- Chimera-users - RBVI Mailing Lists

drawing molecules
by Kathleen.Zocher＠ernaehrung.uni-giessen.de 14 Jul '08

14 Jul '08

Dear Sir or Madam, I`ve just one question concerning some special tools of Chimera. Is it possible to draw small molecules (ligands) within chimera? I can not find some information for this problem in the manual. For further docking experiments I just need a 3D-structure which is minimized (in a mol2 file). Many thanks in advance! Sincerely yours Kathleen Zocher ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Question about bond length modification
by Benjamin G.S. Horsman 14 Jul '08

14 Jul '08

Hello, I have what appears to be simple problem but is I can't find the solution in previous mailing list queries. My problem is that I am unable to modify the lengths of any bonds in a PDB molecule. I am rather frustrated with myself over such a stupid problem, having tried dozens of times over dozens molecules to get it right but to no avail. Any possible solutions from the community? I am using MacpyMol to generate PDB structures and Chimera v1 build 1470. Thanks for any help, Ben

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Re: [Chimera-users] [Chimera-announce] Chimera production release
by Elaine Meng 13 Jul '08

13 Jul '08

Hello Yao, Don't worry, the new versions still include the ability to fit map in map. It is simply that two tools were combined into a new tool with a slightly different name. Changes in this production release relative to the previous one include: "Fit Model in Map" and "Fit Map in Map" (Volume Data) — * merged into new "Fit in Map" tool * can update fit values continuously * can simulate map from atomic coordinates, report map-map correlation current documentation: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ fitmaps/fitmaps.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 12, 2008, at 11:49 PM, Yao Cong wrote: > Hello Chimera developer, > > Appreciate your great efforts to make Chimera an perfect tool for > Cryo-EM study. > > I and many of my colleges notice that in your latest versions, you > omit the "fit map into map" module, which is very convenient in > many cases. Is there a specific reason for that? And we all > consider it will be very helpful if you could add this function > back in your next version, maybe daily release? Otherwise, we still > keep the old version to have that function and meanwhile install > your newer version to enjoy the newer functions. > > Thanks, > Yao > ----------------------- > Yao Cong, Ph.D. >

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Creating abridged multimer
by Francesco Pietra 12 Jul '08

12 Jul '08

I am posting again after having once again subscribed In order to create an abridged multimer made of non covalently bound subunits (from available pdb of subunit) which is the preferable route? (1) Load the monomer, delete substructures, and then assemble an abridged multimer? Are the headers furnished with the monomer OK for the abridged subunit? (2) Build the unabridged multimer and proceed to simplify each subunit the same way? Thanks francesco pietra

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distance measurements on surfaces
by Daniel Hautzinger 11 Jul '08

11 Jul '08

Dear all, from the Volume Visualization Tour, I discovered the topography command that now allows me to dsiplay atomic force microscopy data (basically bitmap images with grey scales representing height). In that way I got some very nice images. I also found out how to scale the voxel size, so the scale of the structures should be correct. To test this, and to be able to add some length markers, I wanted to measure distances on the surface generated by the topography command. But while that seems possible for volume data (by setting markers), I had no success with the surface representation of my data nor the original image (which is handled as kind of a volume, but a single slice) when it came to setting markers or measuring distances in another way. Did I miss anything, or is that just not possible? I am using build number 2509, because of the topography feature. Setting markers is described as working by setting the marker in the first maximum in the line of sight at the click position. For surfaces, you could just take the position of the visible pixel clicked. Or maybe it is possible to convert surfaces to volumes? Thank you for your help Daniel Hautzinger

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changing selection color
by Michael DiMattia 10 Jul '08

10 Jul '08

Hi all, I have a quick question regarding a figure I am trying to make. I have a multi-chain protein loaded with each subunit surface-rendered individually. We wanted to find a way to highlight the outline of one of the subunits in the 3d surface rendering and selecting the surface of the chain works really well for this in Chimera. The familiar green outline highlights the subunit well, even though I realize this is probably not the primary purpose for such highlighting. I imagine it is just to let the user know what is selected. But if i were to use the selection highlighting to show such an outline in a figure, i was wondering if it is possible to change the color of the selection outline from green to any other color or if it is possible to change the width of the outline. I realize it's a long shot, but thought I'd ask anyway in case anyone has tried this before. Many thanks Mike DiMattia

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Chimera production release
by Elaine Meng 10 Jul '08

10 Jul '08

Hi everybody, A new production release, version 1.2540, is now available from: http://www.cgl.ucsf.edu/chimera/download.html#production Many improvements and new features have been added since the previous production release (Nov 2007), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html For the time-challenged, here are just a few of the reasons you may want to use the new version: 1) new fetch types: - comparative models from ModBase - protein pocket data from CASTp database - small molecule structures from Pub3D - small molecule structures built from SMILES strings 2) surface improvements: - increased reliability - surface areas automatically calculated - Actions menu, other tools work on more types of surfaces 3) appearance: - default lighting changed to improve POV-Ray results - larger default scale - helix ribbon insides can be colored separately - 2D labels can include Greek letters and other symbols 4) new tools: Axes, EnsembleCluster, Solvate, Structure Diagram 5) new commands: export, mclip, molmap, perframe, ribinsidecolor, shape, solvate, topography, vop See the release notes for details. The production release includes versions for Windows, Mac/X11, Linux, SGI IRIX, and HP Tru64. The Mac Aqua version has been improved significantly, but for now remains a snapshot download: http://www.cgl.ucsf.edu/chimera/download.html#snapshots Enjoy! The Chimera Team

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Multiscale models and surface coloring
by David Sept 10 Jul '08

10 Jul '08

I need to create a series of images of large protein complexes, and since it is tedious to do this through the menus, I am trying to script this for Chimera. I want to create low-res, EM looking surfaces and color the individual protein chains different colors. So far, I can read in multiple structures and create the surfaces, but I can't figure out how to change the coloring. Here's what I have: ---- test.py ------- from chimera import openModels m = openModels.open('model-1.pdb')[0] import MultiScale d = MultiScale.show_multiscale_model_dialog() d.make_multimers([m]) chimera.viewer.viewAll() ---- test.py ------- The above python script work and makes very nice blobs. I can color the entire structure (say red) by adding something like: d.select_all_chains_cb() d.change_color_cb((1, 0, 0, 1)) but I can't figure out how to select individual chains and color them (not sure how to use select_chains). This also gets more complicated when I load in two structures at the same time and they have common chain letters. Since I found a way to get this (almost) working in python, I've been sticking with it, but if this can easily be done directly using a chimera command file, I'm happy to do that. Any help is appreciated. Thanks, Dave ---------------------------------------------------- David Sept, Ph.D. Associate Professor Biomedical Engineering and Center for Computational Biology Washington University, Campus Box 1097, St. Louis, MO 63130 Phone: (314) 935-8837 Fax: (314) 935-7448 dsept(a)biomed.wustl.edu http://habanero.ibme.wustl.edu

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Coloring different set of marker with different radius
by Bui Khanh Huy 08 Jul '08

08 Jul '08

Hi, I tried to color my EM electron density and thought that if I can color different maker sets with different radii, that would make thing much easierMy idea is to color one set using radius a, then select another set, color with radius b. But then the color from the first set disappeared. . Is there any way to do that? Best regards, Huy

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Mac Chimera in-window menu bars
by Thomas Goddard 07 Jul '08

07 Jul '08

Hi Kevin, The Chimera Aqua version has a menu bar at the top of the screen as normal Mac applications do and also at the top of the graphics window. I agree there should be a preference setting to eliminate the in-window menu bar. Here's the reason for this weirdness. There are 13 Chimera dialogs that have their own menu bars and menus. Use of these involves switching between actions in the main window and the dialog repeatedly. With menus for the active window only shown at the top of the screen this interaction becomes very tedious. For this reason I added menu bars within each Chimera window that has its own set of menus. Those in-window menus don't work very well. If you post one menu then put the pointer over an adjacent menu it will not pop up. An even worse atrocity in Aqua Chimera is that it implements "focus follows mouse". As the pointer is moved over the various Chimera windows the one underneath becomes active. This again was added because common Chimera usage involves switching frequently between windows and the normal Mac "click to focus" behavior is inconvenient for this. We would like instead to use "click through" where the first mouse click on a window both activates that window and presses the button or activates the entry field that was clicked on. I have not been able to do this in Aqua Tk, the windowing toolkit we use. The problem we're facing is that the Chimera user interface with its many windows and frequent switching between windows is poorly suited to the Mac GUI conventions. The in-window menus and focus-follows-mouse mode are a first stab at a compromise solution -- still much to be desired. Tom Kevin Walzer wrote: The latest build of Chimera from 7/3/08 on OS X/Aqua (10.5.4) includes menubars at the top of the screen (the standard OS X behavior) *and* on the main toplevel window itself, as on Windows and X11. This behavior is simply weird--two menus? It can only b e regarded as a bug, not a feature. What purpose does it serve? The correct Mac behavior can be restored by commenting out lines 1470-1476 of tkgui.py. If some of your Mac users are requesting this kind of behavior in menubars, at the very least the non- standard window-based menubar should be a preferences item that can be toggled off.

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