February 2010 - Chimera-users - RBVI Mailing Lists

Density map in Chimera
by Pancera, Marie (NIH/VRC) [C] 17 Feb '10

17 Feb '10

Hi, I opened an electron density map in chimera. For some reason it is forming a box and I am not quite sure how to get the density outside of the box (to cover symmetry molecules etc...) Thanks for helping me with that. Best regards, Marie

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copyright permission
by M P Williamson 17 Feb '10

17 Feb '10

Hi folks. I am getting near to the end of writing a book called How Proteins Work (to be published by Garland, hopefully this fall). I would like to include a figure showing anisotropic B factors for a protein, and the best image I have come across is of heme on your website, http://www.cgl.ucsf.edu/chimera/feature_highlights/ellipsoids.png I would like to include this image in the book. Could you let me know if there are copyright restrictions on the image, and how you would like me to refer to it? Thanks Mike Williamson

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help
by Giuseppe Falini 17 Feb '10

17 Feb '10

Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe

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writing a trajectory to multiple pdbs
by Dan Gurnon 16 Feb '10

16 Feb '10

Hi everyone, How would one write a trajectory read into MD Movie to a series of pdb files instead of one large file? I don't see a suitable option specified for the "write" command, and for "Save PDB" it seems the option of multiple files is only available when multiple models are selected. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Hydrogen Atoms
by Elaine Meng 16 Feb '10

16 Feb '10

On Feb 14, 2010, at 11:31 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am working on calculating the Solvent accessible Surface Area on > the antigen interaction region. I am confused about adding/removing > hydrogen's, my question is will there be a change in SASA if you > have or not have hydrogen's atoms added. > Thank You. > -Thiru > Hi Thiru, Yes, it will be different with and without hydrogen, because the molecule is treated as a set of spheres where each atom is a sphere. There will be more small bumps on the surface when there are hydrogens. Also, the radii of the other atoms may change because there are different defaults for structures with and without hydrogens, as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> I think surface area calculations are usually done on structures without hydrogens. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html P.S. you may want to use "measure buriedArea" (or maybe you are already doing that): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedAr… >

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reference for saving pdb
by Samuel Coulbourn Flores 12 Feb '10

12 Feb '10

Hi Guys, I'm having what I am sure is a trivial problem. When I save my PDB coordinates, I am asked what the reference is, and choose a density map. But when I read those coordinates back in, they are translated/rotated from where they should be and no longer match the density map. Can you tell me what is the correct procedure for setting the reference? Thanks Sam

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Row interleaved stereo and Zalman monitors under Linux
by David Bhella 12 Feb '10

12 Feb '10

Hello again! I have just installed a Zalman M220W monitor on one of our workstations under OpenSuse 11.1, after a small amount of fiddling to get it working with dual head mode it seems to be behaving. In Amira it gives beautiful 3D, although the assignment of left and right eye views seems fairly random, as Amira has the option to reverse left and right eye views this is not a problem. In Chimera however with row interleaved stereo I seem to always get the views the wrong way around. It took me a while to work out why it didnt seem to be giving good depth and it was quite disconcerting to look at while viewing cryoEM 3D reconstructions, however with a pdb file it was quite obvious that my right eye was getting the left eye view. There only seems to be the option of reversing the views for sequential stereo however.... I would be grateful if anyone could advise me on how I can fix this. 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 Skype: d.bhella 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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Shadows
by David Bhella 12 Feb '10

12 Feb '10

Hi, I just updated my Chimera installation to 1.4.1 (Mac OSX aqua), and I noticed that for some reason shadows are not so nicely rendered in standard 3x3 super-sampled output. They look very blocky, much as they always have done in the viewer. In version 1.4 I always got very nice shadows when I saved an image. I am trying to save images of an isosurface view of a 3D reconstruction. Is there a setting I need to adjust to get high quality shadows back again? 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 Skype: d.bhella 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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session writing
by Jean-Paul Armache 11 Feb '10

11 Feb '10

hello, i would like to ask whether it would be possible to save sessions with relative path, instead of absolute one ? it is a bit complicated to move the sessions between different platforms with the absolute one. thank you, best, jp armache

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Re: [Chimera-users] 64-bit version of Chimera for windows
by Tom Goddard 11 Feb '10

11 Feb '10

Hi Pu, Greg Couch in our lab is working on a 64-bit version of Chimera for Windows 7. It should be available in a month or two if we don't run into overwhelming difficulties. Tom > Hi Tom, > > Do you have 64-bit version chimera for windows. Our computer manager asked me > this question. > > Happy Chinese New Year. > > Best regards > > > Pu Qian > > >

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Chimera-users February 2010