[Chimera-users] Commands for multiscale models?

Tom Goddard goddard at sonic.net
Wed Dec 3 14:07:55 PST 2014


Hi Darrell,

  You can create multiscale models with the sym command, for example,

	open 1ej6
	sym #0 surface true

If you just open a viper model (.vdb suffix) or fetch it from the web Chimera it shows a similar depiction (image attached)

	open viperID:1ej6

But there is no command to tell it to replace some specified subunits with atomic or ribbon depictions, or to change colors of individual subunits.  You can get all proteins as atomic models, just omit the “surface true” from the sym command, but that takes alot of memory for say a large virus.  But then commands can work on any subunit to create surfaces, change colors, change display styles.

  How do you want to tailor the multiscale model appearance?

	Tom




On Dec 3, 2014, at 1:41 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:

> Hi Chimera friends,
> 
> I was reading this post from 2009 that indicates that there are no Chimera commands for multiscale models:
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004009.html
> 
> Is it still the case that there are no Chimera commands for manipulating the multiscale models? I saw the blue-tongue virus example script for doing something similar using Python itself:
> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/bluetongue.py
> 
> I want to script the loading of an arbitrary VIPERdb model and then create multiscale model surfaces for every chain (not just the copies). Can it be done with Chimera commands? Or do I need to work up my Python-fu?
> 
> Thanks,
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
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