Hi,
I am a new user of chimera and I already have a question.
I have an protonated aspartic acid in my protein and I was wondering,
is it possible to add hydrogen atom to aspartic acid with chimera?
Thanks
Virginie
What Tom says below is all true, but as he intimated in his previous
mail if you are willing/able to use Chimera as your Python
interpreter (typically as "chimera --nogui script.py") then things
should work. There are some caveats. Chimera ignores the PYTHONPATH
environment variable in order to avoid using libraries from
incompatible Python installations, therefore to have Chimera find
locally installed packages that you want to use you need to set the
CHIMERAPATH variable, which Chimera uses in a fashion similar to
PYTHONPATH. Another thing is that you can't pass arguments to your
script in the conventional fashion since Chimera itself processes all
arguments. If you need to pass values to your script, you need to
use environment variables as detailed in the FAQ here: http://
www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett(a)cgl.ucsf.edu
http://www.cgl.ucsf.edu
On May 8, 2006, at 9:27 PM, Thomas Goddard wrote:
> Hi Jim,
>
> Importing Chimera from your Python script to use its
> functionality is
> something we have put very little effort into supporting. I have done
> this in an nuclear magnetic resonance assignment program called Sparky
> that is based on Python to run Chimera as a structure viewer.
> Below is
> the code that starts Chimera from the Sparky Python interpretter.
>
> There are many problems.
>
> You need to set an environment variable to tell the operating system
> where the Chimera shared libraries are before you start Python. See
> example below.
>
> You need to use the Python included with Chimera because Chimera
> uses a modified Python. Ick. The modification allows Chimera objects
> like Molecules to be given new attributes. There is also some other
> issue on the Mac where a stock Python can't find the init_chimera()
> method in shared library _chimera.so.
>
> If you start the Chimera graphical user interface then you will need
> to run the Tk event-loop to get Chimera to update the graphics. But
> then Chimera will not return to your script that started it. So my
> example below does not start the event-loop.
>
> If you start Chimera in nogui mode, it quits as soon as it processes
> any arguments which would probably prevent your script from calling
> into
> Chimera after that as Chimera has cleaned up.
>
> When I used the script below and then opened a PDB file on my Mac OS
> 10.4.6 system the screen went dim and a message told me to hold the
> power button down to do a hard reboot! Probably a graphics driver
> issue.
>
> As you can see we really haven't worked much on this type of
> Chimera use.
>
> Tom
>
> ----
>
> Example starting Chimera on a Mac from Python:
>
> $ export CHIMERA="/Users/goddard/Desktop/Chimera 2199.app/Contents/
> Resources"
> $ export DYLD_LIBRARY_PATH=$CHIMERA/lib
> $ "/Users/goddard/Desktop/Chimera 2199.app/Contents/Resources/bin/
> python2.4"
> Python 2.4.2 (#1, Jan 30 2006, 11:15:23)
> [GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import start_chimera
>>>> start_chimera.start_chimera()
>>>>
>>>> # Now you could "import chimera" and do some stuff.
>>>>
>
> ---
>
> The following is the start_sparky.py file used in the above example:
>
> #
> ----------------------------------------------------------------------
> -------
> #
> start_count = 0
> def start_chimera():
>
> setup_chimera()
>
> import chimeraInit
> try:
> chimeraInit.init(argv = [], nogui = False, eventloop = False,
> exitonquit = False)
> except SystemExit, value:
> # Chimera raises SystemExit sometimes when it can't start.
> # Have to catch it here or Sparky will exit.
> import traceback
> traceback.print_exc()
> raise EnvironmentError, 'Chimera failed to start'
> except:
> global start_count
> if start_count == 1:
> warning = '''
> Chimera can only be started once per Sparky session.
> This is a limitation in all versions of Chimera released so far
> (through March 2004).
>
> '''
> import sys
> sys.stdout.write(warning)
> raise
>
> start_count += 1
>
> #
> ----------------------------------------------------------------------
> -------
> # Do initial Chimera setup that only needs to be done once even if
> Chimera
> # is started and quit several times.
> #
> chimera_setup = False
> def setup_chimera():
>
> global chimera_setup
> if chimera_setup:
> return
> chimera_setup = True
>
> import os
> if not os.environ.has_key('CHIMERA'):
> raise EnvironmentError, 'CHIMERA environment variable not set.'
>
> chimera_path = os.environ['CHIMERA']
> import os.path
> if not os.path.exists(chimera_path):
> raise EnvironmentError, 'CHIMERA environment variable gives non-
> existent directory ' + chimera_path
>
> chimera_python = os.path.join(chimera_path, 'share')
> chimera_lib = os.path.join(chimera_path, 'lib')
> import sys
> if sys.platform == 'win32':
> chimera_site_packages = os.path.join(chimera_path, 'bin', 'Lib',
> 'site-packages')
> else:
> chimera_site_packages = os.path.join(chimera_path, 'lib',
> 'python2.4',
> 'site-packages')
>
> sys.path.insert(0, chimera_site_packages)
> sys.path.insert(0, chimera_python)
> sys.path.insert(0, chimera_lib)
>
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