- Chimera-users - RBVI Mailing Lists

CC calculation
by Qing Xie 26 Jan '12

26 Jan '12

Hi, Can anyone help me with calculating correlation coefficient from a .pdb model to a .mrc map? Thank you! Qing

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Morph conformation: Starting all movies in the same time
by Damien Larivière 26 Jan '12

26 Jan '12

Dear all, I have 4 MD movies (corresponding to 4 morph conformations) in the viewport like in the image below. Is it possible to start all the movies in the same time? It would be thus possible to better appreciate visually how much far or close are the different deformations. Thanks Damien Chimera

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Creating a single pdb file from multiple pdb files
by Steven Bottomley 25 Jan '12

25 Jan '12

Hi It is possible to create a single (preferably weighted) protein structure (pdb file) from two or more related protein structures (pdb files)? I guess that this would be something like creating a single (weighted average) of NMR ensemble structures but using any chosen pdb file. Thanks for any help! Regards Steven

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how to make rotation slabs smaller
by Moumita Dutta 25 Jan '12

25 Jan '12

Hello, I am trying to measure rotation using the "measure rotation showslabs t" command in chimera which gives very large slabs. How can I make the slabs smaller ? Any help gratefully appreciated. Thanks

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show viewdock models via command line
by Eric Pettersen 24 Jan '12

24 Jan '12

On Jan 24, 2012, at 6:59 AM, Alex Schneider wrote: > Is there a way to activate/show (...not only select) a loaded > dockview frame using the chimera COMMAND LINE (show frame 1, show > frame 10, show frame 20 ...)? I tried different commands, using > models.submodels combinations, no success, I can select different > submodels, but, I cannot bring them on the screen without clicking > on the dockviewe window. You can show a viewdock model with the 'modeldisp' command, e.g.: modeldisp #0.5 modeldisp turns display of the entire model on without changing the display state of individual atoms, so that if you had undisplayed hydrogens previously for instance, hiding the model with ~modeldisp and then showing it with modeldisp would keep the hydrogens hidden. With tonight's daily build you can activate a model for motion with select 0.5 (and deactivate it with ~select). Prior to tonight's build there was a problem parsing submodel numbers in the select command and you would have to use this kludgey alternative: select 0.5-5 --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Intersurf
by George Tzotzos 24 Jan '12

24 Jan '12

've used intersurf to show the interface area between two different protein sub-units. I'm attaching an image. Is it possible to increase the transparency of the interface area shown in red? I found no way to do so. Many thanks in advance for any suggestions Regards George PS. No attachment as it is 33.5 Mb. By the way, is there a way to reduce the size of tiff images without compromising the quality?

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Intersurf + one more question
by George Tzotzos 24 Jan '12

24 Jan '12

've used intersurf to show the interface area between two different protein sub-units. I'm attaching an image. Is it possible to increase the transparency of the interface area shown in red? I found no way to do so. Many thanks in advance for any suggestions Regards George PS. No attachment as it is 33.5 Mb. By the way, is there a way to reduce the size of tiff images without compromising the quality?

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Re: [Chimera-users] Chimera-Viewer IDEA
by Eric Pettersen 23 Jan '12

23 Jan '12

On Jan 20, 2012, at 6:00 AM, Alex Schneider wrote: > Is there a standalone Chimera-Session-viewer or a way to create such > an viewer? It should be a small tool which can only display, zoom, > rotate a chimera-py-session-file with its bondstyle, background > color AND dockview conformers WITHOUT having the comprehensive > options of the full chimera package, f.e. (options just imaginary): > > chimera-viewer.exe peptidewithhbonds.py -fullscreen > chimera-viewer.exe peptide_10conf_20picosec.py -startmovie > > The idea is to use the small tool just to view a chimera-session > without changing the style or without manipulating bonds or anything > else, JUST VIEW (o:. You could use that tool for presentations at a > conference. > > Normally I manipulate my molecules with chimera and export a vrml- > file for that task. BUT: > > I want to view my dynamic results as rotatable trajectory. I use the > dockview tool for that task. > > Ok, I know, I can just use the full chimera package to visualize my > results, but I just want to tell you my idea. Hi Alex, We don't have plans for the "Chimera Lite" you describe, but we do have some plans that nonetheless may be of some help. One thing we have right now (in the 1.6 daily build) is "WebGL" export [under File...Export], which modern browsers can show directly without any plug-ins (though many browsers currently need to have this cutting- edge capability explicitly "turned on" by the user, see: get.webgl.org) This may be more convenient than showing VRML. The generated HTML file, when shown in a browser, supports the normal "embedded trackball" Chimera mouse motions for rotating and scaling. We are actively working on improving the performance of exported WebGL, but it still can be slow for large systems. We also intend to leverage WebGL further and implement a subset of Chimera directly as HTML displayable in modern web browsers. This will take some time to get going and even then display of trajectories is doubtful. It's a lot closer to your Chimera Lite idea though. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu P.S. Thanks for the compliments in the original mail! I trimmed them off the above so that other people just got the "meat". :-)

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Procedure for modelling a homo-dimer?
by Ashfield, Thomas 23 Jan '12

23 Jan '12

hi, As a novice Chimera user I'm just wondering if it's possible to model a homo-dimer using Modeller with Chimera as the user interface? I'm familiar with the steps required to model the structure of a single chain but I'm not sure how to alter the procedure for a homo-dimer.. Any help is much appreciated, Tom Ashfield / Indiana University

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inertia axis
by Luca Pellegrini 23 Jan '12

23 Jan '12

Hello, Can you please explain how the inertia axis is calculated in: Tools -> Structural analysis -> Structure Measurements -> Define Axes when one uses the 'Selected atoms' and 'Mass weighting' option? Formally one can define three principal axes of inertia for an object, but only one axis seems to be calculated. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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