June 2008 - Chimera-users - RBVI Mailing Lists

saving 2 maps for difference
by Gabriel Lander 09 Jun '08

09 Jun '08

I have 2 density maps, and use the "fit in map" function to best align the 2 of them. I'd like to use this fitting to create a difference map, but the original maps are not the same size. Does anyone know how to save both maps to the same grid in Chimera? For now I've been using the "subregion selection" tool in combination with "resampling voxel size", but if someone has a more direct method it'd be much appreciated. Thanks, -gabe

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<< Plotting Gaussian MO >>
by Hatuey Hack 09 Jun '08

09 Jun '08

Hi all, I have a cube file with the Molecular Orbitals calculated with Gaussian. When I load the cub file into Chimera, I am only seen half of the orbital surface. I would like to know what should I do to get the whole molecular orbital surface colored (as usually) with only to colors (each on for one half). Regards, Hatuey

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gaussian orbitals, Chimera-users Digest, Vol 62, Issue 11
by Jonathan Hilmer 09 Jun '08

09 Jun '08

Hatuey, If I remember correctly, you need to open the density map twice, then contour at the same level for both maps: one at the positive value and the other negative. Each map is colored independently, so they can be depicted however you want. Jonathan On Mon, Jun 9, 2008 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. << Plotting Gaussian MO >> (Hatuey Hack) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Jun 2008 10:24:29 -0300 > From: "Hatuey Hack" <hatuey.hack(a)gmail.com> > Subject: [Chimera-users] << Plotting Gaussian MO >> > To: chimera-users(a)cgl.ucsf.edu > Message-ID: > <612c95fa0806090624l5395ab11k6c9b235379e1a4fe(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a cube file with the Molecular Orbitals calculated with Gaussian. > > When I load the cub file into Chimera, I am only seen half of the > orbital surface. > > I would like to know what should I do to get the whole molecular > orbital surface colored (as usually) with only to colors (each on for > one half). > > Regards, > > Hatuey > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 62, Issue 11 > ********************************************* >

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Molecular voodoo
by Tom Goddard 06 Jun '08

06 Jun '08

While debugging a bit of Chimera code I stumbled upon molecular voodoo. Stick pins in any evil molecule. Ask your doctor if this treatment may be right for you. A snake toxin (PDB 1a0m) has been fully cursed in the attached image. I attach the voodoo doll Chimera script for your amusement. You open voodoodoll.py in Chimera and then ctrl-right-mouse-button lets you place pins. Works in Chimera production release 1.2470 and newer. Tom def mouse_down_cb(viewer, event): from VolumeViewer import slice xyz_in, xyz_out = slice.clip_plane_points(event.x, event.y) from chimera import selection selection.clearCurrent() from VolumePath import place_marker place_marker(xyz_in) place_marker(xyz_out) from chimera import mousemodes as m m.addFunction('hide triangle', (mouse_down_cb, None, None)) m.setButtonFunction('3', ['Ctrl'], 'hide triangle')

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smoothening the edge of molecular surface
by Maurice Ho 06 Jun '08

06 Jun '08

Is there any way to smoothen the edge of molecular surface when only part of it would be displayed? It's quite often that a couple of triangles sticking out from the edges which makes the image a bit absurd. Please kindly advice. rgds, Maurice Ho

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Installing Chimera in Ubunty Hardy
by David 05 Jun '08

05 Jun '08

Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu for 6 gb of ram that couldn't be used in XP 32 bits. I need help installing Linux version of Chimera, I have read and goggled web for instructions, and none of them seems to work, I run .exe in terminal (knowing linux doesn't use .exe i find this confusing) and nothing happens, I try that Chmod command and running again and nothing too... Im a really beginner here in linux, also browsed Ubuntu forums for help and at least till today have got no answer. All help would be greatly appreciated. sincerely, David Bulnes Abundis

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Chimera - quantitative possibilities using surfnet?
by mgochin＠touro.edu 05 Jun '08

05 Jun '08

I am wondering if it is possible to get numerical values for areas / volumes of molecular cavities and indentations drawn by surfnet in either the Interface or Selected Atoms mode. Any help is appreciated. - Miriam Gochin

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coloring residues according to electrostatic force
by Maurice Ho 05 Jun '08

05 Jun '08

How to color residues of a protein according to the electrostatic potential map generated by APBS? I could only color the molecular surface by loading the potential map. Please kindly advice. Thanks and regards, Maurice Ho

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OS X aqua version
by Glenn Millhauser 03 Jun '08

03 Jun '08

Hi Folks, I just saw the mac aqua version at the download site and decided to give it a try. Layout looks terrific. However, it seems to move molecules much more slowly than the X windows version. I'm running on a macbook (intel) with inherent limited graphics capabilities, so perhaps that's the problem. Any comments? thanks, g Glenn Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 459 2935 fax 831 566 3337 cell glennm(a)chemistry.ucsc.edu http://chemistry.ucsc.edu/~glennm

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making a plane through the atoms of a ring and Distance measurements
by David Chenoweth 03 Jun '08

03 Jun '08

Dear Chimera team, I would like to make a plane through the atoms of an aromatic ring and then measure a distance from an atom to the ring centroid. I would also like to measure the angle between the normal to the ring plane and the line joining the centroid and the atom I am measuring from. It would also be nice if I could specify the dimensions, color, and transparency of the plane. In addition it would be great to be able to make multiple planes through atoms, select and color them separately, and measure the angles at the intersection of the planes. Just wondering if there is a way to do this with Chimera. Thanks in advance, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

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Chimera-users June 2008