- 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 08 Jul '08

08 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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Tile Structure default view
by Eduardo Sanz Garcia 07 Jul '08

07 Jul '08

I would like to request an extra feature for chimera, if it is not there already. I normally open multiple structures in chimera and then I use the "Tile Structure" button to visualize them in an array. This is nice, for example, to visualize the evolution of a cryo-EM 3D reconstruction. I would like that chimera could open multiple structures in an array view by default. Could a "Default view" button be added to the Tile Structure window, so that the "Border scale" value setting is saved and then the next time I open several structures they would be displayed in array view? Thank you very much.

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renumbering pdb
by bustik＠gmx.net 05 Jul '08

05 Jul '08

dear chimera-users, i am just starting to use chimera, so this will be a really simple question to you (although i didn't find anything about this in the manual...): is there a simple command to change residue numbers in a pdb file (i built up a homology model and want to elevate all residue numbers in the model the same amount)? thanks in advance sebastian -- Sebastian Kruggel Eppendorfer Weg 17d D 20259 Hamburg fon: +49 (0)40 4192 9579 mobil: +49 (0)151 1789 2232 e-mail: bustik(a)gmx.net

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graphics performance: amira v. chimera
by Matthew Dougherty 03 Jul '08

03 Jul '08

I loaded a MRC file, isosurfaced it, gave it a transparency around 0.48, and generated a vrml in chimera. I loaded the vrml into amira. initial comparison: I reloaded the vrml into chimera, I turned off the fog on chimera, moving the object around the refresh rate seems to be around 8 fps. On amira it seems to be around 24fps. results: The graphics on Chimera seems to be better during the rotation of transparent objects: full rotation in chimera is flawless, full rotation in amira results in flipping of the object (vertices in back quantum-ly jump to the front, front vertices go to back, looks like a z buffer error) periodically at 180 degrees, making it useless for many camera positions. Any comments or suggestions?

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OS X Chimera
by Christopher Vavricka 02 Jul '08

02 Jul '08

I have OS X 10.4.11 and I am trying to run Chimera. When I start Chimera.app it tells me to start X windowing system (Apple X server). X11 is not located in my applications/utlilties folder. How do I get this application? Is it on my installation disc for OS X? Regards, Chris Vavricka

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(no subject)
by Levy, Hazel C. 02 Jul '08

02 Jul '08

Hi, I am a postdoctoral researcher and an enthusiastic Chimera user. We are trying to finish up a manuscript to submit tomorrow to JSB and we have been frantically trying to figure out how to convert from Chimera's "contour level" to the more conventional "sigma level" for density map viewing at different noise levels. We understand that the higher the contour level the smaller the map volume displayed (less noisy), but we are not quit sure how to report this as a sigma level. Each map that we are comparing has a different contour range assigned, I am wondering if sigma level corresponds to some proportion of the maximum volume. Please let us know how to do this conversion or please point us in the direction toward the person that can help us. Thanks you so much...this information will settle a long-standing mystery for us. Hazel Levy

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Mutate by D- res...
by Yasser Almeida Hernández 30 Jun '08

30 Jun '08

Can Chimera mutate by D-residues? If this is possible, how i can do it? Thanks... -- Yasser Almeida Hernández Estudiante, 4to Año Bioquímica Facultad de Biología Universidad de la Habana

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Dummy atoms
by Jean Didier Pie Marechal 30 Jun '08

30 Jun '08

Dear all, I think the question was already posted but I can't find it. I would like to make an atom I placed as an helium to a Dummy: What is the corresponding atom type in Chimera? All the best JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimarts, Juny 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 21 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: how could u know the order of atoms? (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 23 Jun 2008 14:22:31 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] how could u know the order of atoms? > To: Kamal Al Nasr <k_alnasr(a)yahoo.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <8901DE4E-D117-4B18-968B-D3095AD735D4(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote: > > > Dear Sir/Madam, > > > > I am using Chimera viewer..and it is a great viewer ever... > > Thanks! I'm glad you like it. > > > I kindly have a question... how could you know (from PDB file) > the > > coorect bonding between atoms? I mean that how could you know > that > > this atom is connected with CA not N nor C.....do u have all > these > > bonds stored already in a database? or you use atom positions to > > determine that? > > For standard amino and nucleic acids, Chimera has templates > containing the correct connectivity. For non-standard residues it > bases the connectivity on inter-atomic distances, with a few added > heuristics (e.g. hydrogens can only have one bond). > > The templates are accessible in the Python layer with the > chimera.restmplFindResidue() function. You can look in the > Rotamers > extension for examples of its use. The distance-based connectivity > > function is also available for an entire molecule as > chimera.connectMolecule(). It takes the molecule as its only > argument and adds bonds to it. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

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"Floating exception" error message
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

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"Floating exception" error message
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

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(no subject)
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

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hydrophobic pocket
by bala 27 Jun '08

27 Jun '08

Dear Chimerian's, How do i detect hydrophobic pockets in a protein using chimera ?. Thanks in advance, Bala

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Re: [Chimera-users] Question about avi files in chimera
by Tom Goddard 27 Jun '08

27 Jun '08

Hi Jaap, The AVI files produced by Chimera movie recorder use the MSMPEG-4v2 (Microsoft MPEG4 version 2) video codec and the encoding is done by the open source ffmpeg program. The file size depends on the movie recorder "bit rate" setting (default 2000 Kbits/sec = 250 Kbytes/sec = 15 Mbytes/min). Changing this setting allows you to trade off file size versus image quality. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… Tom Jaap Brink wrote: > > Hi Tom, > > > > I was wondering given the size difference in avi files that chimera > generates versus other program (Video Edit Magic for instance), which > video codec is being used? I searched the list of embedded software > packages in chimera and found the library of libavcodecs. > > > > Thanks in advance, > > > > Jaap >

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upcoming production release
by Greg Couch 26 Jun '08

26 Jun '08

Hello, We are currently getting ready to put out another chimera production release. At this point, we consider the daily builds to be release candidates, so please download one and try it out. Not all of the daily builds will be production releases, in particular, the Mac OS X Aqua version is not quite ready, and will be a snapshot release. And the Linux off-screen OpenGL version is experimental and will probably stay as a daily build. Greg Couch UCSF Computer Graphics Lab Daily builds: <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> New features: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>

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Re: [Chimera-users] how to draw lines in Chimera
by Elaine Meng 25 Jun '08

25 Jun '08

On Jun 24, 2008, at 4:24 PM, Qing Xie wrote: > Hi, > I'm trying to draw a bunch of axes from center (0,0,0). I could do > this > in 'O' by calling this macro: > > begin_object symax > colour blue > stick_xyz 139.05, -0.00, -16.25, -139.05, 0.00, 16.25, 0.25 > stick_xyz -111.40, 43.12, 73.02, 111.40, -43.12, -73.02, 0.25 > stick_xyz -107.48, 80.74, 39.10, 107.48, -80.74, -39.10, 0.25 > stick_xyz -66.72, 119.11, -31.00, 66.72, -119.11, 31.00, 0.25 > stick_xyz 50.41, 73.78, -107.77, -50.41, -73.78, 107.77, 0.25 > stick_xyz 100.65, 0.20, -97.31, -100.65, -0.20, 97.31, 0.25 > stick_xyz -68.88, 113.16, 45.26, 68.88, -113.16, -45.26, 0.25 > stick_xyz -39.02, 80.98, -107.34, 39.02, -80.98, 107.34, 0.25 > stick_xyz 10.15, 0.20, -139.64, -10.15, -0.20, 139.64, 0.25 > stick_xyz 50.47, -73.42, -108.00, -50.47, 73.42, 108.00, 0.25 > end_object symax > > Since I had to use some features in Chimera, do you know what > commands I > should combine to do similar things above? > Thank you! > Sincerely, > Qing Hi Qing, You can make a BILD file defining the objects, for example containing the following: .color medium blue .cylinder 139.05 -0.00 -16.25 -139.05 0.00 16.25 1 .cylinder -111.40 43.12 73.02 111.40 -43.12 -73.02 1 .cylinder -107.48 80.74 39.10 107.48 -80.74 -39.10 1 .cylinder -66.72 119.11 -31.00 66.72 -119.11 31.00 1 .cylinder 50.41 73.78 -107.77 -50.41 -73.78 107.77 1 .cylinder 100.65 0.20 -97.31 -100.65 -0.20 97.31 1 .cylinder -68.88 113.16 45.26 68.88 -113.16 -45.26 1 .cylinder -39.02 80.98 -107.34 39.02 -80.98 107.34 1 .cylinder 10.15 0.20 -139.64 -10.15 -0.20 139.64 1 .cylinder 50.47 -73.42 -108.00 -50.47 73.42 108.00 1 and open it in Chimera to create the objects. I also attached this below as the file sticks.bild to be opened directly in Chimera. I didn't think 0.25 looked that good, but you can edit the file to whatever radius (and color, etc.) that you want. The BILD language also includes many other objects: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.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

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Re: [Chimera-users] find levels and morph conformations
by Thomas Goddard 24 Jun '08

24 Jun '08

Hi Ed, The Morph Conformations tool works with submodels. It will not work between two models or submodels that have different numbers of chains. The error message you get means that you are giving it models with different numbers of chains. Tom Edward Brignole wrote: > Tom, > > ... I'd like to use morph conformations between two pdbs each > composed of the same submodels/chains. I've tried to do this through the > dialog but it displays an error telling me "cannot interpolate the > models have different numbers of chains". The only way I can see to do > this is to write the pdb as a mol2 so that all atoms are in a single > model without submodels, open the mol2, and run morph conformations. > Is there another method or is this the simplest? > > Thanks, > Ed

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