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pemsley / coot

Software for macromolecular model-building
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
GNU General Public License v3.0
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infinite stream of "INFO:: found bad THR chiral atom" messages #14

Closed wojdyr closed 8 years ago

wojdyr commented 8 years ago

I downloaded 4q4w from pdb and expanded it using iotbx.pdb.expand_ncs.

$ coot 4q4w_ncs.pdb
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/lib/data/monomers/
INFO:: Reading coordinate file: /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/share/coot/standard-residues.pdb
 PDB file /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
initalize graphics molecules...done.
^[[1m(filter-fileselection-filenames-state)^[[0m
^[[1m(get-active-map-drag-flag)^[[0m
^[[1m(use-graphics-interface-state)^[[0m
INFO:: coot.py imported

** (coot-bin:20379): WARNING **: Trying to register gtype 'GMountMountFlags' as enum when in fact it is of type 'GFlags'

** (coot-bin:20379): WARNING **: Trying to register gtype 'GDriveStartFlags' as enum when in fact it is of type 'GFlags'

** (coot-bin:20379): WARNING **: Trying to register gtype 'GSocketMsgFlags' as enum when in fact it is of type 'GFlags'
INFO:: coot_python initialized
Running python script /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Evening Wojdyr, Welcome to Coot. 0.8.3
^[[1m(set-display-intro-string "Good Evening Wojdyr, Welcome to Coot. 0.8.3")^[[0m
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
^[[1m(use-graphics-interface-state)^[[0m
^[[1m(filter-fileselection-filenames-state)^[[0m
^[[1m(get-active-map-drag-flag)^[[0m
^[[1m(use-graphics-interface-state)^[[0m
Coot Scheme Scripting GUI code found and loaded.
^[[1m(set-display-intro-string "Good evening ,,,. Welcome to Coot")^[[0m
^[[1m(set-display-lists-for-maps 0)^[[0m
^[[1m(handle-read-draw-molecule-with-recentre "4q4w_ncs.pdb" 1)^[[0m
INFO:: Reading coordinate file: 4q4w_ncs.pdb
 PDB file 4q4w_ncs.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 14/582
INFO:: NCS chain comparison 6/582
INFO:: NCS chain comparison 3/582
INFO:: NCS chain comparison 156/507
INFO:: NCS chain comparison 3/507
INFO:: NCS chain comparison 2/453
Molecule 0 read successfully
DEBUG:: there were 3 types with no dictionary
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB

and so on. Coot window is not responding. The output is perhaps finite, I killed it after waiting a couple minutes.

bernhardcl commented 8 years ago

Can you send or post the pdb (I assume 4q4w was ok). That would help in finding the issue (unless Paul already knows). B

wojdyr commented 8 years ago

If you get 4Q4W and run

iotbx.pdb.expand_ncs 4q4w.pdb

or, if you don't have phenix installed, run this instead:

ccp4-python $CCP4/lib/py2/site-packages/cctbx_project/iotbx/command_line/pdb_expand_ncs.py 4q4w.pdb

This will output 4q4q_ncs.pdb - that's this file.

pemsley commented 8 years ago

Can't reproduce in 0.8.4-pre.