- Chimera-users - RBVI Mailing Lists

Reduce mesh density?
by Maja Divjak 13 Mar '13

13 Mar '13

Hello Chimera, I would like to export some protein models in obj format and I was wondering if there is some way of reducing the mesh complexity when I do that please? I am using the models for animations in Maya and when I use the mesh reduce feature in Maya, Im getting some rather odd results, so was wondering if I can actually simplify the models first in Chimera? Thank you for your time, Maja Divjak Walter and Eliza Hall Institute, Melbourne, Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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Re: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it?
by Elaine Meng 11 Mar '13

11 Mar '13

Hi Boaz, Sounds perfectly reasonable to me -- that CASTp surface is actually just parts of the molecular surface calculated by Chimera (using MSMS). Although the area/volume values in the pocket list dialog are those calculated by castp, the display is the Chimera molecular surface for just the set of atoms reported by castp to comprise the pocket, minus any disconnected bits. After displaying the surface for any pocket, you can see the MSMS surface model for the protein listed in the Model Panel, for example. Thus you can feel free to use any of the surface-coloring approaches in Chimera that you like (APBS ESP, Coulombic ESP, residue conservation, etc. etc.), and just uncheck "colored by hydrophobicity" in the CASTp pocket list dialog. That option was just provided for convenience because people often like to evaluate pocket hydrophobicity. I hope this helps, 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 Mar 11, 2013, at 3:14 PM, Boaz Shaanan wrote: > Hi, > I'd like to colour a surface generated by castp by electrostatic potential rather than by the hydrophobicity values. I read in the .dx file from apbs and colour accordingly. The result makes sense to me in terms of +ve/-ve values,as obtained by "walking" on the surface (using the mouse) and taking into account the low dielectric values that apbs assigns to residues inside the protein during the calculation. Am I missing something about the way chimera handles the .dx file and doing something completely insane? > Thanks for your input. > Boaz

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ViewDock: flexible receptor residues in different chains
by Jérôme Hénin 11 Mar '13

11 Mar '13

Hi everyone, When viewing Autodock Vina results in ViewDock, I hit a problem that I think is due to insufficient parsing of the PDBQT file. I have flexible receptor residues in two identical chains, say, Leu15 in chain A and Leu15 in chain B - these sidechains are part of the PDBQT file. However, ViewDock apparently ignores chain identifiers in that file, so it is unable to distinguish between these two residues, and it creates mangled bonds linking them while some other bonds are missing. I don't know how much work it would be to parse chain identifiers from the PDBQT file, I would have a go at it if I was more of a Python person, but I really am not. Best, Jerome

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Re: [Chimera-users] internal coordinates (z-matrix) in chimera (Chinh Su Tran To)
by Visvaldas K. 08 Mar '13

08 Mar '13

Dear Chinh, I am not sure if you can do multiple (batch) conversions in chimera, but the tool you seek could be openbabel, using command line or openbabel gui. On the command line you can issue, for one molecule (it's for Linux): babel my.mol my.gzmat This creates Gaussian style Bond-Angle-Torsion a.k.a. Z-matrix coordinates. For batch processing, you can use: babel *.mol -ozmat -m Best regards, Vis

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comparing angles in 28 structures
by Elaine Meng 08 Mar '13

08 Mar '13

Hi Paola, Other than measuring the angle in each one, the only other idea I have is to open the 28 structures as a single trajectory in the MD Movie tool. You can only do that if each file has the same atoms with the same names. Then you can plot the angle across the 28 "frames" in the trajectory. However, if the structures do not have the exactly the same atoms, I don't know any other method than opening and measuring each one individually. There are several trajectory input options including multiple PDB files, although in that case you would need to give the files names including numbers and ending in ".pdb". The MD Movie tool including input options is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h…> After you open the trajectory, you can use the MD Movie controller to "play" through the 28 frames. You can plot values such as the angle of interest, see the MD Movie menu: Analysis.... Plot <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#p…> I hope this helps, 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. this is a "user" question, so chimera-users(a)cgl.ucsf.edu (CC'd here) is a better place to send it than chimera-dev, which is for programming questions On Feb 21, 2013, at 12:30 PM, Paola Peshkepija wrote: > Good afternoon, > I am a new chimera user. I am using Chimera to look at the backbone dihedral angle variations for 28 GFP structures. I was wondering if there is a way I can look at the changes in dihedral angles using the 28 structures altogether rather than looking at each structure individually. Please, let me know. > Thank you in advance for your help! > Paola

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Chimera Tutorial in Boston area
by Scooter Morris 06 Mar '13

06 Mar '13

Hi all, I'll be teaching a Chimera tutorial scheduled as part of the VizBI conference <http://vizbi.org/2013/> in Cambridge, MA. See the Program <http://vizbi.org/2013/Program/> for information about what we'll be covering, or just bring your favorite structure and we'll explore some of Chimera's new features. -- scooter

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Re: [Chimera-users] How to fork/specify a web browser
by Greg Couch 06 Mar '13

06 Mar '13

Forgot to include list in reply. -------- Original Message -------- Subject: Re: [Chimera-users] How to fork/specify a web browser Date: Wed, 6 Mar 2013 09:23:11 -0800 From: gregc(a)cgl.ucsf.edu To: Yasha Karant <ykarant(a)csusb.edu> > For certain of the tutorials, help files, etc., Chimera linux displays a > comment to use a web browser in order to use a URL file://foobar . > How does one configure Chimera to automatically use a specified browser > to diplay the URL generated by Chimera? I have not been able to find a > preferences setting for this, nor an answer on the web or in the Chimera > manuals/help. I have not perused the source code for Chimera to find a > solution. > > Yasha Karant > Chimera uses Python 2.7's webbrowser module to open files in a web browser. For Linux, if you are using a GNOME or KDE desktop environment, then it will use the default browser that is configured for that environment. Otherwise, it looks for firefox (and derivatives), kfm, konqueror, galeon, epiphany, skipstone, opera, mosaic, and grail(!). You can override the the search order with the BROWSER environment variable. You may have noticed that Google's chrome is not on that list. Chrome support is included in Python 3's webbrowser module. But, that support would only be needed if you are not using a GNOME or KDE desktop environment. I will look into how much work it would be to backport Python 3's webbrowser module to Chimera. HTH, Greg

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How to fork/specify a web browser
by Yasha Karant 05 Mar '13

05 Mar '13

For certain of the tutorials, help files, etc., Chimera linux displays a comment to use a web browser in order to use a URL file://foobar . How does one configure Chimera to automatically use a specified browser to diplay the URL generated by Chimera? I have not been able to find a preferences setting for this, nor an answer on the web or in the Chimera manuals/help. I have not perused the source code for Chimera to find a solution. Yasha Karant

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Guessing net charge
by Miro Moman 05 Mar '13

05 Mar '13

Hello, When computing partial charges in Chimera, the user is prompted to indicate the net charge of the "non-standard" residues. However, more often than not, the suggested value is correct. I would like to know how this guess is made and whether or not the net charge of small organic molecules can be guessed in batch mode using Chimera (or other tools). Best regards, Miro Moman -- http://www.e-moman.eu

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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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