February 2013 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Re: [Chimera-users] Chimera on a virtualbox
by Greg Couch 04 Apr '13

04 Apr '13

(No real need to involve the list, we'll figure this out and report back) -------- Original Message -------- Subject: Re: [Chimera-users] Chimera on a virtualbox Date: Tue, 05 Feb 2013 17:22:51 -0800 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: chris.wood(a)stfc.ac.uk It appears as if you missed the: export LD_LIBRARY_PATH=$CHIMERA/lib before running gdb because the import of libgfxinfo.so failed. And there should be a space between "break" and "_exit" in the gdb command. -- Greg On 02/05/2013 04:38 PM, chris.wood(a)stfc.ac.uk wrote: > > Hi Greg, > > I know that doing anything with graphics within virtual machines is > not always a brilliant idea, but I have seen Chimera work in > VirtualBox and I wanted to get to the bottom of why mine doesn't... > > I've got the latest graphics driver on my host (and I run Chimera > successfully on it anyway). I've run the commands you suggested, with > the following output > > $ gdb $CHIMERA/bin/python2.7 > > GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04 > > Copyright (C) 2012 Free Software Foundation, Inc. > > License GPLv3+: GNU GPL version 3 or later > <http://gnu.org/licenses/gpl.html> > > This is free software: you are free to change and redistribute it. > > There is NO WARRANTY, to the extent permitted by law. Type "show copying" > > and "show warranty" for details. > > This GDB was configured as "x86_64-linux-gnu". > > For bug reporting instructions, please see: > > <http://bugs.launchpad.net/gdb-linaro/>... > > Reading symbols from /home/ccw/.local/chimera-1.7/bin/python2.7...done. > > (gdb) break_exit > > Undefined command: "break_exit". Try "help". > > (gdb) run $CHIMERA/share/__main__.py --debug > > Starting program: /home/ccw/.local/chimera-1.7/bin/python2.7 > $CHIMERA/share/__main__.py --debug > > [Thread debugging using libthread_db enabled] > > Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". > > Traceback (most recent call last): > > File "/home/ccw/.local/chimera-1.7/share/__main__.py", line 69, in > <module> > > value = chimeraInit.init(sys.argv) > > File "/home/ccw/.local/chimera-1.7/share/chimeraInit.py", line 594, > in init > > import chimera > > File "/home/ccw/.local/chimera-1.7/share/chimera/__init__.py", line > 16, in <module> > > from _chimera import BBox, Camera, Color, ColorGroup, > DirectionalLight, LODControl, Lens, LensViewer, Light, Material, > MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, > OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, > PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, > TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform > > ImportError: libgfxinfo.so: cannot open shared object file: No such > file or directory > > [Inferior 1 (process 4025) exited with code 01] > > (gdb) bt > > No stack. > > I guess the lack of libgfxinfo.so is fairly significant, and I assume > that the result from bt is all part of the problem? > > Thanks, > > Chris > > *From:*chimera-users-bounces@cgl.ucsf.edu > [mailto:chimera-users-bounces@cgl.ucsf.edu] *On Behalf Of *Greg Couch > *Sent:* 05 February 2013 23:26 > *To:* Chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] Chimera on a virtualbox > > (Forgot to send reply to whole list) > > -------- Original Message -------- > > *Subject: *** > > > > Re: [Chimera-users] Chimera on a virtualbox > > *Date: *** > > > > Tue, 05 Feb 2013 13:51:47 -0800 > > *From: *** > > > > Greg Couch <gregc(a)cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu> > > *To: *** > > > > chris.wood(a)stfc.ac.uk <mailto:chris.wood@stfc.ac.uk> > > Hi Chris, > > So what are you trying to do with Chimera inside a virtual machine? > Presumably, you're not trying to use it graphically because > virtualized graphics performance is usually abysmal. Chimera benefits > immensely from direct access to the graphics hardware. So that leaves > using Chimera as a server, and for that the headless version of > Chimera is usually better -- the headless version uses a software > implementation of OpenGL and thus avoids any driver issues. > > That said, this bug is still likely to be related to OpenGL support in > VirtualBox. Make sure the computer that VirtualBox is running on has > an up-to-date OpenGL graphics driver. It doesn't matter what > VirtualBox does if the underlying system has a bad graphics driver. > > To confirm that the bug is in the graphics driver, get a backtrace of > where the error occurs by using gdb as follows in a Terminal window > (and assuming there is a symbolic link to the chimera binary on your > path): > > % export CHIMERA=`chimera --root` > % export LD_LIBRARY_PATH=$CHIMERA/lib > % gdb $CHIMERA/bin/python2.7 > (gdb) break_exit > (gdb) run $CHIMERA/share/__main__.py --debug > (gdb) bt > > The '%' and '(gdb)' parts are the shell and gdb prompts, > respectively. The output from the bt command will probably be in > Chimera's molecular drawing code (as opposed to drawing the UI). If > you need help interpreting the chimera backtrace, you can send it to me. > > HTH, > > Greg > > On 02/05/2013 12:48 PM, chris.wood(a)stfc.ac.uk > <mailto:chris.wood@stfc.ac.uk> wrote: > > Hello all, > > I'm trying to run Chimera on VirtualBox. The installation > completes fine, but when I try and run the program (|cd| to the > bin directory and run |./chimera|) I see > > X Error of failed request: BadDrawable (invalid Pixmap or Window > parameter) > > Major opcode of failed request: 72 (X_PutImage) > > Resource id in failed request: 0x480006a > > Serial number of failed request: 1382 > > Current serial number in output stream: 1388 > > I've tried enabling / disabling hardware virtualization & 3D > acceleration, but to no avail. Although people do seem to have > problems with chimera on a virtualbox, it normally seems to be a > problem with OpenGL, which this doesn't seem to be. > > Has anyone seen this error before? Is there anything else I'm > missing? I can't even work out if it's a hardware, VirtualBox, or > OS problem... > > ** > > *System:* > > VirtualBox 4.2.4 > Guest additions 4.2.4 > > Guest OS: Ubuntu 12.04 > Host OS: Windows 7 professional > > Thanks in advance! > > Chris > > ------------------- > > Dr Chris Wood > > STFC Rutherford Appleton Laboratory > > Didcot > > OX11 0QX > > chris.wood(a)stfc.ac.uk <mailto:chris.wood@stfc.ac.uk> > www.ccpem.ac.uk <http://www.ccpem.ac.uk> > > > Tel: +44(0)1235 567864 > > Tel: +44(0)7909 586624 > Fax: +44(0)1235 567801 > > -- > Scanned by iCritical. > > > -- > Scanned by iCritical. > >

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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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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 01 Mar '13

01 Mar '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 01 Mar '13

01 Mar '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 01 Mar '13

01 Mar '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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Chimera-users February 2013