[Chimera-users] Commands for multiscale models?

[Tom Goddard]

Hi Darrell,

  If you instead just open the PDB model (not the ViperDB one) you can use the sym commmand “surfaces all” option, for example,

	open 1ej6
	sym #0 surfaces all
	~modeldisp #0
	focus
	scale 0.9

Here I open the PDB, make the surfaces, hide the original atomic model, zoom to show the full virus, then zoom out a little bit.  If you prefer to use the Viper .vdb files where Chimera automatically makes the depiction that excludes the surface for the original subunit then you can instead do

	open viperID:1ej6
	sop showPieces #1

The sop surface operation command shows all the surface subunits including the hidden ones.

	Tom



On Dec 3, 2014, at 2:20 PM, Hurt, Darrell (NIH/NIAID) [E] <darrellh at niaid.nih.gov> wrote:

> Hi Tom,
> 
> Thanks for the quick reply. I'm trying to take advantage of the default behavior of Chimera that, when it opens a VIPER structure, it automagically makes the symmetry mates. What I'm trying to do is alter the default picture to hide the ribbons of the "loaded" coordinates and show a multiscale surface for those loaded coordinates (so that the entire virus is pretty surfaces — see attached).
> 
> Thanks!
> Darrell
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Bethesda office: 301-402-0095
> Rockville office: 240-669-2741
> Mobile: 301-758-3559
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> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
> Date: Wednesday, December 3, 2014 5:07 PM
> To: Darrell Hurt <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>>
> Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
> Subject: Re: [Chimera-users] Commands for multiscale models?
> 
> 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
> 
> [cid:E8D04F98-8ECA-4F52-AC55-EE0E523EA9BF at cgl.ucsf.edu]
> 
> 
> 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)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Bethesda office: 301-402-0095
> Rockville office: 240-669-2741
> Mobile: 301-758-3559
> Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<https://twitter.com/niaidbioit> , @NIH3Dprint<https://twitter.com/nih3dprint>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
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