[Chimera-users] Scripting to write / save multiple models into single pdf file

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 8 16:04:42 PST 2010

On Mar 7, 2010, at 10:13 AM, Elaine Meng wrote:

> On Mar 7, 2010, at 5:12 AM, Sumitro Harjanto wrote:
>> Hi Meng,
>> I would like to use chimera to help me with a process of combining  
>> receptors and ligands that were modelled separately (in separate  
>> files)
>> So here is my intended framework:
>> For each iteration:
>> 	• open “template.pdb” template file (which contains the receptor/ 
>> ligand complex) I used to model the receptor and ligand
>> 	• open the receptor_model.pdb
>> 	• open the ligand_model.pdb
>> 	• match receptor to template
>> 	• match ligand to template
>> 	• close template.pdb
>> 	• save the models in their current position into a single new pdb  
>> file.
>> I was exploring the feasibility of using the command “write” but I  
>> am not too sure if it will allow me to save the complex as a single  
>> pdb file..?
>> On a side note, if it’s possible, any suggestion on how to optimise  
>> the run time since I might be running this for a large number of  
>> iterations ..? I read somewhere about switching off the GUI to save  
>> time, does it help..?

Hi Sumitro,
	I don't have any really great suggestions for making things faster.   
Using --nogui will probably speed things up since Chimera won't have  
to build display lists for your structures.  Also, you should probably  
open your structures with the "noprefs" keyword so that Chimera  
doesn't do a lot of work figuring about what parts of your structure  
to ribbon, which to ball-and-stick, etc. (see the docs for the "open"  
	Did you need help with the scripting itself?  It wasn't really clear  
from your mail whether you had all that under control or not...


                         Eric Pettersen
                         UCSF Computer Graphics Lab

> Hi Sumitro,
> You can't save multiple models in one file with the "write" command,  
> but you can use "write"  multiple times, one for each model you want  
> to save.  If you make sure to save each model "relative" to the same  
> model, they will be in the correct positions with respect to each  
> other when you reopen the files.  See the "relative" keyword:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
> Or, if you really need to have them in a single file, you can use  
> the "combine" command to create a new single model from multiple  
> models.  You would do that after the matching, but before saving the  
> PDB file.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
> I can't answer about how to script for multiple models, or how much  
> faster it might be to use noGUI, so I'm sending this to the chimera- 
> users list.
> In the future, please send Chimera questions to the chimera-users at cgl.ucsf.edu 
>  list, because I might be away from work or (like now) others may be  
> better able to answer the question.

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