Commands for multiscale models?
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/blueton... 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.
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/blueton...
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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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 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. From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Date: Wednesday, December 3, 2014 5:07 PM To: Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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@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/blueton... 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. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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 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.
From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Date: Wednesday, December 3, 2014 5:07 PM To: Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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@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/blueton...
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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (2)
-
Hurt, Darrell (NIH/NIAID) [E] -
Tom Goddard