedded]. (set-display-intro-string "Good morning Jobi,,,,. Welcome to Coot") load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "parse-pisa-xml.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "americanisms.scm" load "group-settings.scm" (set-display-lists-for-maps 0) load "tips-gui.scm" load "check-for-updates.scm" load "extensions.scm" error (not syntax error) Traceback (most recent call last): File "<string>", line 1, in <module> NameError: name 'coot_has_pygtk' is not defined error (not syntax error) Traceback (most recent call last): File "<string>", line 1, in <module> NameError: name 'coot_has_pygtk' is not defined error (not syntax error) Traceback (most recent call last): File "<string>", line 1, in <module> NameError: name 'coot_has_pygtk' is not defined error (not syntax error) Traceback (most recent call last): File "<string>", line 1, in <module> NameError: name 'coot_has_pygtk' is not defined load "shelx-extensions.scm" (filter-fileselection-filenames-state) (get-active-map-drag-flag) WARNING:: Can't run script: coot_test.py no such file. (use-graphics-interface-state) (command-in-path? *probe-command*) On Tue, Nov 1, 2011 at 5:21 AM, Nathaniel Echols wrote:

On Fri, Oct 28, 2011 at 3:33 AM, Jobichen Chacko wrote:

...

Dear Nat, I already tried two versions, both downloaded from the following site. I suspect this problem is because of ubuntu. Can you recommend any specific build of coot for ubuntu. I have no problem in opening the maps and models from Refmac, it opens nicely. Do you think is it a dependency issue??

Sorry for the slow response - I started downloading it and quickly forgot.  This build worked for me:

http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/coot-0.6.2-binary-...

The only Ubuntu system we have is 64-bit, so I didn't try any of the 32-bit (aka "i686") builds.

I also forgot to send the standard script I use for debugging this problem, which I've attached to this message.  All it does is print some additional debugging information about the Python interpreter to the console.  It is run like this:

coot --script coot_test.py

-Nat

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