February 2013 - Chimera-users - RBVI Mailing Lists

robust molecular surface calculation
by Francois Berenger 21 Feb '13

21 Feb '13

Hello, Is there any plan to plug some alternative molecular surface calculation algorithm into chimera? I have seen some interesting articles about isosurface and gaussian density functions: "Yu, Z., Jacobson, M. P. and Friesner, R. A. (2006), What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. J. Comput. Chem., 27: 72–89. doi: 10.1002/jcc.20307" "What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules DOI: 10.1002/jcc.20307" http://onlinelibrary.wiley.com/doi/10.1002/jcc.20307/abstract The algorithm looks simple, robust and even parallelizable. I kind of guess that's the algorithm used in MOE when I look at their triangulation. Regards, Francois.

3 5

A way to extract mesh data?
by Hyeong-Tae Jou 20 Feb '13

20 Feb '13

Hi list, I wonder if it is possible to extract mesh data when drawing volume data. Thanks for your help in advance. Regards, Hyeong-Tae Jou ----------------------- Korea Institute of Ocean Science and Technology

2 2

Center
by Sebastian Mock 20 Feb '13

20 Feb '13

Hi, is it possible to center a molecule absolute? I have to molcules and want to center one in the absolute center of the other one. Or e.g. center both in coordinate system on 0.0,0.0,0.0 The "center" command only centers the camera. But I need to move the molecules, not the camera view. Greets Sebastian

2 1

New user-visualizing coulombic
by Minor, Armond 20 Feb '13

20 Feb '13

Hello, I am just starting out using the program for a project with my Biochemistry professor. We are trying to develop a simple procedure to visualize the Coulombic surface of short DNA sequences. I have very little experience working with Chimera and do not know if I am going about it in correct way that will yield meaningful data. I have tried following the instruction but must of them seem to be for people who are more familiar with the programs than I am. Basically what I have tried is opening a pdb file, running PDB2PQR, opening the pqr file then running APBS on that. I am not sure what to do with the .dx file that comes out and how to use it to color the surface. If I use it to color the Electrostatic potential map I get a range of values that seem to be not what my professor is expecting. If I instead use the coulombic surface tool I get values like she expects but I am not sure if these are connected to the .dx file or just the pdb2pqr file. Any help would be greatly appreciated thank you. Armond Minor Student, Biochemistry, SUNY Oneonta

3 5

Draw schemas with Chimera ?
by Benjamin SCHWARZ 20 Feb '13

20 Feb '13

Hi list, I wonder if it is possible to draw "simplified schemas", such as those that can be found in biology publications where a protein complex is represented by a superimposition of ellipses, each ellipse representing a different protein in the complex, and their 2D placement reflects their known interactions in the complex (cf, for instance http://www.erasmusmc.nl/proteomics1/files/PBAP.jpg). This question triggered several interrogations : 1.) Is it possible in Chimera to draw 2D ellipses that would always reorient towards the screen as the scene rotates the same way the labels do 2.) Is it possible to draw ellipsoids ? 3.) Is it possible to save a picture in SVG format ? Thanks for your help, and thanks once more for the wonderful tool you provide us --Ben

3 3

Drug-Protein Interaction
by kanika sharma 20 Feb '13

20 Feb '13

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*

3 5

2. Unit of electrostatic surface coloring within Chimera
by Boaz Shaanan 19 Feb '13

19 Feb '13

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(a)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(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Tuesday, February 19, 2013 7:53 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 118, Issue 20 Send Chimera-users mailing list submissions to chimera-users(a)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(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)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(a)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(a)h-da.de> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] Algorithm for areaSAS calculations Message-ID: <0781A55E8298FD4CBCAAA70C4AF2EDB6350489B0BA(a)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(a)external.merckgroup.com To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Unit of electrostatic surface coloring within Chimera Message-ID: <OF57DE4D54.6BC4EDF1-ONC1257B16.004734C6-C1257B16.004845D9(a)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(a)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. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. 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(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Drug-Protein Interaction Message-ID: <CAAo-yeL3vs_KH76GdFQT0iP39-K2zcYRuBvmUG8pgfTxt8ivAQ(a)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*

1 0

Unit of electrostatic surface coloring within Chimera
by Florian.Capito＠external.merckgroup.com 19 Feb '13

19 Feb '13

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 Grüssen/ With best regards Florian Capito MM-PTD-New Downstream Darmstadt Location A17/217 Postcode: A046/509 Phone: +49 6151 72-7168 Email: florian.capito(a)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. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer.

2 1

meaning of evidence in PDB/UniProt Info
by Luis M. Sánchez 19 Feb '13

19 Feb '13

In PDB/UniProt Info some features have a line with a numeric value for evidence. For example: N-linked (GlcNAc...) (complex) evidence=1 2 3 7 8 9 10 12 What do those numbers means? Thanks for a great program and best regards -- Luis M. Sánchez

2 2

Algorithm for areaSAS calculations
by Korbus, Michael 19 Feb '13

19 Feb '13

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

2 1

Chimera-users February 2013