Hi Nancy, The script assumes you only have one model open and flips that model in its entirety. Here’s a slightly tweaked version that flips all open molecular models: from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): for a in m.atoms: crd = a.coord() crd.x = 0 - crd.x a.setCoord(crd) You don’t have to type it into the IDLE shell. Instead, you could save the above into a file whose name ends in ‘.py’ (indicating it’s a Python file). The you could run the script simply by opening it in Chimera with File→Open or the “open” command. I don’t know what you read on GitHub, but if you really need to restrict the script to working on a model with a particular ID#, it’s possible to make the script do that. Let me know if that’s what you need. It would be weird to flip just part of a model. Consider a model with two chains where the Z coordinate of all the atoms are in the range 30-40. Flipping the Z coordinate of one of the chains would move it far away from the other chain. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 1, 2018, at 8:32 AM, Chu Ji <nancyji0217@gmail.com> wrote:
Hi Eric,
I was trying to get a mirror image of a PDB model and came across your thread. I know that you are typing in m = chimera.openModels.list()[0] for a in m.atoms: crd = a.coord() crd.z = 0 - crd.z a.setCoord(crd) in the Gen Control>IDLE section, but I also read on GitHub that I should change the [0] in openModels.list()[0]to the model specifier. What does that mean exactly? I tried to type in the PDB ID to replace the 0 but nothing happened…Could you show me an example? What if I want to flip Chain B of a certain model or just the entire model?
Thank you so much for your help! Looking forward to hearing from you.
Best, Nancy
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