- Chimera-users - RBVI Mailing Lists

docking sphere visualization
by Trent E. Balius 02 Nov '11

02 Nov '11

Dear Chimera-user list, I believe, currently, Chimera can not visualize docking spheres (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand) files directly, in order to do so, we need to create a pdb file of the spheres and then visualize them. It would be vary helpful for DOCK users if we could visualizes spheres directly from the .sph files produced by sphgen (http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Sphgen) or sphgen_cpp. Radius and color information could then also be displayed. This might be a helpful new feature to be included in a future release of Chimera. Thank you, Trent E. Balius Graduate Student, Rizzo Group, Department of Applied Mathematics and Statistics, Stony Brook University. Office: Math Tower 3-129, Phone: (631) 632-8519 URL: http://www.ams.sunysb.edu/~tbalius/

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MD plotting
by Eric Pettersen 01 Nov '11

01 Nov '11

Hi all, For any of you using Chimera's MD Movie for trajectory playback, I just added the ability to plot atomic distances, angles, and dihedrals for your trajectory. You can click (or drag) on the plot to go to the corresponding frame. You create a plot by using the "Plot" submenu in MD Movie's Analysis menu. Most of the functionality is available in the current daily build, but tomorrow's build will have a couple of additional features: dumping plot values to a file, and showing the numeric value of the plot for the current frame in the list of plots (the value is blanked during playback since updating it slows down playback too much). Feedback welcome. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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alpha helix representation problem
by larif sofiene 29 Oct '11

29 Oct '11

greeting after a MD simulation of an in silico induced mutation A80P (located in an alpha helix) in a monomeric protein i get this strange alpha helix (a wire represented helix) http://imageshack.us/photo/my-images/573/alphahelix.jpg/ is it the induced mutation that break down the alpha 3 helix and disturb orientation of the helix axis or a problem with chimera not recognizing the helix (in sequence tool the helix is no more color filled as alpha helix after inducing mutation) thank you for this piece of art which is CHIMERA :)

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managing CONECT table
by Francesco Pietra 27 Oct '11

27 Oct '11

Hello: In preparing a model comprising various fragments I would like to suppress from the PDB CONECT table two connections to the central transition metal. I wonder whether there are rules for such manipulations. Chimera detects (as a bond) only one of these two connections. thanks francesco pietra

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Re: [Chimera-users] periodic box visualization
by Eric Pettersen 26 Oct '11

26 Oct '11

On Oct 26, 2011, at 4:52 AM, Giovanni Pavan wrote: > Dear all, > when a periodic system is visualized into Chimera (e.g., a periodic > waterbox), is it possible to visualize explicitly the borders of the > periodic box (defined for instance in the last line of coordinate/ > restart files in case of AMBER format structures)? > Last, is it also possible to see the periodic images of the original > box along X, Y & Z axes? How? > I thank you in advance for the support and I look forward to > receiving any feedback from you. Hi Giovanni, I'm sorry but neither of these is currently possible in Chimera. You'll have to use another visualization program (VMD?) if you need these capabilities. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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periodic box visualization
by Giovanni Pavan 26 Oct '11

26 Oct '11

Dear all, when a periodic system is visualized into Chimera (e.g., a periodic water box), is it possible to visualize explicitly the borders of the periodic box (defined for instance in the last line of coordinate/restart files in case of AMBER format structures)? Last, is it also possible to see the periodic images of the original box along X, Y & Z axes? How? I thank you in advance for the support and I look forward to receiving any feedback from you. Bye Giovanni Dr. Giovanni Maria Pavan SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI) Centro Galleria 2, Manno 6928, Switzerland. e-mail: giovanni.pavan(a)supsi.ch skype: giovanni_pavan phone: +41 58 666 65 60

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periodic box visualization
by Giovanni Pavan 26 Oct '11

26 Oct '11

Dear all, when a periodic system is visualized into Chimera (e.g., a periodic waterbox), is it possible to visualize explicitly the borders of the periodic box (defined for instance in the last line of coordinate/restart files in case of AMBER format structures)? Last, is it also possible to see the periodic images of the original box along X, Y & Z axes? How? I thank you in advance for the support and I look forward to receiving any feedback from you. Bye Giovanni

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Fwd: Re: Upgrade your video/graphics driver. hirose
by Greg Couch 25 Oct '11

25 Oct '11

Forgot to send reply to the list. -------- Original Message -------- Subject: Re: [Chimera-users] Upgrade your video/graphics driver. hirose Date: Tue, 25 Oct 2011 15:02:04 -0700 From: Greg Couch <gregc(a)cgl.ucsf.edu> To: HIROSE Junzo <hirose(a)fupharm.fukuyama-u.ac.jp> This is a common error with Intel integrated graphics and older Intel graphics drivers. The solution, if your system is new enough, is to go to the system vendor's website support pages and download (and install) the graphics driver update. Sometimes the graphics driver is referred to as a video driver. Good luck, Greg On 10/24/2011 03:14 AM, HIROSE Junzo wrote: > Dear Sir > > Side View doesn't work. I got the following command in Side View. > > > Unable to share graphics data with main window. > Upgrade your video/graphics driver. > > > How can I resolve this problem? > > > Dr. Junzo HIROSE > > > ****************************************** > > Fukuyama Univ. > JAPAN > > TEL 084-936-2111 > Email: hirose(a)fupharm.fukuyama-u.ac.jp > > **************************************** > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Question
by Anna Starus 25 Oct '11

25 Oct '11

Hello, I am having difficulty to depict some bonds as solid lines or some as dashed lines for the bonds that are coordinated to the metal. For some reason when I changed one bond to dashed all of the bonds also change to that. How could I ungroup the coordinating bonds to the metal and be able to make some of them dashed and some solid? I would greatly appreciate the help. Thank you, Anna

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delegate
by Zoe Cournia 24 Oct '11

24 Oct '11

Hello, I am trying to use the "delegate" command from the Midas program in Chimera, but the error message I get is that "delegate is not yet implemented". Is there an available "Extension Mechanism" in chimera? If not, is it possible to get the source code for Midas in order to compile it and use it with delegate? Thanks a lot for any help. Best Zoe -- ------------------------------- Dr. Zoe Cournia Investigator - Lecturer Level Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece zcournia(a)bioacademy.gr Office: +302106597195 Lab: +302106597568 Cell: +306944223123 -------------------------------

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