Dear Coot Community, I'm having a few issues installing/running Coot 0.5-pre osx ppc. I have a G4 Powerbook and G4 mac mini, both running 10.4. First the powerbook and mini were hanging with the start (coot) image and the startup log says: ...(looks normal)..... There are 2 data in /sw/share/coot/lib/data/monomers/u/UR.cif Reading coordinate file: /sw/share/coot/standard-residues.pdb PDB file /sw/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 ** (coot:439): WARNING **: Error loading pixmap file: /sw/share/coot/pixmaps/smiles.png art_render_invoke: no image source given Having read the earlier posts ABOUT "art_render_invoke" I decide to move my sw/ to sw.old/ and reinstall fink as well as coot and all its dependencies. It now launches but still gives errors in the startup log... see attached. I am able to load a model, but am unable to upload any CNS maps (I used model_map_twin.inp) an error to do with headers. I guess the format must be wrong? As for the mini, I did almost everything the same as the powerbook except, as an extra step prior to renaming and reinstalling everything, I downloaded and installed the stand-alone 0.4.2 (I think) pre-compiled binary from Bill Scott's site. But I still got the same hanging on the startup image with the same warning art_render_invoke. I then moved sw/ to sw.old and repeated as above. What is strange is that after reinstalling everything I still get the 0.4.2 startup image even though apt-get give me "Sorry, coot is already the newest version" when I try to install now (ie. 0.5-pre) I feel like this is all a bit confusing, if anything needs further clarification please ask. Thanks in advance, Mark Collins |
[gunks:~] mnc% coot If have found this software to be useful, you are requested to cite: Coot: model-building tools for molecular graphics Emsley P, Cowtan K ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2126-2132 Part 12 Sp. Iss. 1 DEC 2004
The reference for the REFMAC5 Dictionary is:
REFMAC5 dictionary: organization of prior chemical knowledge and
guidelines for its use
Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S,
Long F, Murshudov GN
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
60: 2184-2195 Part 12 Sp. Iss. 1 DEC 2004
If using "SSM Superposition", please cite:
Secondary-structure matching (SSM), a new tool for fast
protein structure alignment in three dimensions
Krissinel E, Henrick K
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
60: 2256-2268 Part 12 Sp. Iss. 1 DEC 2004
Acquiring application resources from /sw/share/coot/cootrc
INFO:: splash_screen_pixmap_dir /sw/share/coot/pixmaps
INFO:: Colours file: /sw/share/coot/colours.def loaded
WARNING:: Coot REFMAC dictionary override COOT_REFMAC_LIB_DIRfailed to find a di
ctionary /usr/local/coot/share/coot/lib
There are 117 data in /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /sw/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in /sw/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in /sw/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in /sw/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in /sw/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in /sw/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in /sw/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in /sw/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in /sw/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in /sw/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in /sw/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in /sw/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in /sw/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in /sw/share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in /sw/share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in /sw/share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in /sw/share/coot/lib/data/monomers/s/SER.cif
There are 2 data in /sw/share/coot/lib/data/monomers/t/THR.cif
There are 2 data in /sw/share/coot/lib/data/monomers/v/VAL.cif
There are 2 data in /sw/share/coot/lib/data/monomers/t/TRP.cif
There are 2 data in /sw/share/coot/lib/data/monomers/t/TYR.cif
There are 2 data in /sw/share/coot/lib/data/monomers/p/PO4.cif
There are 2 data in /sw/share/coot/lib/data/monomers/s/SO4.cif
There are 2 data in /sw/share/coot/lib/data/monomers/g/GOL.cif
There are 2 data in /sw/share/coot/lib/data/monomers/e/ETH.cif
There are 2 data in /sw/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in /sw/share/coot/lib/data/monomers/a/AR.cif
There are 2 data in /sw/share/coot/lib/data/monomers/a/AD.cif
There are 2 data in /sw/share/coot/lib/data/monomers/c/CR.cif
There are 2 data in /sw/share/coot/lib/data/monomers/c/CD.cif
There are 2 data in /sw/share/coot/lib/data/monomers/g/GR.cif
There are 2 data in /sw/share/coot/lib/data/monomers/g/GD.cif
There are 2 data in /sw/share/coot/lib/data/monomers/t/TD.cif
There are 2 data in /sw/share/coot/lib/data/monomers/u/UR.cif
Reading coordinate file: /sw/share/coot/standard-residues.pdb
PDB file /sw/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
Cell: 40.631 109.18 93.243 90 90 90
art_render_invoke: no image source given
art_render_invoke: no image source given
initalize graphics molecules...done.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
DEBUG:: stating pydirectory /sw/share/coot/python
INFO:: loading coot.py from /sw/share/coot/python/coot.py
Running python script /sw/share/coot/python/coot.py
INFO:: coot.py loaded
INFO loading coot python modules
Running python script /sw/share/coot/python/coot_load_modules.py
Loading: coot_utils.py
Loading: filter.py
Loading: coot_lsq.py
Loading: shelx.py
Loading: get_ebi.py
Loading: local_code.py
Loading: hello.py
Good Evening Mnc, Welcome to Coot.
(set-display-intro-string "Good Evening Mnc, Welcome to Coot.")
Loading: mutate.py
Loading: refmac.py
Loading: libcheck.py
Loading: gap.py
Loading: fitting.py
Loading: raster3d.py
Loading: povray.py
Loading: generic_objects.py
Loading: ncs.py
Loading: cns2coot.py
Loading: tips.py
Loading: americanisms.py
Loading: group_settings.py
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
Loading scheme files from /sw/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"
WARNING: (net http client): imported module (net http message) overrides core bi
nding `version'
load "local-code.scm"
load "hello.scm"
Good evening mcollins. Welcome to Coot.
(set-display-intro-string "Good evening mcollins. 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 "ncs.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 "extensions.scm"
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(filter-fileselection-filenames-state)
(handle-read-draw-molecule-with-recentre "/Users/mnc/Desktop/bindividual_twin4k.
pdb" 1)
Reading coordinate file: /Users/mnc/Desktop/bindividual_twin4k.pdb
PDB file /Users/mnc/Desktop/bindividual_twin4k.pdb has been read.
Spacegroup: P 43
Cell: 71.651 71.651 37.102 90 90 90
Symmetry available for this molecule
INFO:: NCS chain comparison 72/84
INFO:: fill_ghost_info Constructed 1 ghosts
Ghost 0 name: "NCS found from matching Chain B onto Chain A"
Molecule 0 read successfully
(filter-fileselection-filenames-state)
CCP4 map filename: /Users/mnc/Desktop/1FoFc-4k.map
INFO:: map file type was determined to be CNS type
allocating space in read_ccp4_map
attempting to read CNS map: /Users/mnc/Desktop/1FoFc-4k.map
CNSMAPfile: can't get number of header lines
WARNING:: failed to read /Users/mnc/Desktop/1FoFc-4k.map
DEBUG:: Erasing the back molecule 1 which says that it has molecule number 1
Read map /Users/mnc/Desktop/1FoFc-4k.map failed
