On Feb 22, 2012, at 2:06 PM, Kevin D. Walker wrote:
I want to change the geometry of a selected atom by executing a command line script. I would like to proceed as follows:
1) select [atom-id] (this is the easy part)
...then I want to apply a script for the following interpretation
2) modify structure; set Element to 'C'; bonds to '4'; geometry to 'tetrahedral'
Is there a command script for this series?
Well, there is no command version of this part of Build Structure. Nonetheless everything is doable by calling the underlying Python. I've attached a Python script that does exactly what you requested above. It's got some explanatory comments. You would definitely want to look through it before running it because it offers some options for how you want the modified atom named. You would run the Python script from a regular command script with "open ~/c4.py" (assuming you named it c4.py and put it in your home directory). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu