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

Jobichen Chacko jobichenc at gmail.com
Mon Oct 31 19:34:00 PDT 2011


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 <nechols at lbl.gov> wrote:
> On Fri, Oct 28, 2011 at 3:33 AM, Jobichen Chacko <jobichenc at gmail.com> 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-Linux-x86_64-ubuntu-10.04.2-python-gtk2.tar.gz
>
> 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
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>


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