Hi Florian, The units for the electrostatic surface generated by APSB (andDelphi) are kT/e, which is what Chimera uses for determining the threshold when colouring the electrostatic surface. I'm quite sure that's the case. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of chimera-users-request@cgl.ucsf.edu [chimera-users-request@cgl.ucsf.edu] Sent: Tuesday, February 19, 2013 7:53 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 118, Issue 20 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Algorithm for areaSAS calculations (Korbus, Michael) 2. Unit of electrostatic surface coloring within Chimera (Florian.Capito@external.merckgroup.com) 3. Drug-Protein Interaction (kanika sharma) 4. Re: New user-visualizing coulombic (Elaine Meng) 5. Re: session file/HID (Tom Goddard) 6. Re: questions about modeller and task panel (Elaine Meng) 7. Re: Drug-Protein Interaction (Elaine Meng) 8. Re: Algorithm for areaSAS calculations (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Feb 2013 10:27:44 +0100 From: "Korbus, Michael" <michael.korbus@h-da.de> To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] Algorithm for areaSAS calculations Message-ID: <0781A55E8298FD4CBCAAA70C4AF2EDB6350489B0BA@Virgon.h-da.local> Content-Type: text/plain; charset="us-ascii" Dear Ladies and Gentlemen, I have a question concerning calculation of areaSAS with chimera. Which algorithm is used? A Shrake-Rupley based algorithm? Thank you for your help. Sincerely, Michael Korbus Michael Korbus Dipl.-Ing. Biotechnologie (FH) Hochschule Darmstadt University of Applied Sciences Fachbereich Chemie u. Biotechnologie Schnittspahnstr. 12 D-64287 Darmstadt Tel +49/6151/16-8630 Fax +49/6151/16-8404 ------------------------------ Message: 2 Date: Mon, 18 Feb 2013 14:09:24 +0100 From: Florian.Capito@external.merckgroup.com To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Unit of electrostatic surface coloring within Chimera Message-ID: <OF57DE4D54.6BC4EDF1-ONC1257B16.004734C6-C1257B16.004845D9@merck.de> Content-Type: text/plain; charset=ISO-8859-1 To whom it may concern, I am using Chimera to color surfaces of proteins according to electrostatic potential files calculated by APBS. Now, in Chimera, there is the option to select a threshold, e.g. at which value the surface should be colored in red and at which value it is colored in blue. Now i would like to know in which unit this threshold works? Is it kcal (mol?e)-1? While this has been described for the Coloumbic surface coloring within Chimera Help, I could not find any explanation for this in the help menu, when loading external APBS potential files into Chimera. Thank You very much for Your time and help!!! Mit freundlichen Gr?ssen/ With best regards Florian Capito MM-PTD-New Downstream Darmstadt Location A17/217 Postcode: A046/509 Phone: +49 6151 72-7168 Email: florian.capito@external.merckgroup.com Merck KGaA Frankfurter Str. 250 D 64293 Darmstadt Homepage: http://www.merck.de Pflichtangaben finden Sie unter http://mandatories.merck.de Mandatory information can be found at http://mandatories.merck.de This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. 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Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. ------------------------------ Message: 3 Date: Mon, 18 Feb 2013 12:24:37 +0100 From: kanika sharma <ksharma997@gmail.com> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Drug-Protein Interaction Message-ID: <CAAo-yeL3vs_KH76GdFQT0iP39-K2zcYRuBvmUG8pgfTxt8ivAQ@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position? -- *Regards,* * * *Kanika Sharma*