Hi there, I’ve tried searching the archives and found some interesting information, but nothing specific to this question. Elaine’s response was particularly helpful: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html
From the documentation, it seems that Chimera only displays solvent-excluded surfaces: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/representation.html#...
I understand that I can map solvent-accessibility to this surface using “Render Attributes”, but I would like to display the actual solvent-accessible surface. I want to do this because it is my understanding that electrostatic potential mapping to a solvent-accessible surface is often more informative than to a solvent-excluded surface: http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostat... Can it be done? 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 3B62G Bethesda, MD 20892 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) 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're definitely right in that the potential at the solvent-accessible surface (SAS) is more directly what the contacting atom centers would "see." It also varies less sharply there as compared to the solvent-excluded surface (SES) that Chimera displays. For these reasons, both Electrostatic Surface Coloring and Coulombic Surface Coloring tools (by default) actually use the values 1.4 angstroms out from the SES (so approximately at the SAS) even though the coloring is at the SES. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html> There are options in those tools to change the offset, so it could be zero to just show the values exactly at the displayed surface. You can simulate an SAS in Chimera by increasing all the VDW radii by 1.4 and making the probe for surface calculation as small as possible. You can't get exactly the SAS because the probe cannot be zero. For example, commands: open 1zik; preset apply int 2 del solvent; rep sphere surf vdwdef +1.4 setattr s probeRadius 0.5 I find that many papers and programs claim to be showing the SAS but aren't really. It has an interesting soap-bubbly appearance that I rarely see in published images. Nevertheless you can change the offset to zero in the ESP-coloring tool and try this almost-SAS surface to see what it looks like. Just remember to avoid calculations that rely on reasonable VDW radii after inflating their values. I hope this helps, Elaine P.S. I thought your name sounded familiar.. We were happy to see that you teach some molecular graphics classes including Chimera! Thanks! ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 17, 2010, at 8:46 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi there,
I’ve tried searching the archives and found some interesting information, but nothing specific to this question. Elaine’s response was particularly helpful: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html
From the documentation, it seems that Chimera only displays solvent-excluded surfaces: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/representation.html#...
I understand that I can map solvent-accessibility to this surface using “Render Attributes”, but I would like to display the actual solvent-accessible surface. I want to do this because it is my understanding that electrostatic potential mapping to a solvent-accessible surface is often more informative than to a solvent-excluded surface: http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostat...
Can it be done?
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 3B62G Bethesda, MD 20892 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public)
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 http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, This is a perfect answer. Thank you! The issue of SES and SAS surfaces is often confused and not well understood because it is not apparent to novice users what the differences are. I'm glad to see that Chimera recognizes this problem and "offsets" the values. You guys are always one step ahead of me! I use a similar hack of VDW radii in PyMOL: http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Display _solvent_accessible_surface I humbly suggest that a nice feature for Chimera might be a button or checkmark or panel or something to specify which surface should be generated. Thanks for your rapid response! I'm supposed to teach next week and this was something I didn't know how to do in Chimera! Best wishes, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62G Bethesda, MD 20892 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) 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: Elaine Meng <meng@cgl.ucsf.edu> Reply-To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Date: Fri, 17 Sep 2010 13:08:38 -0400 To: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Display solvent-accessible surface?
Hi Darrell, You're definitely right in that the potential at the solvent-accessible surface (SAS) is more directly what the contacting atom centers would "see." It also varies less sharply there as compared to the solvent-excluded surface (SES) that Chimera displays. For these reasons, both Electrostatic Surface Coloring and Coulombic Surface Coloring tools (by default) actually use the values 1.4 angstroms out from the SES (so approximately at the SAS) even though the coloring is at the SES.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor. html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic. html>
There are options in those tools to change the offset, so it could be zero to just show the values exactly at the displayed surface.
You can simulate an SAS in Chimera by increasing all the VDW radii by 1.4 and making the probe for surface calculation as small as possible. You can't get exactly the SAS because the probe cannot be zero. For example, commands:
open 1zik; preset apply int 2 del solvent; rep sphere surf vdwdef +1.4 setattr s probeRadius 0.5
I find that many papers and programs claim to be showing the SAS but aren't really. It has an interesting soap-bubbly appearance that I rarely see in published images. Nevertheless you can change the offset to zero in the ESP-coloring tool and try this almost-SAS surface to see what it looks like. Just remember to avoid calculations that rely on reasonable VDW radii after inflating their values.
I hope this helps, Elaine
P.S. I thought your name sounded familiar.. We were happy to see that you teach some molecular graphics classes including Chimera! Thanks!
----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 17, 2010, at 8:46 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi there,
I¹ve tried searching the archives and found some interesting information, but nothing specific to this question. Elaine¹s response was particularly helpful: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html
From the documentation, it seems that Chimera only displays solvent-excluded surfaces: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/representation.html#... urfaces
I understand that I can map solvent-accessibility to this surface using ³Render Attributes², but I would like to display the actual solvent-accessible surface. I want to do this because it is my understanding that electrostatic potential mapping to a solvent-accessible surface is often more informative than to a solvent-excluded surface: http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostat... cs-in-pymol#TOC-Surface-potentials
Can it be done?
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 3B62G Bethesda, MD 20892 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public)
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 http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Hurt, Darrell (NIH/NIAID) [E]