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997 bytes added ,  06:49, 19 June 2020
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==Installing Coot on Windows==
 
==Installing Coot on Windows==
Please refer to the [http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-download.html WinCoot install and download] page.
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Please refer to [https://github.com/bernhardcl/coot/releases Bernhard Lohkamp's WinCoot download] page.
    
==Installing Coot on Linux==
 
==Installing Coot on Linux==
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[[Image:a_zalman_zm_m220w__2d_35_pic.jpg|150px|thumb|right|3d lcd]]
 
[[Image:a_zalman_zm_m220w__2d_35_pic.jpg|150px|thumb|right|3d lcd]]
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Control stereo separation / depth in coot 0.9: the transformation between the eyes is no longer a rotation and is now a shear. Which means that now we don't get part of the map showing up in the left eye but not the right (or vice versa).
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This is documented in Section 3.4.1, e.g.
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set_hardware_stereo_angle_factor(0.5) # for the Python fans
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Hardware stereo failure: try the line
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(set-display-lists-for-maps 0)
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in ~/.coot for coot 0.9 - see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind2002&L=COOT&P=R312 and https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;49fa8d15.2006
    
==== Zalman Stereo ====
 
==== Zalman Stereo ====
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===External Links===
 
===External Links===
====[http://www.ysbl.york.ac.uk/~emsley/coot/doc/user-manual.html On-line User Manual]====
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====[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html On-line User Manual]====
====[http://www.ysbl.york.ac.uk/~emsley/coot/ Coot's home page]====
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====[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Coot's home page]====
 
====[http://www.mail-archive.com/coot@jiscmail.ac.uk/ Current mailing list archives]====
 
====[http://www.mail-archive.com/coot@jiscmail.ac.uk/ Current mailing list archives]====
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====[http://www.ysbl.york.ac.uk/~emsley/coot/mbox/ Mailing list archives: (no longer) current]====
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====[http://www.ysbl.york.ac.uk/~emsley/coot/mbox-2004-2005/ Mailing list archives: 2004-05]====
      
==Scheme Scripts==
 
==Scheme Scripts==
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Q: Is it possible to deactivate the nomenclature errors check? Sometimes this check is not very useful and it becomes rather annoying when one has several molecules loaded only wants to look at the structures...
 
Q: Is it possible to deactivate the nomenclature errors check? Sometimes this check is not very useful and it becomes rather annoying when one has several molecules loaded only wants to look at the structures...
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A: Add to your ~/.coot or whatever:
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A: The [https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#set_002dnomenclature_002derrors_002don_002dread Coot manual] should help: Add to your ~/.coot or whatever:
 
  (set-nomenclature-errors-on-read "ignore")
 
  (set-nomenclature-errors-on-read "ignore")
 
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In case you are using the python file, e.g. “.coot.py”, I think you have to change this to “set_nomenclature_errors_on_read ignore”.
    
==NCS edits==  
 
==NCS edits==  
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A: Turn up the radius a bit and use (set-symmetry-shift-search-size 3) . I would have thought that 2 is big enough, but maybe not in this case.
 
A: Turn up the radius a bit and use (set-symmetry-shift-search-size 3) . I would have thought that 2 is big enough, but maybe not in this case.
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== specify Coot download directory, like specifying backup dir by COOT_BACKUP_DIR? ==
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here is my working startup.py (of course replace src folder with your preferred location):
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import os
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try:
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    os.symlink('/ccp4/xray/tmp/', 'coot-download')
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except:
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    pass
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(Eugene Osipov on 22/04/2020 14:43)
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