Eric Pettersen pett at cgl.ucsf.edu
Wed May 5 15:18:24 PDT 2004

On Tuesday, May 4, 2004, at 11:38 PM, riccardodesantis at fastwebnet.it 

> Hallo,
> my name is Riccardo De Santis and I'm a new user of CHIMERA.
> I'd like to know how run the program from the command line.
> I've tryed with the command NOGUI but the program doesn't start.
> Another question is: how can I use matchmaker (in the graphic menu) to 
> match
> the molecules from the command line? Which is the istruction to type?
> Thank you in advance,
> Riccardo De Santis.

Hi Riccardo,
	Unlike Chimera's predecessor Midas, running Chimera in nogui mode 
("chimera --nogui") doesn't expect or allow commands on standard input 
(e.g. typing in the shell window).  Instead, you use one or more file 
name arguments on the "chimera --nogui" command line to have Chimera 
execute the commands you want.  When you say that "the program doesn't 
start ", I'm guessing you ran "chimera --nogui" with no file name 
arguments, which resulted in Chimera exiting since it had no files to 
	You can put normal Chimera commands in a file and have Chimera execute 
those.  Such files should either end in ".cmd" or ".com" or be prefixed 
with "cmd:" or "com:" on the Chimera startup command line.  So if you 
have such a file named "make_alignment" with Chimera commands you want 
executed then "chimera --nogui cmd:make_alignment" would execute it.  
You can do the same with files of Python code, ending such files in 
".py" or prefixing them with "python:".
	As for MatchMaker, right now it is too closely tied to the GUI dialog 
to be called from nogui mode.  I will work on disassociating the 
underlying computation from the graphical interface so that it can 
become a command-line command.  The hydrogen-bond finder has recently 
been given this kind of treatment and is callable from the command line 
in the release we will be making later this week.  I'll send mail when 
the same is true for MatchMaker.
	It is possible to "remote control" MatchMaker in GUI mode, so that as 
long as a window system is available, you could write scripts that 
automate MatchMaker functions.  They just can't be run in nogui mode.  
But they can be run in an analogous manner to the above (e.g. "chimera 
python:make_alignment") -- it's just that windows and so forth will pop 
up until Chimera finishes.  If you would want to do this, let me know 
and I can send more details.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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