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@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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