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

[Jobichen Chacko]

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 at 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 <nechols at lbl.gov> wrote:
> On Mon, Oct 31, 2011 at 7:34 PM, Jobichen Chacko <jobichenc at gmail.com> 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
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>