On Aug 20, 2009, at 11:23 AM, Damien Larivière wrote:
Hi Eric and Elaine,
Thank you very much for your answers !
I was blocked in fact by the "cd command" that does not work on my machine for opening a file. I reported the bug this morning.
I will be looking into that.
So, I have used Eric's suggestions and it works very well.
I am not a python programmer (but I know Matlab well enough). So in Chimera I would like to open successive pdb files (dock000i.pdb with i = 1 to 20) and perform some actions on each one and then close each session that are previously saved in a Chimera session. The loop "for" in Matlab starts with "for i = 1:20" then the block of actions and ends with "end". What's about in Python programming ?
As Elaine mentioned, if you need to do looping you will need to resort to Python. There is a function in Chimera named runCommand which allows you to execute Chimera commands in Python, so that way you don't have to spend a lot of time figuring out the equivalent Python functions. This lets us write your script pretty easily in Python:
I suggest the following but I know it can't work:
for i = 1 to 20 open C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring \Bond_Set\Docking_Hex\Results_190809\dock\dock000i.pdb color orange red :38-227.A color blue :228-356.A color magenta :203-227.A color green :261-271.A color green :297-307.A save C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring \Bond_Set\Docking_Hex\Results_190809\dock\dock000i.py close session end
from chimera import runCommand as rc for i in range(1, 21): rc(r"open C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring \Bond_Set\Docking_Hex\Results_190809\dock\dock%04d.pdb" % i) rc("color orange red :38-227.A") rc("color blue :228-356.A") rc("color magenta :203-227.A") rc("color green :261-271.A") rc("color green :297-307.A") rc(r"save C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring \Bond_Set\Docking_Hex\Results_190809\dock\dock%04d.pdb" % i) rc("close session") The script is really pretty self-explanatory except for a couple of tricky things. One is that the quoted strings that contained backslashes needed to be preceded by an 'r' (marking them as a "raw" string) to prevent Python from doing special backslash processing on the string. The other is getting the zero-padded version of 'i' into the open and save commands. This is accomplished with the special text %04d which means replace that text with a zero-padded 4-digit decimal integer. The "% i" after the string indicates that the variable 'i' should be used in the text replacement. Good luck! :-) --Eric Eric Pettersen UCSF Computer Graphics Lab