- Chimera-users - RBVI Mailing Lists

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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View Dock plugin
by James Starlight 22 Apr '13

22 Apr '13

Dear Chimera users! I have a question about the View Dock plugin. >From some servers usually I've obtained pdb file of the target protein as well as separate file consisted of all predicted posses which I can visualize in Chimera. So I wounder to know 1- How I could hide hydrogen bonds as well as protein's side chains of the residues which are in contact with the ligands ( on the default both of that two options are turned ON) 2- How I could properly save some poses as the separate pdb models ? E.g when I chose to same target.pdb with the #1_pose from the chimera saving menu I obtain protein and ligand with the surrounded residues as two models in one pdb file ( so I must manually merge it in one model and delete residues from the second model). Does it possible to obtain protein-ligand complex as one model as the output? Thanks for help, James

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multiple volumes' orientation in space
by Yunji Wu 22 Apr '13

22 Apr '13

Dear all -- I am a total newb to Chimera, and I have an issue which I feel like can be easily resolved with your help. I am trying to make a 'structure-based schematic' with the purpose of clarifying the locations of the domains of a complicated crystal structure. There are 12 domains in this structure that I want to represent as 'blobs', and they are oriented in space in a very confusing way, especially if represented as the standard ribbons or cartoons. I used pdb2mrc (in EMAN2) to create 25Å maps from my .pdb files for (with the command e2pdb2mrc.py -R 25 H.pdb K.mrc). These show up fine individually in Chimera, but the separate maps are not oriented properly in space. It looks like the map volume files have no instructions about where to be in space relative to the coordinate files that generated them. If I take a single .pdb file with all 4 chains and generate a single .mrc file, I obviously get something that has the chains correctly oriented. This is less useful and satisfying, since I'd like to make separate chains into separate map volumes so I can color them separately (for example: chains H,K,L,M as H.pdb, K.pdb, L.pdb, M.pdb into H.mrc, K.mrc, L.mrc, M.mrc). When these 4 volumes are plotted in Chimera, they appear to be semi-randomly piled in the middle of the viewing field, with no correlation to the original pdb coordinates (attached screenshot of volumes from 4 chains, calculated from 4 individual pdb files). Is this just a result of a preset in Chimera that I am not aware of that needs to be adjusted? If I plot the original pdb file with the 4 chains from which these volumes were generated, there is no spatial correlation between the structure and the volumes. In trying to solve this, I know that "Fit to Map" will allow the coordinates to be fit into the map volume, but I cannot seem to fit the separately map to the individual chains, which would be a longer way around the issue. Is there some way to do this, or to just create maps that are oriented properly in space relative to each other? Thank you so much for your help, Yunji Wu

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Radius of gyratiion
by George Tzotzos 22 Apr '13

22 Apr '13

Hi everybody, I've search the archive to find a script for measure protein radius of gyration. I came across the following link: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007257.html I'm now trying to find the actual script <radius-of-gyration.py>. Any ideas how to retrieve it? Many thanks in advance George

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euler angle
by Jingchuan Sun 19 Apr '13

19 Apr '13

Hi, After I rotate a volume to a specific orientation, and "save map as" in "volume viewer", the saved volume are still in the original orientation. Could I save it in the new orientation. If I could display the current euler angles, I can rotate it in other software. But how could I display euler angle after rotation? Thanks! Jim

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Doubt
by Víctor J. Gallardo López 19 Apr '13

19 Apr '13

Good Morning Mr./Ms., I have a bit problem with the molecular modeling. I have a dímer (the two chains of this protein are the same sequence) and I want to put 34 residues at the N-terminal in each chain. I load my fasta (with this residues addition) in chimera and I blast a protein structure in the PDB that has the same residues as my protein without this addition. When I modeller (homology) my fasta, the programm only gives me one of the chain with this addition but I need the whole protein (with the two chains and with this residue addition for each chain as well). How can I do it? I hope you resolve my problems. Thanks you for you attention. Sincerely, Víctor J. Gallardo

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Generating trajectory of a user-defined plane
by Lili Peng 18 Apr '13

18 Apr '13

Hi, I am interested in measuring the deviation of an helical segment with respect to the initial structure in a GROMACS trajectory. I have already uploaded my *.tpr and *.trr files into MD Movie and have defined a plane through the helical segment within the initial structure. Is it possible to define another plane through the same helix and track the intersection angle throughout the trajectory? Thank you, Lili

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python script running OUTSIDE chimera possible?
by frederick lee 18 Apr '13

18 Apr '13

hello chimera experts, as far as i know, python scripting for chimera is done within the context of chimera like chimera --nogui myscript.py parameters ... is it possible to run myscript.py without the need of the chimera executable and use import statements of some sort to access the chimera module(s) like python myscript.py parameters best regards, fred

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selecting amino acids and labeling
by Gonzalez, Mireya 18 Apr '13

18 Apr '13

To whom it should concern I am working on some docking structures. Previously I used to have Quimera version 1.7 installed in my computer. Recently I downloaded the version 1.8 but I am having problems identifying the amino acids that are in contact with my compound using the cursor. This function is inactivated. Furthermore if I hold the key Ctrl for selecting them and labeling it is also not doing it at all. Any help with this issue will be greatly appreciated. Mireya Gonzalez

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question
by sunwei_223 18 Apr '13

18 Apr '13

Dear sir I have some question in using your excellent Chimera. How can i set 5 symmetry to a 3 symmetry map? thank you

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AutoDock Vina and hydrogens
by Elaine Meng 16 Apr '13

16 Apr '13

Hello, Users of the AutoDock Vina interface in Chimera 1.7 should be aware of a potential "gotcha": the structures should include hydrogens, at least the "polar" (potentially H-bonding) ones. For the receptor, this is generally taken care of because the "add hydrogens in Chimera" option in the AutoDock Vina interface is turned on by default. However, there is no corresponding option for the ligand in that interface: instead, you need to add hydrogens to the ligand beforehand, for example with Chimera AddH. Polar hydrogens are needed for Vina to correctly recognize the atom types, to correctly calculate docking scores. In the current daily build (and for future releases) we have built in more protections so that if there are no hydrogens and you haven't added them with Chimera, they will still be added by the AutoDock prep scripts before the docking calculation. Recent fixes: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#bug_fixes> Download the daily build: <http://www.cgl.ucsf.edu/chimera/download.html#daily> Best, 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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Tube representation of the motion projections along the eigen vectors
by Prasanna Venkatesh 16 Apr '13

16 Apr '13

Dear all, I request you to give me the steps for "Tube representation of the motion projections along the eigen vectors" in Gromacs. Please give me step wise details with the input file types required. Thank you in advance. Prasanna.

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docking with flexible side-chains
by Thomas Evangelidis 16 Apr '13

16 Apr '13

Dear Chimera developers, Isn't docking with flexible side-chains supported in the AutoDock Vina GUI? I am surprised I didn't find any pertinent information about it in the documentation or the mailing list archives. thanks, Thomas -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tevang(a)pharm.uoa.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Technical problem!
by Narges Mortezaei 16 Apr '13

16 Apr '13

Dear Sir/Madam We have confronted with kind of problem using chimera. We have constructed an structure of P-pili containing subunits and epitopes. A few cylinders that are representing arms of antibody have also been added to the model. The problem comes when we want to copy the cylinders to make more out of them. I do select corresponding cylinder, but when it comes to copy in Model Panel a copy option is not activated. I also tried "mcopy" command, but it did not work as well. Would you please give me some hints how to copy these kind of objects. Sincerely, Narges Mortezaei

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(no subject)
by Muhammad ALi 16 Apr '13

16 Apr '13

hi can we make a DNA model with chimera???

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pdb
by Muhammad ALi 16 Apr '13

16 Apr '13

when I download a ligand from PDB site it contains may ligand molecules ..and kindly tell me how to get a single ligand????

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Radial density plots
by Pranav Shah 15 Apr '13

15 Apr '13

Hi Tom, I am trying to plot a graph of average density as a function of radius in Chimera v1.7. I tried the code that you wrote for Padma in an earlier post. However, Chimera spits up this error "Accelerators file C:\Program Files\Chimera 1.7\share\Accelerators\radial_density.py has no register_accelerators() function." when I try to load the radial_density.py in the keyboard shortcuts menu. Could you tell me how this bug can be fixed? Awaiting your assistance, Warm regards, Pranav Shah Postgraduate student (Infection and Immunobiology), College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK.

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