[Chimera-users] [chimera-dev] Dividing a model into seperate models - one for each chain

[Tom Goddard]

Hi Mateusz,

   Ok, your Python can be changed in a simple way, for example

     from chimera import openModels
     for m in openModels.list():
       id = m.oslIdent()
       command="write "+id+" "+o_path+"/"+id[1:]+".pdb"
       runCommand(command)

The m.oslIdent() gives the string "#0.1" or for models with no sub-id 
"#0".  The id[1:] gives "0.1" so you don't get the "#" in the file 
name.  The cryptic "oslIdent" stands for object selection language 
identifier.

     Tom


Mateusz Dobrych?op wrote:
> Hi Tom,
>
> Thank you very much for your response.
>
> My exact problem is that I'm trying to find a way to automatically 
> save all the models (and submodels) that are opened in Chimera at a 
> time. It's easy when models are numbered #0, #1, #2 etc - then, I use:
>
> opened=openModels.list()
> howmany=len(opened)
> while howmany>=0:
>      command="write "+str(howmany)+" "+o_path+"/"+str(howmany)+".pdb"
>      runCommand(command)
>      howmany-=1
>
> Unfortunately, when I split, let's say, #0 that contains 3 chains, and 
> then use the above code, I get an error:
>
> MidasError: 3 model ids match "0"
>
> So maybe there's a different way to do it? I'd like to save #0.1, #0.2 
> and #0.3 to seperate files. I know it's possible from Chimera's 
> interface, but I have no idea how to do it when my script doesn't have 
> any info about the number of submodels etc.
>
> Thank you for your time once again,
> Mateusz
>
> 2012/5/9 Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
>
>     Hi Mateusz,
>
>      The "split #0" command produces separate models for each chain.
>      They are numbered #0.1, #0.2, #0.3, ... with the same primary id
>     number (0) and different secondary id numbers.  You can use these
>     two-part id numbers in any Chimera command (e.g. color blue #0.2),
>     or you can refer to all the models using #0.  There is currently
>     not a way to change the id numbers of models.
>
>        Tom
>
>
>         Hello,
>
>         Is there a command / a way to split a model into seperate
>         models (one for each chain)? I know there is the "split"
>         command, but it divides the model into submodels.
>
>         Mateusz
>
>
>

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