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

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