- Chimera-users - RBVI Mailing Lists

Movie recording
by Ibrahim Moustafa 24 Sep '08

24 Sep '08

Dear Chimera team, I have a problem with making a movie of morphed conformations in chimera (only for chimera 1.2548 installed on my laptop running XP). After doing the ³morph² when trying to record the movie I got the following error message: ³Error stopping/encoding movie: MidasError: Keyword and¹ does not match any known keywords² I don¹t understand the error message and what does it mean by ³keyword and²? I¹m not running a script. I don¹t have this problem with the Mac version of Chimera. The funny thing is that I was able to create a movie on the windows version a week ago. I¹m not sure if this problem has relation with XP and perhaps some new updates! Any idea how to solve this problem? many thanks for your great help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Creating and visualizing a plane
by James Nettles 23 Sep '08

23 Sep '08

I'm not sure if this is a function available in Chimera. I have a protein system with three residues which define a plane, or floor, relative to an active site. I would like to display a translucent plane passing through the alpha carbon of these three residues to shoot an image. Further, I would like to quantify deviation of mobile regions relative to this plane. Thanks, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine ________________________________________________________

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Scale_bar Gradient Color
by Anindito Sen 22 Sep '08

22 Sep '08

Hi All A simple question- How do I color the scale bar (in a gradient form). Also Has anyone experienced the problem of scale bar giving an incorrect measurement when a density map in .dat format is displayed in Chimera? Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Show position in volume
by Magnus Gedda 22 Sep '08

22 Sep '08

Hello, I'm quite new to Chimera and have a small but annoying problem. I can place a marker in the volume and move it around, but I cannot find a way to see the xyz coordinate of the marker. How do I do this? Is there any other way to find out the xyz coordinates of a position in the volume? Best regards, Magnus

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VRML scene
by Eduardo Sanz García 19 Sep '08

19 Sep '08

Is it possible to export a VRML scene of only what it is been displayed in the window instead of the whole model? I wasn't able to open in chimera X3D files exported with chimera itself. Does chimera only writes but not read X3D files? Thank you.

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Colouring surfaces from EM density maps
by David Bhella 19 Sep '08

19 Sep '08

I am looking at some rather noisy cryo-tomography data and I would like to create something akin to icosahedral and spherical sections, using different shapes (cylinders, ellipses etc). I have found spherical and icosahedral sectioning to be a valuable way to represent density and would like to use this in other types of structure. Is it possible to colour the surface of an imported VRML object in the same way as spheres and icosahedra are in the tools>volume data>surface colour dialogue? In my current chimera installation, VRML objects are not listed in this window.... The sort of effect I want to achieve is similar to that described here: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icossu… except that I want to use custom geometries.... Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

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code 5 error
by steve field 18 Sep '08

18 Sep '08

Hello' I am trying to render a surface depiction on various fluorescent protein molecules. The program seems to work with some but not others. A code 5 error message displays. Any insight into what is causing this? PyMol is able to depict the surface from the same PDB file and Chimera works with other molecules, but not the one I need. Any thoughts would be appreciated. Thank you, steve field _________________________________________________________________ Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!5…

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Re: [Chimera-users] [chimera-dev] Hydrophobicity
by Elaine Meng 18 Sep '08

18 Sep '08

On Sep 18, 2008, at 9:54 AM, Leo O'Young wrote: > Hi Elaine, > > Thanks for such a quick and detailed response. > I am looking to get the Hydrophobicity-Surface model so > the it will look smoother...the edges not so rough. > I am not very technical, hopefully I am making some sense. > I have attached a file. > > Thanks again, > Leo Hi Leo, In that case, I think you want to change the "vertex density" surface parameter mentioned in the previous message. That uses a greater number of points and thus triangles in the surface, leading to a smoother appearance. However, be aware that doing this may decrease the interactivity (slow down responses to movements with the mouse) depending on your computer, so you may need to experiment a little to find a happy medium. Actually the picture you sent is of a rather small molecule, so I don't think there will be any slowdown. If you were showing a huge protein or several proteins it would be more likely. Best, Elaine

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Re: [Chimera-users] [chimera-dev] Hydrophobicity
by Elaine Meng 18 Sep '08

18 Sep '08

On Sep 17, 2008, at 10:14 PM, Leo O'Young wrote: > > I am new to the list, I am wondering if it is possible to increase > the geometry > of the Hydrophobicity-Surface models. > > Thanks, > Leo Hi Leo, Welcome! The "hydrophobicity" in the preset is just a coloring scheme, so I will set that aside and discuss molecular surfaces. I am not sure what you mean by "increase the geometry." There are several ways you can adjust molecular surfaces in Chimera: change vertex density, probe radius, and also the radii of the underlying atoms. It is a molecular surface by the Richards definition, also known as the solvent-excluded surface, made of probe contact and re- entrant patches; it shows the VDW surface of the structure except with crevices smoothed. Currently Chimera does not show the solvent- accessible surface, which is where the probe center goes. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > If you mean you want to make the surface "bigger" to enclose a greater volume, that can be done by increasing the VDW radii of the atoms, and to a lesser extent, increasing the probe radius, which will smooth the crevices more. One way to increase VDW radii is with a command; this would increase all radii by 0.7 A, for example: vdwdefine +0.7 (the command ~vdwdefine changes the radii back to defaults). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html#changing > To change probe radius or other parameters of an existing molecular surface: - Ctrl-click the surface to select it - open the Selection Inspector (click the greenish button on the lower right corner of the Chimera window or choose Actions... Inspect from the menu) - in that dialog, Inspect "MSMS surface", and then edit the various parameters as desired <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html#msmsprop > You can also set preferences to use different parameters for surfaces created in the future, so you don't have to change each one after you create it. To do that, choose Favorites... Preferences, go to the New Surfaces category, change parameters as desired and click Save. That only pertains to surface parameters, not VDW radii of atoms, however. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surf… > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Protonating ASP and GLU
by Francesco Pietra 18 Sep '08

18 Sep '08

Is there any special reason why, in the AddH option, side chains are only considered for HIS (with full options)? Why similar options are not given to protonate GLU and/or ASP at the carboxylate? The general option to consider H-bonding does not work in my case for such residues close to one another in space with Chimera (the two O atoms of two ASP residues are at 2.56A from one another). Even Reduce, supposed to protonate close lying carboxylates, failed in my case. This is why I would consider to add that option in future versions of Chimera. Thanks francesco pietra

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