[chimera-dev] Match->Align command line option?

[Eric Pettersen]

On Sep 13, 2012, at 11:55 AM, Chetanya Pandya wrote:

> Hi Eric,
> 
> Thanks for your detailed reply...it has been really useful! As instructed, I've installed today's daily build on my machine (running Fedora 15 32 bit). I've written a python script(see attached) which (hopefully) does what I want.
> 
> Unfortunately, the script is unable to save the alignment as a file. It spits out an error which I'm unable to comprehend (see attached log file).
> 
> Any help would be appreciated!

Well, Multalign Viewer was designed a decade ago and has no non-GUI version.  Therefore, the script cannot be run in nogui mode if it creates an MAV instance.  So you have two options.  One is simply to run your script in GUI mode.  The Chimera window will come up and you will have to remain logged in until it finishes.  The other is to get tomorrow's daily build, where I've modified makeAlignment so it is possible to just get the list of aligned Sequences instead of a MAV instance.  That list can then be used to write the output file.  The changes to your script would be in the makeAlignment call:

seqs = makeAlignment(chains, makeMAV=False)

and the way you call save:

save(f, None, seqs, {})

(and remove the mav.Quit() call, obv.)

> 
> Thanks,
> --Chetanya
> 
> P.S. - I would like to read more about the various packages and their functions. I can't seem to find a detailed writeup/manual. Can you direct me to a good source?

This is probably our Achilles' heel -- there really isn't a good source.  On the Programmer's Guide page there are links to the help() output for the main Chimera molecular data classes (which can also be viewed with the help() command in the IDLE tool).  If you know a tool doesn't something similar to what you want, you can find out how it does it by looking in the source for the tool (all in <chimera installation>/share).  If you know a command does what you want, use runCommand to run it, or look at the command's source (in share/Midas/__init__.py unless the command is implemented by a tool).  Lastly, and probably most importantly, just asking here on the chimera-dev mailing list if you're stumped.  And with our spotty programmer documentation, it's easy to get stumped!

--Eric


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