Hi Damien, Eric's answer is perfect, I just wanted to add that you can try out each command by typing it into the Command Line (shown by choosing "Favorites... Command Line" from the menu). In other words, a Chimera command script is just a text file containing the same lines that could be entered at the Command Line. You can see a list of all commands by choosing "Help... User's Guide" from the menu and then clicking the "commands" link in the page that appears. That commands index also has a section near the bottom entitled "Chimera Command Files" with links to several example files. There are also many example commands in the tutorials (again under the Help menu). Another kind of script is Python code, which is sometimes needed if there is no Chimera command for what you want to do, or you need to loop through a large number of structures. Best, Elaine On Aug 19, 2009, at 11:22 AM, Eric Pettersen wrote:

Hi Damien, You can use "open" with the full path to the file, or you can "cd" to the folder and then just use the file's name. See below...

On Aug 19, 2009, at 6:44 AM, Damien Larivière wrote:

...

Dear all,

Sorry for this simple question : Is there an example of how to use a command in a script ? For example, the command "open" is described in the documentation but I confess (i'm not a programmer) that I do not understand how to use it for opening a pdb file in a specific directory : C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock0001.pdb

I would like to create a script that does :

1/ Open a PDB file (dock0001.pdb)

Either: open C:\Users\damien\ ... \Results_190809\dock001.pdb

-or-: cd C:\Users\damien\ ... \Docking_Hex\Results_190809 open dock001.pdb

The latter might be better if you are going to save files and would like them to go into that folder as well without specifying a big long path.

...

2/ open Tools - Structure analysis - Sequence 3/ select residues 203 to 227 chain A

sel :203-227.A

":203-227.A" is the "atom specifier" for residues 203 to 227 of chain A. There is an extensive explanation of atom specifiers here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ frameatom_spec.html

...

4/ Actions Color Red

color red sel

...

5/ open Tools - Structure analysis - Sequence 6/ select residues 54 to 87 chain A

sel :54-87.A

...

7/ Actions Color Magenta

color magenta sel

If the only reason you are making the selection is in order to color it magenta (i.e. you aren't going to do any other operations on it) then you could just cut out the selection step and:

color magenta :54-87.A

--Eric

Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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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