[Chimera-users] Problem using Chimera

Eric Pettersen pett at cgl.ucsf.edu
Tue Nov 17 10:21:53 PST 2015

Hi Tatiana,
	“read” reads files that contain Chimera commands (like “color red”, “ribbon”, etc.) not Python commands.  You would use the “open” command to read Python files (as well as many other types of files of course).  Make sure the file name ends in “.py” so the open command recognizes it as a Python file.
	You may want to look through the Chimera Programmer’s Guide (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>) to get more familiar with how Chimera is organized at the Python level.  Also, the “extremely basic primer” for looping through data files in Chimera and performing actions on them would seem to be very relevant to what you’re doing.  It’s linked from the Programmer’s Guide and the direct URL is http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
	So is a “SCF” file a sequence chromatogram file?  If so, getting Chimera to read and display that is doable, maybe via matplotlib, maybe in the Sequence viewer.  You will undoubtedly need to ask more questions really.  FYI programming questions would be best sent to the chimera-dev list rather than the chimera-users list.
	I hope it goes well.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Nov 17, 2015, at 1:56 AM, BRUXELLES Tatiana (ETU VIE) <tatiana.bruxelle at etu.unistra.fr> wrote:
> Dear Sir, dear Madam
>      I am a Master student at the Université de Strasbourg in France and I am currently doing an internship in a bioinformatics lab : the LBGI in Strasbourg. One of my tasks during this internship is to make Chimera read about 80 files with the extensions .scf. The problem is that software doesn't to be able to read my command file. I can't even make it read a print instruction. To execute those files I use the command : read File_name in command line on chimera. I am gonna join the files so you can see. Could you suggest a solution to my problem ?
> Kind regards, Bruxelles Tatiana
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