Editing Cealign plugin (section)

== Troubleshooting ==

Post your problems/solutions here.

=== Unicode Issues in Python/Numpy ===
'''Problem''': Running/Installing cealign gives
<source lang="python">
Traceback (most recent call last):
  File "/home/byron/software/pymol_1.00b17/pymol/modules/pymol/parser.py",
line 308, in parse
  File "/home/byron/software/pymol_1.00b17/pymol/modules/pymol/parsing.py",
line 410, in run_file
  File "qkabsch.py", line 86, in ?
    import numpy
  File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 36, in ?
    import core
  File "/usr/lib/python2.4/site-packages/numpy/core/__init__.py", line 5, in ?
    import multiarray
ImportError: /home/byron/software/pymol/ext/lib/python2.4/site-packages/numpy/core/multiarray.so:
undefined symbol: _PyUnicodeUCS4_IsWhitespace
</source>
where the important line is
<source lang="python">
undefined symbol: _PyUnicodeUCS4_IsWhitespace
</source>

This problem indicates that your Numpy Unicode is using a different byte-size for unicode characters than is the Python distribution your PyMOL is running from.  For example, this can happen if you use the pre-built PyMOL and some other pre-built Numpy package.



'''Solution''': Hand-install Numpy.


=== LinAlg Module Not Found ===
'''Problem''': Running CE Align gives the following error message:
<source lang="python">
run qkabsch.py
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/parser.py", line 285, in parse
parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names)
File "/usr/lib/python2.4/site-packages/pymol/parsing.py", line 407, in run_file
execfile(file,global_ns,local_ns)
File "qkabsch.py", line 86, in ?
import numpy
File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 40, in ?
import linalg
ImportError: No module named linalg
</source>



'''Solution''': You do not have the linear algebra module installed (or Python can't find it) on your machine.  One workaround is to install [http://www.scipy.org/ Scientific Python]. (on debian/ubuntu this can be done by: sudo apt-get install python-scipy) Another is to reinstall the Numpy package from source, ensuring that you have the necessary requirements for the linear algebra module (linpack, lapack, fft, etc.).

=== CCEAlign & NumPy Modules Not Found ===
'''Problem''': Running CE Align gives the following error message:
<source lang="python">
PyMOL>run cealign.py
Traceback (most recent call last):
  File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parser.py", line 297, in parse
  File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 408, in run_file
  File "/usr/local/pymol/scripts/cealign-0.1/cealign.py", line 59, in ?
    from ccealign import ccealign
ImportError: No module named ccealign
run qkabsch.py
Traceback (most recent call last):
File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parser.py", line 297, in parse
File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 408, in run_file
File "qkabsch.py", line 86, in ?
import numpy
ImportError: No module named numpy
</source>



'''Solution''': This problem occurs under [http://www.apple.com/macosx Apple Mac OS X] if (a) the Apple's python executable on your machine (/usr/bin/python, currently version 2.3.5) is superseded by [http://fink.sourceforge.net/ Fink]'s python executable (/sw/bin/python, currently version 2.5) and (b) you are using [http://delsci.com/rel/099/#MacOSX precompiled versions of PyMOL] (MacPyMOL, PyMOLX11Hybrid or PyMOL for Mac OS X/X11). These executables ignore Fink's python and instead use Apple's - so, in order to run CE Align, one must install NumPy (as well as CE Align itself) using Apple's python. To do so, first download the [http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103 Numpy source code archive] (currently version 1.0.1), unpack it, change directory to numpy-1.0.1 and specify the full path to Apple's python executable during installation: <tt>sudo /usr/bin/python setup.py install | tee install.log</tt>. Then, donwload the [http://www.pymolwiki.org/index.php/Cealign#The_Code CE Align source code archive] (currently version 0.2), unpack it, change directory to cealign-0.2 and finally install CE Align as follows: <tt>sudo /usr/bin/python setup.py install | tee install.log</tt>.
[[User:Lucajovine|Luca Jovine]] 05:11, 25 January 2007 (CST).

=== The Function SimpAlign() is not found ===
'''Problem''': Running CE Align gives the following error message:
<source lang="python">
PyMOL>cealign 1CLL,1GGZ
Traceback (most recent call last):
  File "C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 203, in parse
    result=apply(kw[nest][0],args[nest],kw_args[nest])
  File "py24/Lib/cealign.py", line 177, in cealign
    curScore = simpAlign( matA, matB, mol1, mol2, stored.mol1, stored.mol2, align=0, L=len(matA) )
NameError: global name 'simpAlign' is not defined
</source>
I am running PyMOL v. 0.99rc6 on Win XP Professional x64 edition version 2003 sp2 and have followed the windows install procedure as described above.

'''Answer''': This simply means that PyMOL couldn't find the simplAlign function.  To let PyMOL know about this, you must run the following commands before running [[cealign]]:
<source lang="python">
run /your/path/to/cealign/qkabsch.py
run /your/path/to/cealign/cealign.py
</source>
but most people that use cealign would just put these two lines in their '''.pymolrc''' file.

=== Short Alignments Don't Work ===
If you are trying to align fewer than 16 residues then use [[align]], [[super]], or [[optAlign]].  CE uses a window size of 8; and to build a path of more than one window, you need 2*8=16 residues.  I will insert some code to re-route small alignments to one of the aforementioned alignment algorithms.

=== It Worked A Second Ago! ===
[[Image:Rewind.png|thumb|right|Showing the rewind button to rewind to state 1.]]

If you were using cealign (or alignto) and now the commands don't work -- that is, they return an RMSD, but don't actually superimpose the objects, then you have a simple problem dealing with states.  Most likely the cause of this oddness was (1) when you issued "cealign prot1, prot2" one of them was actually an ensemble of states or (2) you are trying to align to proteins with only one state, but are not looking at state one (because the last protein you were considering had more than one state and you quit editing that protein on a state that's not state 1).  To fix this, use the rewind button to get the proteins back into state 1 & reissue the cealign/alignto command.

=== file is not of required architecture ===
This error happens on a Mac when you compile one bit of code with gcc-4.0/g++-4.0 and then try to make a library with code compiled from gcc-4.2/g++-4.2.  If you recent installed Snow Leopard (Mac OS X 10.6) then this might bother you when you try to install Cealign or even PyMOL.  To get around this, ensure that you're building all components with the same gcc/g++ executable.  Here's how I did it,
<source lang="bash">
# sudo rm /usr/bin/gcc /usr/bin/g++
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc
# sudo ln -s /usr/bin/g++-4.0 /usr/bin/g++
</source>

I commented out those lines to stop people from blindly copy/pasting possible harmful lines.  Please ensure that your /usr/bin/gcc and /usr/bin/g++ are actually symbolic links, otherwise you could be doing bad things to your computer.  In my case, I only relinked gcc and not g++, hence the error.