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. 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 ? 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 Many thanks for your help Damien Eric Pettersen a écrit :
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...
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