[Chimera-users] [chimera-dev] Dividing a model into seperate models - one for each chain
goddard at sonic.net
Wed May 9 14:00:22 PDT 2012
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"
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
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:
> while howmany>=0:
> command="write "+str(howmany)+" "+o_path+"/"+str(howmany)+".pdb"
> 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,
> 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.
> 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.
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