MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
Hi there, I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command? Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing? Thanks! Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> 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.
I may have to use the Multiscale Coloring command tool that is not distributed with Chimera as documented here: http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html This seems to work well. Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> 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: Darrell Hurt <darrellh@niaid.nih.gov> Date: Wed, 20 Aug 2008 10:46:16 -0400 To: <chimera-users@cgl.ucsf.edu> Conversation: MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ??? Subject: MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ??? Hi there, I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command? Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing? Thanks! Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> 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.
Dear Darrell, You are looking at out-of-date information. The latest production release and current documentation include "msc": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/msc.html> and it is cross-referenced in the "see also" list near the top of the Multiscale Models page: <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multiscale/...
Actually, "msc" was also in the previous production release, Nov 2007. I usually recommend searching your local copy of the documentation (Help... Search Documentation in the Chimera menu) before Googling and/ or searching the Chimera Web site, as the latter are more likely to turn up old information. However, I understand it can be hard sometimes to come up with the right search terms! Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 20, 2008, at 8:00 AM, Darrell Hurt wrote:
I may have to use the Multiscale Coloring command tool that is not distributed with Chimera as documented here:
http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html
This seems to work well.
Darrell
Hi Darrell, You need to use the multiscale coloring command "msc". Here's an example using Chimera commands (Favorites / Command Line): open viperID:1p58 color blue :86.A msc #1 :86.A 15 The first command opens a dengue virus model from the VIPERdb database. Then I color residue 86 of chain A blue. That just colors the atoms of the residue not the surface. Then the msc command colors the multiscale surfaces (model identifier #1 seen in Favorites / Model Panel) making the surface color match the blue of residue 86 within 15 Angstroms of that residue. After I open the model and before coloring it I can change its resolution by pressing the Select All button at the top of the Multiscale dialog, then change the Resolution value in the middle of that dialog and press Resurface. A resolution value of 0 will make very high resolution solvent excluded molecular surfaces. The lighting effects will look better on lower resolution surfaces (e.g. 5 Angstroms). I've attached an example image. Tom Darrell Hurt wrote:
I may have to use the Multiscale Coloring command tool that is not distributed with Chimera as documented here:
http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html
This seems to work well.
Darrell
------------------------------------------------------------------------ *From: *Darrell Hurt <darrellh@niaid.nih.gov> *Date: *Wed, 20 Aug 2008 10:46:16 -0400 *To: *<chimera-users@cgl.ucsf.edu> *Conversation: *MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ??? *Subject: *MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
Hi there,
I’m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can’t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command?
Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing?
Thanks!
Darrell
Thank you. The answers from Elaine Meng and Tom Goddard are definitely what I was looking for. Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> 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@cgl.ucsf.edu> Date: Wed, 20 Aug 2008 12:17:22 -0400 To: "Hurt, Darrell (NIH/NIAID) [C]" <darrellh@niaid.nih.gov> Cc: <chimera-users@cgl.ucsf.edu> Conversation: [Chimera-users] MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ??? Subject: Re: [Chimera-users] MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ??? Hi Darrell, You need to use the multiscale coloring command "msc". Here's an example using Chimera commands (Favorites / Command Line): open viperID:1p58 color blue :86.A msc #1 :86.A 15 The first command opens a dengue virus model from the VIPERdb database. Then I color residue 86 of chain A blue. That just colors the atoms of the residue not the surface. Then the msc command colors the multiscale surfaces (model identifier #1 seen in Favorites / Model Panel) making the surface color match the blue of residue 86 within 15 Angstroms of that residue. After I open the model and before coloring it I can change its resolution by pressing the Select All button at the top of the Multiscale dialog, then change the Resolution value in the middle of that dialog and press Resurface. A resolution value of 0 will make very high resolution solvent excluded molecular surfaces. The lighting effects will look better on lower resolution surfaces (e.g. 5 Angstroms). I've attached an example image. Tom Darrell Hurt wrote:
I may have to use the Multiscale Coloring command tool that is not distributed with Chimera as documented here:
http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html
This seems to work well.
Darrell
------------------------------------------------------------------------ *From: *Darrell Hurt <darrellh@niaid.nih.gov> *Date: *Wed, 20 Aug 2008 10:46:16 -0400 *To: *<chimera-users@cgl.ucsf.edu> *Conversation: *MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ??? *Subject: *MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
Hi there,
I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command?
Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing?
Thanks!
Darrell
participants (3)
-
Darrell Hurt -
Elaine Meng -
Tom Goddard