[Chimera-users] Chimera scripting with --nogui can't write pdb files

[Eric Pettersen]

Hi Rebecca,
	The basic problem is that your two commands aren't Python commands, they're Chimera commands and therefore produce syntax errors when executed as Python.  If you just put those commands in a file named close.com instead, this should work for you:

chimera --nogui pdb1.pdb pdb2.pdb close.com

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jun 24, 2014, at 1:31 PM, rswett at chem.wayne.edu wrote:

> Hey guys, i've been trying to put together a command line only set of scripts that will do some selection processing and save a pdb without going through the gui.
> 
> If I use the command
> chimera --nogui  --script close.py pdb1.pdb pdb2.pdb
> 
> where close.py contains
> 
> select #0 za<3 & #1:HOH
> write selected 1 output.pdb
> 
> I should get the residues that match that selection criteria saved as the pdb output.pdb, correct?
> 
> I get SyntaxError: invalid syntax for line 2 even though this works OUTSIDE a script. as in, if I just run chimera command line and enter those commands sequentially, it works. I also noticed that within the gui I need  "#1" and outside it only works with '1" as the model number.
> 
> I've also tried doing this with a python script:
> 
> chimera --nogui --nostatus --script "close.py pdb1.pdb pdb2.pdb output.pdb"
> 
> this should pass whatever I enter as $1 $2 $3 as arguments to my script, correct?
> 
> So close.py for this version contains
> 
> open (sys.argv[1])
> open (sys.argv[2])
> select #0 za<3 & #1:CVX
> write selected 1 (sys.argv[3])
> 
> which also pukes on the pdb write. I couldn't find any other way to write a pdb using python syntax, I assume the way i'm doing it is wrong, but I couldn't find a write.pdb function during my digging.
> 
> Does anyone have suggestions for writing a pdb based on a selection without going through the gui? I plan on batching this up for a huge number of files and directories and going through the gui would be far too time consuming.
> 
> Rebecca
> 
> 
> 
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