[Chimera-users] Distance Grid SES calculation available?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Tue Jan 6 13:50:06 PST 2015


Hi Tom,

Thank you for sharing so publicly. It works wonderfully and oh so fast! I do not want to get in the way at all of the progress of Chimera 2, so I hope this doesn't put you too off course. Long live UCSF Chimera!

Thanks and Happy New Year!
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, 4A31
North Bethesda, MD 20892-2135
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 at sonic.net<mailto:goddard at sonic.net>>
Date: Tuesday, January 6, 2015 3:01 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] Distance Grid SES calculation available?

Hi Darrell,

  Ok, there is a secret Chimera 1 option to the surface command to let you use the distance grid SES calculation:

surface #0 grid 0.5

The value of the grid option is the grid spacing and 0.5 Angstroms is reasonable, smaller values will produce a more finely triangulated surface.  This surface cannot be colored to match the atom colors in the same way as a normal molecular surface because it lacks an association between surface points and atoms (although the color zone tool can get the same effect if you need it).  This is an undocumented feature because if we add all our cool new features to Chimera 1 then we will never have time to get Chimera 2 produced.  But since you need it here it is.

Tom



On Jan 5, 2015, at 8:49 PM, Hurt, Darrell (NIH/NIAID) [E] <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>> wrote:
Hi Chimera friends,
This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here:
http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html
The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces).
Is there some way to call the routine, especially in a script? Python maybe?
Thanks,
Darrell
--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
5601 Fishers Lane, 4A31
North Bethesda, MD 20852
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 at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users





More information about the Chimera-users mailing list