- Chimera-users - RBVI Mailing Lists

Chimera - Question
by Peter Murphy 13 Mar '07

13 Mar '07

Hi, I have a quick question about your program. Normally (on a day to day basis) I use fairly basic features of chimera (coloring, etc) to produce pictures of crystal structure images (for presentations, papers, etc). Rarely do I have to use the more advanced features of chimera (Solvent accessible surface area, distance calculations, etc) so I don`t have a good idea of the limits of your program. Thus, I figured I would check to see if what I wanted to do is out of the scope of your program. I have a few crystal structures which I want to align (I now understand how to do this based on your online tutorial (thanks)), but what I really want to do is feed a third structure into the consensus structure (or if there is no consensus structure, just feed a known sequence into a known crystal structure to see if the sequence could form that structure. Is there anyway to do this in your program.. Thanks for any help you may be able to provide, -- Peter Murphy, B.Sc., M.Sc Candidate Atlantic Research Center Dalhousie University Halifax, Nova Scotia, Canada

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Rotated density maps
by Thomas Goddard 13 Mar '07

13 Mar '07

I added two Chimera commands "newmap" and "addmaps" that allow extracting a rectangular piece of a density map with axes that are rotated relative to the original map. http://www.cgl.ucsf.edu/chimera/experimental/resample_map/resamplemap.html This is useful for extracting substructures from electron microscope tomograms. It is not part of current Chimera distributions but can be obtained as a separate plug-in from the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It is called "Resample Map Commands" on that web page because data values from the original map are interpolated (i.e. resampled) on the new rotated grid. Tom

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~longbond
by Boaz Shaanan 12 Mar '07

12 Mar '07

Hi, I'm trying to use ~longbond to hide a long bond in the Calpha trace of a model (270-280 in ijsc_a) but the bond refuses to disappear. The bond is not there when atoms are shown in full and only shows up in the Calpha trace (atoms->show chain trace). I type ~longbond in the command line after the trace is on and nothing happens. What am I missing ? I'd appreciate your advice. Thanks, Boaz Boaz Shaanan, Ph.D. Associate Professor 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] independent movement
by Elaine Meng 12 Mar '07

12 Mar '07

Hi Michel, namesel is a newer command added after version 1.2304 - get the recent snapshot to use this command: http://www.cgl.ucsf.edu/chimera/download.html#snapshots The release notes for this snapshot list what has changed since 1.2304: http://www.cgl.ucsf.edu/chimera/1.2349/docs/relnotes/snapshot.html The links I included in previous messages were to "development" documentation, which will always be newer than what you have (although mostly the same if you have a recent version). The documentation included with a download is more synchronized - you can access and search your local copy of the documentation using the Chimera Help menu. ----- 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 Mar 11, 2007, at 3:32 PM, michel dedeo wrote: > Elaine and Tom > > Thanks for your help! Savepos and reset will let me do exactly what I > want. It is good to know there are two selection commands as well. > > I have one more question. I can name a selection using the menu but > when I try to use the 'namesel' command I get an error: Unrecognized > command: "namesel". Does this command still exist? > > I am using production version 1 build 2304 2006/10/23 on Windows. > > Thanks again, > > Michel Dedeo > > > On 3/9/07, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: >> Hi Michel, >> >> I think Elaine's suggestion about using the savepos and reset >> commands >> is the best approach. >> >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html >> >> >> The "movemodel" command envisioned in a previous mailing list entry >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-June/000843.html >> >> does not exist. I think I would make two simpler commands if some new >> ones were needed that look like: >> >> spin #1 0.3 0.4 0.5 90 20 >> >> (spin model number 1 about axis (.3,.4,.5) by 90 degrees over 20 >> frames) >> >> slide #1 5.2 8.2 3.1 20 >> >> (translate model number 1 by (5.2,8.2,3.1) over 20 frames). These >> would >> work in screen coordinates by default. But using local coordinates of >> the model or local coordinates of a second model would also be handy: >> >> spin #1 0.3 0.4 0.5 90 20 local #2 >> >> (spin about axis specified in local coordinate system of model #2) >> >> slide #1 5.2 8.2 3.1 20 local >> >> (translate with vector specified in local coordinates of the model). >> >> These local coordinate versions allow the motion to stay the same >> if you >> rotate the whole scene. Neither the spin nor slide command currently >> exists. There are move, turn, and roll commands in Chimera that have >> more limited capabilities, only allowing rotation axes and shifts >> to be >> x, y, or z screen axes. >> >> Tom >> >> >> >> >> >> >>

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Re: [Chimera-users] surface display
by Tom Goddard 09 Mar '07

09 Mar '07

Hi Markus, This is a problem with the surface calculation library MSMS used by Chimera. It crashes on specific PDB files. It is described more in this post: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-February/000685.html which suggest you use Chimera command vdwdefine * * +0.01 to make the atom radii 1/100 Angstrom bigger which may circumvent the crash. Trying to surfce fewer residues generally does not fix the problem because Chimera still computes the whole surface and then just limits the display to the few residues you selected. Here is the Chimera bug report about this problem. http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=1295&database=chime… Tom Markus Voehler wrote: > Tom > > I have installed the new version and the same thing happens. Here is > what I do: > 1) open pdb (3003 atoms) > 2) display round ribbon, hide atoms/bonds > 3) action --> surface --> show also tried it on a smaller selection of > a few residues. > > I have submitted the chimera error report and have attached the crash > report. Any ideas would be appreciated. > > Markus > > > On Mar 9, 2007, at 1:43 PM, Tom Goddard wrote: > >> Hi Markus, >> >> Is your problem with molecular surfaces (menu Actions / Surface / >> show) or contour surfaces of volume data? >> >> In either case you should first try a newer version of Chimera. I >> recommend trying the snapshot 1.2352 released this week (scroll down >> the Chimera download page a little). >> >> http://www.cgl.ucsf.edu/chimera/download.html >> >> Tom >> >

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viewing VRML files in chimera
by preethi＠bu.edu 09 Mar '07

09 Mar '07

Hi, I used an SGI compiled "ivtovrml" program to convert a .iv file to .wrl file in order to view it in Chimera. I got an error, not in VRML97 formatError near line 1: and this was repeated a few times. Is there any other program that is available to convert it to the right VRML format readable by Chimera? I did a little searching on the web and coudnt find one. Thanks in advance, Preethi.

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surface display
by Markus Voehler 09 Mar '07

09 Mar '07

I have a PowerBook G4 and am not able to display surfaces on that laptop (it works fine on the SGI). I am running OSX 10.4.8 and chimera 1.2303 (1006/10/23). Does anybody have similar issues or know what to do about it. Other functionalities of chimera work just fine. Markus

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independent movement
by michel dedeo 09 Mar '07

09 Mar '07

I would like to use Chimera to make a movie in which multiple models or chains move in different directions simultaneously. The movie illustrating myosin thick filament analysis (http://www.cgl.ucsf.edu/chimera/animations/movies/myomovie.mov) is a good example. I am not sure if this post (http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-June/000843.html) on interpolated model motion is relevant, or if the 'movemodel' command imagined there actually exists in some patch that I do not have. If that proves too difficult (I have little programming experience) I would like to be able to hold one model or chain stationary while moving another. I can do this by using the model panel to make one model inactive while entering a movement command to move the active models, but I have not found a way to do this through the command line. Is there a command to activate/inactivate models, or another way to move some models/chains and not others? Thank you for your help. Michel Dedeo Francis Lab Department of Chemistry UC Berkeley

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Stereo using X11 versions
by Eduardo Sanz Garcia 08 Mar '07

08 Mar '07

I have had problems using the stereo capabilites of chimera using stereo glasses. I have two computers: * Mac G5 Quadro PPC + Nvidia FX 4000 with the latest drivers + Chimera X11 version 1.2304 * Fedora Enterprise 2 x Intel Xeon + Nvidia FX 3500 with the latest drivers + Chimera Linux 32-bit version 1.2349 The stereo hardware is correctly installed. I have other applications (X11 pymol) that display stereo nicely in both systems. On the mac, I have been able to display things in stereo but it crashes or displays weird stuff on the screen. On linux, I haven't been able to display things in stereo. Any suggestions? Thank you very much.

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savepos/reset problem with sessions and volumes
by Thomas Goddard 08 Mar '07

08 Mar '07

Hi Christopher, The problem is that Chimera does not preserve the model numbers of volume data sets when it restores a session. Restoring a saved position then moves the wrong models because it remembers the position associated with each model number. There are two Chimera bugs here. First the volume data restored from a session file should use the original model numbers. And secondly, even if the model numbers were to change, the savepos information should be updated to use the new model numbers. These problems exist in all versions of Chimera on all platforms. I'll work on fixing them and send you email if I get it working. I think I can fix the code so that your existing session files will restore correctly using the original model numbers. Tom Christopher Akey wrote: > Tom- > > I am using a build of Chimera from 11/08/2006 for windows. This version > is useful for us because the map to map correlation (fit map) and the > transform as both work nicely. > > However, I tried the savepos/reset within a session today. Set up a new > session that I would not be changing or if so, only by adding additional > files to the end of the listed files. The problem is that when I close > the session and recall it, then the reset commands invariably leave one > or two volumes out of alignment. The problem is that every time I open > the same session, the model list changes order, ie it does not seem to > be completely set in stone. If only one of your aligned images changes > order (actually 2 then), then all your previous commands are for naught, > unless you go ahead and realign them in the current session. Problem is > you don't realize they are misaligned until after you use reset and must > immediately undo move, or you are screwed. Also, you might have a > mixture of brix and mrc files, such that you might not always be able to > recover the right alignment for a file. > > Is this a windows version feature? I have noticed my files not behaving > properly before, but now have pinned it down. > > Do the models and their assoc numbers absolutely remain the same for ALL > MODELS in the linux version or in a newer windows version? > > The savepos/reset is great, you can theoretically recall you previous > figure positions and reshoot them after tweaking a color for a model or > whatever. > > cheers C Akey >

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