- Chimera-users - RBVI Mailing Lists

morph map and movie recording
by Moumita Dutta 26 Apr '13

26 Apr '13

Hello, I am trying to morph more than two maps at a time so I am using vop morph instead of Morph map. I am following the mini-video animation example script of vop morph using the recommended chimera 1.7 version 2013. The script actually recorded the movie but in the movie threshold changed from what I set and it turned some maps to x 90 degree not all and it is not showing the morph animation only the superimposed maps. Another problem is though I remove the dust after loading the maps but it came back in the morph and in the movie as well. How can I fix the problems and generate the movie ? Moumita

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Ubuntu 12.10 and Chimera update #2
by Greg Couch 25 Apr '13

25 Apr '13

Found a better solution to Chimera's problems on Ubuntu 12.10 -- just install Ubuntu 13.04! HTH, Greg

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Re: [Chimera-users] movie recording from morph map
by Elaine Meng 25 Apr '13

25 Apr '13

On Apr 25, 2013, at 1:01 PM, "Moumita Dutta" <dutta(a)bio.fsu.edu> wrote: > Hi Elaine, > I am trying to morph more than two maps at a time so I am using vop morph instead of Morph map. I am following the mini-video animation example script of vop morph like below > > Record the movie > # > > movie record supersample 3 > > wait 1 > movie crossfade > vop morph #0,1 frames 200 > wait 200 > > movie encode morphmap.mp4 morphmap.webm morphmap.ogv bitrate 200. > > It starts recording the movie but it does not stop. > Best, > Moumita Hi Moumita, The first thing to check when following a tutorial or examples is your version of Chimera. The top of the mini-examples page <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> says that they were made with Chimera version 1.7 from March 2012 or newer. In those versions, movie recording will automatically stop when you use "movie record." In older versions, you have to use the "movie stop" command to stop recording before you do the encoding. (I cc'd chimera-users(a)cgl.ucsf.edu -- please use that address for Chimera questions unless your data are private) 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

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Seeking guidance on Volume-volume fitting
by ingvar 25 Apr '13

25 Apr '13

Dear Chimera, I am seeking guidance on what would be best practice in doing volume-volume fitting, and what expectations should I have on number of trial conformations. For instance would it be beneficial to resample one of the volumes to the same grid as the other volume. What about volumes with different resolutions, do this require any special handling. In the case below it would probably be more efficient to just align the principal moments of inertia of the envelopes above the contour level and then do a search from there, though this will only work well if the volumes are very similar. In an initial study I used 3 EM volumes from EMDB, (EMD-5500, EMD-5501, and EMD-2017). They are all 30S E. coli ribosomes of similar resolution (12.9, 14.0, 13.5 Å). I thought that this would be a relatively easy starting point, with the intent to then go on to fit 30S subunit in some of the many E. coli 70S EM volumes that are available. The volumes EMD-5500 and EMD-5501 are in similar orientation, while EMD-2017 is in a completely different orientation. The grids are similar but not identical, 125^3 vs 128^3. I adjusted the contour levels from the EMDB recommended values to make the enclosed volumes more similar in size. Contour levels used: EMD-5500 -2.8 -> -2.5 EMD-5501 -2.8 EMD-2017 39 -> 32 I am using scripts like the one shown here: from chimera import runCommand as rc from chimera.tkgui import saveReplyLog rc("open data/EMD-5500.map") rc("volume #0 level -2.5 transparency 0.5") rc("open data/EMD-5501.map") rc("volume #1 level -2.8 transparency 0.5") rc("fitmap #1 #0 search 50000 metric cam envelope true inside 0.2") saveReplyLog(r'/Users/ingvar/chimera/log/fit5500_5501_loc.txt') It seems correlation about mean is the best metric for volume-volume fitting, and that it is best to only use points inside the envelope. The maps EMD-5500, and EMD-5501 have the unusual feature that the density range is shifted downwards so that the average is well below 0. I was concerned about that and moved the density range, but with the fitmap parameters above that did not seem to have any significant impact (with other sets of parameters the density range appears to be an issue). In this case, it is relatively easy to see when you have found the "good" fit, all other fits have clearly worse statistics. What I was surprised about was the number of trial conformations needed to be reasonable certain to find the "good" fit. 5500 in 5501 7 times in 5000 5501 in 5500 2 times in 5000 5500 in 2017 0 times in 5000 5500 in 2017 8 times in 50000 2017 in 5501 0 times in 5000 Many Thanks, Ingvar Lagerstedt

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morph map and molecule together
by Tom Goddard 24 Apr '13

24 Apr '13

Hi Moumita, You can morph both maps and molecules at the same time. You use commands instead of the morphing dialogs in order to get them to play with perfect synchronization. The basic plan is to create the molecule morph and the map morph using the dialogs as usual. Then load a simple command script that starts both playing at the same time and records the movie. I'm sure this works in Chimera 1.7, probably in 1.6, and maybe in 1.5. Here is an example command script morphing a filament map and fit molecule http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/scripts/movie2.txt and here's the resulting movie http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/images/morph1.mp4 and here is the web page where I explain how this was done http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/animate.html This was a demonstration I gave at the Bay Area Cryo EM meeting in Santa Cruz last summer. Tom -------- Original Message -------- Subject: morph map From: Moumita Dutta To: goddard Date: 4/23/13 10:16 PM > Hi Tom, > > I want to morph a set of density maps and the atomic models fitted > into them together and run the two movies concurrently so that I get a > movie that shows how the density and the atomic models change > together. I have been able to make the two different sets of data > morph independently, but thought it more informative if they morphed > together. > > I was wondering whether this can be done using chimera ? If so which > version supports it ? > > Thanks, > Moumita > > >

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Hide bonds
by Masaki Uchida 23 Apr '13

23 Apr '13

Dear Chimera users Is it possible to hide bonds between spheres (atoms/bonds view)? I have a "pdb" file which is a bead model of a protein generated by SAXS analysis. When I open the file and changed a view to "sphere" under "atoms/bonds", bonds between beads are shown. I believe the bonds are meaningless in this case and would like to show just spheres (beads). Thank you in advance for your help -- ********************************************** Masaki Uchida Department of Chemistry&Biochemistry Montana State University **********************************************

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dock
by LW 23 Apr '13

23 Apr '13

Dear all, As attached, I have a structure of Saposin C in the presence of SDS micelle solved using NMR. I took the first model out of its 20-structure ensemble and generated SapC_one_model.pdb. I also have a PDB file(as attached )built to model SDS micelle surrounded by water. Does Chimera allow people to dock these two molecules and generate a combined PDB file for further analysis? While the structure of Saposin C in the presence of SDS micelle, NMR data indicate that the open hydrophobic core is in contact with SDS micelle. Is it possible to use Chimera to determine the relative orientation of the two molecules where (i), they are in intimate contact, (ii), there is no clash, (iii), the shape complementarity is at its optimal? Any clue would be much appreciated. Levi

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batch production of images
by Benjamin SCHWARZ 23 Apr '13

23 Apr '13

Dear list, I am considering to use chimera to render (a tons of) pictures of models that I generated and issued in nice markerSet (.cmm) files. 1. If I understand well, the only way to do that is through the linux headless version, and there is no way to do that under MacOS X for the moment 2. I should then use the "copy" command. Something like : chimera --nogui --script "myscript.py" where myscript.py should contain something like "from chimera import runCommand; runCommand('copy file pipo.png')" 3. All my models were produced in a same cartesian, and I'd like to keep the orientation and "picture frame" similar for all pictures. What I mean here, is that I'd like to be able to set my camera somewhere, looking in a specified direction, which I would probably do under the chimera GUI; and then, shoot all my pictures from that point of view on a batch mode. How shall I do that (set a point of view for the camera and use it on a batchmode) ? Thanks a lot again for your great job, and your constant answers --Ben

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stereo viewing with consumer graphics cards
by Greg Couch 22 Apr '13

22 Apr '13

In the past, Chimera has always needed a workstation-class graphics card (e.g., AMD FirePro or NVIDIA Quadro) to view molecules in 3D stereo and read dialogs at the same time. Now that there are 3D HDTVs, that has changed. I have just confirmed that with a computer running Microsoft Windows 8, with an AMD Radeon HD 7850 graphics card, and a Panasonic 3D HDTV, that 3D stereo worked without fiddling with any display settings. That is awesome -- "without fiddling with any display settings". Windows 8 is a requirement, Windows 7 will not work. I am unaware of any effort to get Linux to work. There is a good chance that Apple Mac OS X will work and we plan to test that soon. Any recent AMD Radeon HD graphics card with HD3D, or NVIDIA GeForce graphics card with 3D Vision support, should work. I hope to test a NVIDIA graphics card soon to confirm that. And supposedly, any 3D HDTV will work. The 3D HDTV in the test was a Panasonic TC-P50GT25, from 2010/2011, and I expect that any 3D HDTV that support a full resolution stereoscopic 3D format will work well. Non-full resolution formats would work for the 3D stereo images, but the associated 2D dialogs would be unreadable. Happy 3D viewing! Greg

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Distance between atoms at the interface
by Mehdi Talebzadeh Farooji 22 Apr '13

22 Apr '13

Dear Chimera Users, I was wondering if there is a way to show distances between two objects (two chains) and filter them; for instance to display all of the distnaces between atomes of two interacting protein chains which are less than 6 A. Any help would be much appreciated, Mehdi

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