March 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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deleting entries from rapid access list (plain text format)
by Boaz Shaanan 02 Apr '13

02 Apr '13

Hi, Is there a way to delete entries from the rapid access list without having to edit the preferences file? If there isn't such a way, is it possible to request to add such feature? Thanks, 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

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Weird looking stretch in ribbon presentation
by Boaz Shaanan 30 Mar '13

30 Mar '13

Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? Thanks, 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

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distance label decimal places
by matheus froeyen 28 Mar '13

28 Mar '13

Hi, does someone know how I can control the number of decimal places shown in a distance label using the command line? thanks! mathy

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transparency command unrecognized
by Corey Fugate 28 Mar '13

28 Mar '13

I am following the Chimera Movie Making tutorial, but when I use the command "transp 80,r" the command line tells me, "Unrecognized command: "transp". I tried replacing "transp" with "transparency" and got the same result. Can someone explain to me why this isn't working? (I'm using build 1.5.3 on my MacBook. Thanks, Corey

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Reg: Hydrogen Bond Analysis
by Amit Jaiswal 27 Mar '13

27 Mar '13

Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer. -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. ~~~~~~~~~~~~~~~~~~~~~~~~~

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sphere representation for specific atoms
by Xiongzhuo Gao 27 Mar '13

27 Mar '13

Hi, I'm trying to highlight several CA atoms in one protein structure with sphere. I tried a lot followed the suggestions online, but couldn't make that work. Could you please tell me how to do that. Thank you so much. Best, Stephen

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