I upgraded to coot 0.6.2. But still the problem is not rectified. Any suggestions. Jobi On Tue, Oct 25, 2011 at 5:26 PM, Folmer Fredslund wrote:

Dear Jobi,

This version works perfectly 0.6.2 (revision 3562)  [with guile 1.8.7 embedded] [with python 2.6.0 embedded]

I think the 0.6.1 version is quite old.

I would recommend you to update coot.

Best regards, Folmer Fredslund, PhD DTU Systems Biology

2011/10/25 David Cobessi

...

Dear Jobichen, Are you using coot with python? You should use the version of COOT with python in the name (when you download coot). David

On 10/25/2011 10:46 AM, Jobichen Chacko wrote:

...

The same old problem, I tried to add the coot path using preferences. Coot version result:

COOT_PREFIX is /usr/local /usr/local/bin/coot-real --version 0.6.1 (revision 2740)  [with guile 1.8.7 embedded] [with python 2.6.0 embedded]

The coot opens just after phenix-refine job starts  and after the job finishes. But no maps and models are loaded.

Thanks. Jobi _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613    33(0)608164340 Fax:33(0)438785122

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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?? http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/ Jobi On Fri, Oct 28, 2011 at 1:37 AM, Nathaniel Echols wrote:

On Wed, Oct 26, 2011 at 9:47 PM, Jobichen Chacko wrote:

...

I upgraded to coot 0.6.2. But still the problem is not rectified. Any suggestions.

Okay, after seeing the console output, the problem is here:

'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

If you're seeing ImportError anywhere, this almost always means that the Python module paths are not set correctly.  Fixing this is beyond the scope of PHENIX, and I've never been able to figure out why some Coot builds have this problem; you probably need to try a different binary package.  (Where did you download it from?)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

See the output of two commands import stat # precompiled from /usr/lib/python2.7/stat.pyc # /usr/lib/python2.7/genericpath.pyc matches /usr/lib/python2.7/genericpath.py import genericpath # precompiled from /usr/lib/python2.7/genericpath.pyc # /usr/lib/python2.7/warnings.pyc matches /usr/lib/python2.7/warnings.py import warnings # precompiled from /usr/lib/python2.7/warnings.pyc # /usr/lib/python2.7/linecache.pyc matches /usr/lib/python2.7/linecache.py import linecache # precompiled from /usr/lib/python2.7/linecache.pyc # /usr/lib/python2.7/types.pyc matches /usr/lib/python2.7/types.py import types # precompiled from /usr/lib/python2.7/types.pyc # /usr/lib/python2.7/UserDict.pyc matches /usr/lib/python2.7/UserDict.py import UserDict # precompiled from /usr/lib/python2.7/UserDict.pyc # /usr/lib/python2.7/_abcoll.pyc matches /usr/lib/python2.7/_abcoll.py import _abcoll # precompiled from /usr/lib/python2.7/_abcoll.pyc # /usr/lib/python2.7/abc.pyc matches /usr/lib/python2.7/abc.py import abc # precompiled from /usr/lib/python2.7/abc.pyc # /usr/lib/python2.7/_weakrefset.pyc matches /usr/lib/python2.7/_weakrefset.py import _weakrefset # precompiled from /usr/lib/python2.7/_weakrefset.pyc import _weakref # builtin # /usr/lib/python2.7/copy_reg.pyc matches /usr/lib/python2.7/copy_reg.py import copy_reg # precompiled from /usr/lib/python2.7/copy_reg.pyc # /usr/lib/python2.7/traceback.pyc matches /usr/lib/python2.7/traceback.py import traceback # precompiled from /usr/lib/python2.7/traceback.pyc # /usr/lib/python2.7/sysconfig.pyc matches /usr/lib/python2.7/sysconfig.py import sysconfig # precompiled from /usr/lib/python2.7/sysconfig.pyc # /usr/lib/python2.7/re.pyc matches /usr/lib/python2.7/re.py import re # precompiled from /usr/lib/python2.7/re.pyc # /usr/lib/python2.7/sre_compile.pyc matches /usr/lib/python2.7/sre_compile.py import sre_compile # precompiled from /usr/lib/python2.7/sre_compile.pyc import _sre # builtin # /usr/lib/python2.7/sre_parse.pyc matches /usr/lib/python2.7/sre_parse.py import sre_parse # precompiled from /usr/lib/python2.7/sre_parse.pyc # /usr/lib/python2.7/sre_constants.pyc matches /usr/lib/python2.7/sre_constants.py import sre_constants # precompiled from /usr/lib/python2.7/sre_constants.pyc # /usr/lib/python2.7/sitecustomize.pyc matches /usr/lib/python2.7/sitecustomize.py import sitecustomize # precompiled from /usr/lib/python2.7/sitecustomize.pyc # /usr/lib/python2.7/dist-packages/apport_python_hook.pyc matches /usr/lib/python2.7/dist-packages/apport_python_hook.py import apport_python_hook # precompiled from /usr/lib/python2.7/dist-packages/apport_python_hook.pyc import encodings # directory /usr/lib/python2.7/encodings # /usr/lib/python2.7/encodings/__init__.pyc matches /usr/lib/python2.7/encodings/__init__.py import encodings # precompiled from /usr/lib/python2.7/encodings/__init__.pyc # /usr/lib/python2.7/codecs.pyc matches /usr/lib/python2.7/codecs.py import codecs # precompiled from /usr/lib/python2.7/codecs.pyc import _codecs # builtin # /usr/lib/python2.7/encodings/aliases.pyc matches /usr/lib/python2.7/encodings/aliases.py import encodings.aliases # precompiled from /usr/lib/python2.7/encodings/aliases.pyc # /usr/lib/python2.7/encodings/utf_8.pyc matches /usr/lib/python2.7/encodings/utf_8.py import encodings.utf_8 # precompiled from /usr/lib/python2.7/encodings/utf_8.pyc Python 2.7.1+ (r271:86832, Apr 11 2011, 18:13:53) [GCC 4.5.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. import CommandNotFound # directory /usr/lib/python2.7/dist-packages/CommandNotFound # /usr/lib/python2.7/dist-packages/CommandNotFound/__init__.pyc matches /usr/lib/python2.7/dist-packages/CommandNotFound/__init__.py import CommandNotFound # precompiled from /usr/lib/python2.7/dist-packages/CommandNotFound/__init__.pyc # /usr/lib/python2.7/dist-packages/CommandNotFound/CommandNotFound.pyc matches /usr/lib/python2.7/dist-packages/CommandNotFound/CommandNotFound.py import CommandNotFound.CommandNotFound # precompiled from /usr/lib/python2.7/dist-packages/CommandNotFound/CommandNotFound.pyc dlopen("/usr/lib/python2.7/lib-dynload/gdbm.so", 2); import gdbm # dynamically loaded from /usr/lib/python2.7/lib-dynload/gdbm.so import grp # builtin # /usr/lib/python2.7/string.pyc matches /usr/lib/python2.7/string.py import string # precompiled from /usr/lib/python2.7/string.pyc import strop # builtin # /usr/lib/python2.7/dist-packages/CommandNotFound/util.pyc matches /usr/lib/python2.7/dist-packages/CommandNotFound/util.py import CommandNotFound.util # precompiled from /usr/lib/python2.7/dist-packages/CommandNotFound/util.pyc # /usr/lib/python2.7/gettext.pyc matches /usr/lib/python2.7/gettext.py import gettext # precompiled from /usr/lib/python2.7/gettext.pyc # /usr/lib/python2.7/locale.pyc matches /usr/lib/python2.7/locale.py import locale # precompiled from /usr/lib/python2.7/locale.pyc import operator # builtin # /usr/lib/python2.7/functools.pyc matches /usr/lib/python2.7/functools.py import functools # precompiled from /usr/lib/python2.7/functools.pyc import _functools # builtin import _locale # builtin # /usr/lib/python2.7/copy.pyc matches /usr/lib/python2.7/copy.py import copy # precompiled from /usr/lib/python2.7/copy.pyc # /usr/lib/python2.7/weakref.pyc matches /usr/lib/python2.7/weakref.py import weakref # precompiled from /usr/lib/python2.7/weakref.pyc # /usr/lib/python2.7/struct.pyc matches /usr/lib/python2.7/struct.py import struct # precompiled from /usr/lib/python2.7/struct.pyc import _struct # builtin # /usr/lib/python2.7/optparse.pyc matches /usr/lib/python2.7/optparse.py import optparse # precompiled from /usr/lib/python2.7/optparse.pyc # /usr/lib/python2.7/textwrap.pyc matches /usr/lib/python2.7/textwrap.py import textwrap # precompiled from /usr/lib/python2.7/textwrap.pyc dlopen("/usr/lib/python2.7/dist-packages/apt_pkg.so", 2); import apt_pkg # dynamically loaded from /usr/lib/python2.7/dist-packages/apt_pkg.so import aptsources # directory /usr/lib/python2.7/dist-packages/aptsources # /usr/lib/python2.7/dist-packages/aptsources/__init__.pyc matches /usr/lib/python2.7/dist-packages/aptsources/__init__.py import aptsources # precompiled from /usr/lib/python2.7/dist-packages/aptsources/__init__.pyc # /usr/lib/python2.7/dist-packages/aptsources/sourceslist.pyc matches /usr/lib/python2.7/dist-packages/aptsources/sourceslist.py import aptsources.sourceslist # precompiled from /usr/lib/python2.7/dist-packages/aptsources/sourceslist.pyc # /usr/lib/python2.7/glob.pyc matches /usr/lib/python2.7/glob.py import glob # precompiled from /usr/lib/python2.7/glob.pyc # /usr/lib/python2.7/fnmatch.pyc matches /usr/lib/python2.7/fnmatch.py import fnmatch # precompiled from /usr/lib/python2.7/fnmatch.pyc import logging # directory /usr/lib/python2.7/logging # /usr/lib/python2.7/logging/__init__.pyc matches /usr/lib/python2.7/logging/__init__.py import logging # precompiled from /usr/lib/python2.7/logging/__init__.pyc import time # builtin import cStringIO # builtin import thread # builtin # /usr/lib/python2.7/threading.pyc matches /usr/lib/python2.7/threading.py import threading # precompiled from /usr/lib/python2.7/threading.pyc # /usr/lib/python2.7/collections.pyc matches /usr/lib/python2.7/collections.py import collections # precompiled from /usr/lib/python2.7/collections.pyc import _collections # builtin # /usr/lib/python2.7/keyword.pyc matches /usr/lib/python2.7/keyword.py import keyword # precompiled from /usr/lib/python2.7/keyword.pyc # /usr/lib/python2.7/heapq.pyc matches /usr/lib/python2.7/heapq.py import heapq # precompiled from /usr/lib/python2.7/heapq.pyc import itertools # builtin # /usr/lib/python2.7/bisect.pyc matches /usr/lib/python2.7/bisect.py import bisect # precompiled from /usr/lib/python2.7/bisect.pyc import _bisect # builtin dlopen("/usr/lib/python2.7/lib-dynload/_heapq.so", 2); import _heapq # dynamically loaded from /usr/lib/python2.7/lib-dynload/_heapq.so # /usr/lib/python2.7/atexit.pyc matches /usr/lib/python2.7/atexit.py import atexit # precompiled from /usr/lib/python2.7/atexit.pyc # /usr/lib/python2.7/shutil.pyc matches /usr/lib/python2.7/shutil.py import shutil # precompiled from /usr/lib/python2.7/shutil.pyc import pwd # builtin # /usr/lib/python2.7/dist-packages/aptsources/distinfo.pyc matches /usr/lib/python2.7/dist-packages/aptsources/distinfo.py import aptsources.distinfo # precompiled from /usr/lib/python2.7/dist-packages/aptsources/distinfo.pyc # /usr/lib/python2.7/subprocess.pyc matches /usr/lib/python2.7/subprocess.py import subprocess # precompiled from /usr/lib/python2.7/subprocess.pyc import gc # builtin import select # builtin import fcntl # builtin # /usr/lib/python2.7/pickle.pyc matches /usr/lib/python2.7/pickle.py import pickle # precompiled from /usr/lib/python2.7/pickle.pyc import marshal # builtin import binascii # builtin import apt # directory /usr/lib/python2.7/dist-packages/apt # /usr/lib/python2.7/dist-packages/apt/__init__.pyc matches /usr/lib/python2.7/dist-packages/apt/__init__.py import apt # precompiled from /usr/lib/python2.7/dist-packages/apt/__init__.pyc # /usr/lib/python2.7/dist-packages/apt/package.pyc matches /usr/lib/python2.7/dist-packages/apt/package.py import apt.package # precompiled from /usr/lib/python2.7/dist-packages/apt/package.pyc # /usr/lib/python2.7/httplib.pyc matches /usr/lib/python2.7/httplib.py import httplib # precompiled from /usr/lib/python2.7/httplib.pyc import array # builtin # /usr/lib/python2.7/socket.pyc matches /usr/lib/python2.7/socket.py import socket # precompiled from /usr/lib/python2.7/socket.pyc import _socket # builtin import _ssl # builtin # /usr/lib/python2.7/urlparse.pyc matches /usr/lib/python2.7/urlparse.py import urlparse # precompiled from /usr/lib/python2.7/urlparse.pyc # /usr/lib/python2.7/mimetools.pyc matches /usr/lib/python2.7/mimetools.py import mimetools # precompiled from /usr/lib/python2.7/mimetools.pyc # /usr/lib/python2.7/tempfile.pyc matches /usr/lib/python2.7/tempfile.py import tempfile # precompiled from /usr/lib/python2.7/tempfile.pyc # /usr/lib/python2.7/random.pyc matches /usr/lib/python2.7/random.py import random # precompiled from /usr/lib/python2.7/random.pyc # /usr/lib/python2.7/__future__.pyc matches /usr/lib/python2.7/__future__.py import __future__ # precompiled from /usr/lib/python2.7/__future__.pyc import math # builtin # /usr/lib/python2.7/hashlib.pyc matches /usr/lib/python2.7/hashlib.py import hashlib # precompiled from /usr/lib/python2.7/hashlib.pyc import _hashlib # builtin import _random # builtin # /usr/lib/python2.7/rfc822.pyc matches /usr/lib/python2.7/rfc822.py import rfc822 # precompiled from /usr/lib/python2.7/rfc822.pyc # /usr/lib/python2.7/ssl.pyc matches /usr/lib/python2.7/ssl.py import ssl # precompiled from /usr/lib/python2.7/ssl.pyc # /usr/lib/python2.7/base64.pyc matches /usr/lib/python2.7/base64.py import base64 # precompiled from /usr/lib/python2.7/base64.pyc # /usr/lib/python2.7/urllib2.pyc matches /usr/lib/python2.7/urllib2.py import urllib2 # precompiled from /usr/lib/python2.7/urllib2.pyc # /usr/lib/python2.7/urllib.pyc matches /usr/lib/python2.7/urllib.py import urllib # precompiled from /usr/lib/python2.7/urllib.pyc import apt.progress # directory /usr/lib/python2.7/dist-packages/apt/progress # /usr/lib/python2.7/dist-packages/apt/progress/__init__.pyc matches /usr/lib/python2.7/dist-packages/apt/progress/__init__.py import apt.progress # precompiled from /usr/lib/python2.7/dist-packages/apt/progress/__init__.pyc # /usr/lib/python2.7/dist-packages/apt/progress/old.pyc matches /usr/lib/python2.7/dist-packages/apt/progress/old.py import apt.progress.old # precompiled from /usr/lib/python2.7/dist-packages/apt/progress/old.pyc # /usr/lib/python2.7/dist-packages/apt/deprecation.pyc matches /usr/lib/python2.7/dist-packages/apt/deprecation.py import apt.deprecation # precompiled from /usr/lib/python2.7/dist-packages/apt/deprecation.pyc # /usr/lib/python2.7/dist-packages/apt/progress/base.pyc matches /usr/lib/python2.7/dist-packages/apt/progress/base.py import apt.progress.base # precompiled from /usr/lib/python2.7/dist-packages/apt/progress/base.pyc # /usr/lib/python2.7/dist-packages/apt/progress/text.pyc matches /usr/lib/python2.7/dist-packages/apt/progress/text.py import apt.progress.text # precompiled from /usr/lib/python2.7/dist-packages/apt/progress/text.pyc # /usr/lib/python2.7/dist-packages/apt/cache.pyc matches /usr/lib/python2.7/dist-packages/apt/cache.py import apt.cache # precompiled from /usr/lib/python2.7/dist-packages/apt/cache.pyc # /usr/lib/python2.7/dist-packages/apt/cdrom.pyc matches /usr/lib/python2.7/dist-packages/apt/cdrom.py import apt.cdrom # precompiled from /usr/lib/python2.7/dist-packages/apt/cdrom.pyc No command 'setenv' found, did you mean: Command 'netenv' from package 'netenv' (universe) setenv: command not found # clear __builtin__._ # clear sys.path # clear sys.argv # clear sys.ps1 # clear sys.ps2 # clear sys.exitfunc # clear sys.exc_type # clear sys.exc_value # clear sys.exc_traceback # clear sys.last_type # clear sys.last_value # clear sys.last_traceback # clear sys.path_hooks # clear sys.path_importer_cache # clear sys.meta_path # clear sys.flags # clear sys.float_info # restore sys.stdin # restore sys.stdout # restore sys.stderr # cleanup __main__ # cleanup[1] _bisect # cleanup[1] sysconfig # cleanup[1] aptsources # cleanup[1] zipimport # cleanup[1] math # cleanup[1] CommandNotFound # cleanup[1] aptsources.distinfo # cleanup[1] abc # cleanup[1] urllib # cleanup[1] optparse # cleanup[1] lazr # cleanup[1] CommandNotFound.CommandNotFound # cleanup[1] exceptions # cleanup[1] _functools # cleanup[1] _locale # cleanup[1] itertools # cleanup[1] __future__ # cleanup[1] _collections # cleanup[1] array # cleanup[1] aptsources.sourceslist # cleanup[1] _heapq # cleanup[1] sre_constants # cleanup[1] _warnings # cleanup[1] _codecs # cleanup[1] pwd # cleanup[1] CommandNotFound.util # cleanup[1] _struct # cleanup[1] keyword # cleanup[1] posix # cleanup[1] site # cleanup[1] shutil # cleanup[1] strop # cleanup[1] grp # cleanup[1] gettext # cleanup[1] sitecustomize # cleanup[1] _weakref # cleanup[1] _weakrefset # cleanup[1] gdbm # cleanup[1] collections # cleanup[1] locale # cleanup[1] encodings # cleanup[1] logging # cleanup[1] cStringIO # cleanup[1] copy # cleanup[1] apport_python_hook # cleanup[1] encodings.aliases # cleanup[1] encodings.utf_8 # cleanup[1] heapq # cleanup[1] functools # cleanup[1] threading # cleanup[1] atexit # cleanup[1] codecs # cleanup[2] random # cleanup[2] subprocess # cleanup[2] gc # cleanup[2] struct # cleanup[2] tempfile # cleanup[2] apt.cache # cleanup[2] apt_pkg # cleanup[2] string # cleanup[2] textwrap # cleanup[2] ssl # cleanup[2] httplib # cleanup[2] bisect # cleanup[2] signal # cleanup[2] base64 # cleanup[2] rfc822 # cleanup[2] re # cleanup[2] apt.deprecation # cleanup[2] select # cleanup[2] UserDict # cleanup[2] fcntl # cleanup[2] _hashlib # cleanup[2] socket # cleanup[2] thread # cleanup[2] pickle # cleanup[2] traceback # cleanup[2] apt.progress.text # cleanup[2] weakref # cleanup[2] os # cleanup[2] marshal # cleanup[2] _sre # cleanup[2] operator # cleanup[2] posixpath # cleanup[2] errno # cleanup[2] _socket # cleanup[2] binascii # cleanup[2] os.path # cleanup[2] apt.package # cleanup[2] hashlib # cleanup[2] apt.cdrom # cleanup[2] apt # cleanup[2] fnmatch # cleanup[2] sre_parse # cleanup[2] mimetools # cleanup[2] copy_reg # cleanup[2] sre_compile # cleanup[2] _random # cleanup[2] apt.progress.old # cleanup[2] apt.progress # cleanup[2] linecache # cleanup[2] _abcoll # cleanup[2] genericpath # cleanup[2] stat # cleanup[2] _ssl # cleanup[2] warnings # cleanup[2] glob # cleanup[2] urllib2 # cleanup[2] types # cleanup[2] apt.progress.base # cleanup[2] urlparse # cleanup[2] time # cleanup sys # cleanup __builtin__ # cleanup ints: 52 unfreed ints # cleanup floats: 42 unfreed floats jobi@sbl5ser1-Precision-WorkStation-T3500:~$ coot --script coot_test.py 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:16104): 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) # installing zipimport hook import zipimport # builtin # installed zipimport hook 'import site' failed; traceback: ImportError: No module named site (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 * # /usr/local/share/coot/python/coot.pyc has bad mtime import coot # from /usr/local/share/coot/python/coot.py # can't create /usr/local/share/coot/python/coot.pyc 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*) (coot-checked-exit 0) (clear-backups-maybe) INFO:: backup clearout done 917/86400 days ago (stereo-mode-state) (stereo-mode-state) (save-state) On Tue, Nov 1, 2011 at 10:43 AM, Nathaniel Echols wrote:

On Mon, Oct 31, 2011 at 7:34 PM, Jobichen Chacko wrote:

...

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 ... 'import site' failed; use -v for traceback

Wow, that's way more broken than I was expecting.  I think this means a library conflict, but I've only come across this error on Mac.  Can you try one more thing?

export PYTHONVERBOSE=1 coot --script coot_test.py

(If you're using csh or tcsh as your shell, the first line should be "setenv PYTHONVERBOSE 1" instead.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb