- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [chimera-dev] 2-D projection of volume in Chimera
by Tom Goddard 04 Mar '13

04 Mar '13

Hi Jesus, There is a tricky way to do a projection of a map in Chimera. You can use the map binning capability. For example, if map #0 has 144 planes along the z axis I can add all those planes with vop bin #0 binsize 1,1,144 This can be done with a dialog instead of a command using Tools / Volume Data / Volume Filter, filter type bin and type in the bin size as 1 1 144. You also want a view along an axis other than x, y or z it sounds like. To do that you would resample the map on a new rotated grid so that the z axis is along the desired projection axis. The following video shows how to use the Chimera volume dialog subregion selection capability to do that http://www.cgl.ucsf.edu/chimera/videodoc/rotatedbox/ Tom -------- Original Message -------- Subject: Re: [chimera-dev] 2-D projection of volume in Chimera From: Elaine Meng To: Jesus Montoya Date: 3/4/13 11:59 AM > Hi Jesus, > Sorry, I don't think there is a way, currently. Here is the most recent information I could find on that topic: > > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005124.html> > > Regards, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > p.s. For future questions, you may want to send to chimera-users(a)cgl.ucsf.edu (chimera-dev is mainly for programming questions). > > On Feb 26, 2013, at 5:28 PM, Jesus Montoya wrote: > >> Hi, >> >> Is there a way to project a 3-D volume into a single 2-D image plane in Chimera? >> >> For example, I want to load a volume twice into Chimera and view the two copies side by side in an identical orientation (manually set by rotating the volumes with the mouse). >> Then, I want to view one of them as a 2-D projection along the axis that comes out of the screen. >> >> While a "solid" representation of the volume is similar, it is not exactly what I need... >> >> Thanks! >> >>

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Thank You
by Noel Pace 04 Mar '13

04 Mar '13

thank you to all of you who helped me in compiling a DEMO which I will be using for my dissertation project. I will be making this DEMO public once it has been tested and modified accordingly. Noel Pace Malta

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Question about using the volume command
by Henning Stahlberg 04 Mar '13

04 Mar '13

Hi, The command volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid doesn't work on my computer (OSX), Chimera (Version 1.7, build 38197) requests that "Solid level must be <data-value,brightness-level>". What am I doing wrong? Thanks for any suggestions, Henning.

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Work with Volumetric Data
by esserlo＠helix.nih.gov 28 Feb '13

28 Feb '13

Hi, I am using Chimera to render electron density in gaussian cube files and it works well. I am wondering though whether it is possible to integrate the e-density inside the current volume as defined by the closed surface. If there are people with expertise in this field of volumetric data (processing), I would be interested in obtaining C or C++ libraries that provide functions to calculate volume, surface areas etc. Thanks, Lothar

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vop morph map color
by Steve Reichow 28 Feb '13

28 Feb '13

Hi, I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1: vop morph #0,1 The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following: vop morph #0,1 volume #2 color khaki This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks! I am using Chimera Version 1.6 Mac OSX -- ~~~~~~~~~~~~~~~~~~~~~~ *Steve Reichow *Email: slreichow(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~

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Re: [Chimera-users] Question about using the volume command
by Elaine Meng 28 Feb '13

28 Feb '13

Hi Henning, Best to share with the list (cc'd here)... One problem with the solid level is that the second number should be between 0 and 1. However, even when I tried that, I got the same error, so I'm guessing that is a bug. The second issue may also be a bug: I don't know why the style does not change directly between surface and mesh. I'll try a simple test case and submit a bug report for that one too. Sorry for the problems, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 28, 2013, at 12:38 PM, Henning Stahlberg wrote: > Hi Elaine, > > Yes, you are right with the solid level option. > But I still don't understand this. > This here doesn't have any effect, I give the command on the command line: > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > No change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > No change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > No change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > No change of display. > > This leads to an error message in the log window: > volume #5 level 2.30,2.6 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > TypeError: 'NoneType' object is not iterable > File "/Applications/Chimera.app/Contents/Resources/share/VolumeViewer/solid.py", line 213, in update_coloring > cmap, cmap_range = self.colormap() > > (I just submitted a bug report on the above.) > > > And this gives an error message after the "solid" command, but after that the other commands appear to work: > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > Solid level must be <data-value,brightness-level>; no change of display. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > The display changes to surface view. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > Solid level must be <data-value,brightness-level> > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > The display changes to mesh view. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > Solid level must be <data-value,brightness-level> > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface > The display changes to surface view. > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid > No change of display. Error message: > Solid level must be <data-value,brightness-level> > volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh > The display changes to mesh view. > > Do you have an example how to change the display from "mesh" to "surface"? > > Thanks for your help so far, > > Henning. >

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Question about using the volume command
by Henning Stahlberg 28 Feb '13

28 Feb '13

Hi, The command volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid doesn't work on my computer (OSX), Chimera (Version 1.7, build 38197) requests that "Solid level must be <data-value,brightness-level>". What am I doing wrong? Thanks for any suggestions, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62

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Problem with coloring blobs
by Terry Lang 25 Feb '13

25 Feb '13

Hey Guys, I am trying to compare a before-and-after active site. I have the CASTp pockets for each active site (2PXR pocket id 17 and 3H47 pocket id 18). However, both pocket representations have little hang-overs that are not part of the continuous pocket; I'd really just like to show the continuous pocket. I am trying to mask the overhangs and am failing. I tried coloring them white but they block the pocket. I then tried setting them to be transparent but now you can see through the entire blob (I sense a bug there). I can't figure out how to delete just a part of the blob. Other suggestions? Thanks! Terry

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Help with energy minimization
by Kirsten Reimer 25 Feb '13

25 Feb '13

Hi there, I've been using Chimera for several weeks now and I'm having some trouble with the energy minimization tool. I'm attempting to model a small RNA structure, and I keep getting the same error (using all default settings). To be honest I don't know enough about the program to feel comfortable changing the settings. I've attached the .pdb file that I'm using as well as the error message. Is there some way I could get help with this? Thank you! Kirsten Reimer [cid:f40e0cbe-7688-410c-a025-32c781322ff6@unbc.ca] University of Northern British Columbia

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Error on Ubuntu 12.04 in VirtualBox uder Win7 with Nvidia Graphic Card
by Lingyu 25 Feb '13

25 Feb '13

Hi all, I have tried to open Chimera on Ubuntu 12.04 LTS system, which is installed under Win7 system through VirtualBox. The graphic card is from Nvidia company. And I've got below error: abc@ubuntu:~$ chimera X Error of failed request: BadDrawable (invalid Pixmap or Window parameter) Major opcode of failed request: 72 (X_PutImage) Resource id in failed request: 0x480006c Serial number of failed request: 1444 Current serial number in output stream: 1450 Then I tried "chimera --debug-opengl", after I disable all OpenGL features, still it didn't work. Here is the OpenGL information generated by "Chimera Debug Graphics Driver" interface: OpenGL information: Vendor: VMware, Inc. Renderer: Gallium 0.4 on llvmpipe(LLVM 0x300) Version: 2.1 Mesa 8.0.2 OS: Linux 3.2.0-23-generic x86_64 I have seen a previous post "answerpot.com/showthread.php?4472311-Chimera+on+a+virtualbox", which asked a similar question. Can this problem be solved? Thanks in advance! Lingyu

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question about stereo pairs
by Kristin Parent 25 Feb '13

25 Feb '13

To whom it may concern, When creating a stereo image in chimera using the camera view options, what is the default degree of rotation between the left and right image? Can this be changed? Thank you in advance. Kristin -- Kristin N. Parent, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology Michigan State University 603 Wilson Road Room 519 Biochemistry Building East Lansing, MI 48824 Office phone: (517) 432-8434

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Chimera Troubleshoot start-up
by Anthony Vu 25 Feb '13

25 Feb '13

Dear Sir or Madam, I am a undergraduate student at the University of Houston, pursuing a major in Chemistry. The biochemistry class of this major requires to use the Software name Chimera for writing the assigned term paper due at the end of April. However, this will be the very first time to use it. And I do not know how to use it properly, Can you help me in this troubleshoot? Is there any active tutorial in this software? Anthony Vu P.S. Please respond to this email immediately!

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session file/HID
by Dougherty, Matthew T 25 Feb '13

25 Feb '13

I am developing some USB HID midware code utilizing keyboard shortcuts. This is being done using controllermate to generate an organized system of text strings across devices, and corresponding additions in standard_accelerators.py One thing I need to write is an automated method that will increment keyframe names to be used for savepos. On a more general level, how do I create variables in standard_accelerators.py that willbe saved in the session file, so I can retrieve them at a later session? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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spectrum prediction
by francesco oteri 24 Feb '13

24 Feb '13

Dear chimera users, I have been studying the association between a protein and an electrode by MD simulation. In particular I am interested in the relative orientation in respect to the surface. I only have the PM-IRRAS spectrum of the complex. I am wondering if someone knows a method or a software that simulate the PM-IRRAS spectrum or the infrared spectrum of a protein. Thank you in advance, Francesco

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NVIDIA graphics cards: thanks
by compchem compchems 23 Feb '13

23 Feb '13

Greg, Lionel, thank you very much for your kindly help. Your answers are just what I was looking for. My best wishes to you. Dmitry.

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nvidia graphics cards
by compchem compchems 22 Feb '13

22 Feb '13

Hi, What nvidia graphics cards are recommended to work with UCSF Chimera under Debian Linux? What are better - quadro series or geforce? Unfortunately I have seen only special topics about, for example, 3d graphics. So I don't have holistic view of the subject. Many thanks in advance. Dmitry.

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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.

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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

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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

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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

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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

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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*

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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*

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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.

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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

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