Here is what the saved images look like for 2bbv.

Tom



On Dec 11, 2020, at 11:41 AM, Tom Goddard <goddard@sonic.net> wrote:

Hi Yong Liu,

  First start by figuring out the ChimeraX commands to do what you want.  For example, the commands to save an image of chain A shown as atoms could be

open 2bbv

show #1/A only
view
save ~/Desktop/2bbv_chain_A.png

Now the trick is we want to do that for all chains.  The ChimeraX command language has not looping methods so we have to use some Python.  Also you wanted to create a new command that does the 3 commands above with the right chain id and model number substituted in.  I've attached some Python code chain_images.py that does that makes the command.  If you open that Python file in ChimeraX it will define the command then type

chainimages #1

to make the images.  I've put this example Python code on the ChimeraX Recipes web site


If you want ChimeraX to define this command each time you start you can put command "open ~/scripts/chain_images.py" in ChimeraX startup preferences.

  Tom

<chain_images.py>


On Dec 10, 2020, at 10:29 PM, Yong Liu <liuyongbox@gmail.com> wrote:

Hi All,
I would like to save the image of each chain in one command. I have wrote following python code, but it is not working. Is anybody know how to fix it?


# save the image of each chain

def batchSave(session):
chainID_list = info chains
for x in chainID_list:

chainID = chainID_list.split()

ID = chainID[-1]

save "Desktop/ID.png" width 4000 height 4000 transparentBackground true


def register_command(session):
 from chimerax.core.commands import CmdDesc, register
 desc = CmdDesc()
 register('batchSave', desc, batchSave, logger=session.logger)

register_command(session)

Best,
Yong Liu
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