Re: [Chimera-users] Surface representation

Hi, I would like to know if there is a way to build a surface representation from a pdb file of a dummy atom saxs model in chimera. The file consist only of CA atoms. I could simulate this by increasing the vdw radius but the model becomes way to big. Thanks James
Hi James, You can use Multiscale Models to make a contour surface that encloses the "atoms." The tricky part may be adjusting the contour surface parameters to get the desired smoothness and enclosed total volume. At least in my tests, Chimera did not like the columns in your file after the B-factor column, so I made a version with those removed and opened it with "File... Open" before proceeding. I will send you that file in a separate message. (1) for purposes of comparison to the surface, I displayed the atoms as spheres with the radius 3.75 (this value was given in comments in the file) using the following commands: setattr a radius 3.75 rep sphere You can show the command line with Favorites... Command Line. (2) started Multiscale Models (under Tools... Higher-Order Structure), clicked the "Make models" button near the bottom. This generates the contour surface but hides the spheres. To also show the spheres, Ctrl-click on the surface to select it, and then in the "Style" line of the dialog, choose "Show also.. Spheres". To see spheres inside the surface, make it transparent; set Transparency to some fraction, say 0.3. (3) Then you can fiddle with the contour surface parameters in the Multiscale Models dialog. Many are hidden but can be shown by checking the box next to "..." I got a fairly decent enclosure of the spheres with all default parameters except setting the "Threshold atom density" for "CA only" to 0.0006 instead of the default 0.002. You could also fiddle with the smoothing parameters and resolution if that is not good enough. If you have some idea of what total volume the surface should enclose, that can be evaluated with Measure Volume and Area (under Tools... Volume Data). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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

Hi James, I just added a Chimera command molmap to make a density map from an atomic model. It sums Gaussians for each atom. If your pseudo-atom saxs model is opened as model id 0 you would run it like molmap #0 3.75 and it will create the map and display it with volume viewer. Here the resolution is 3.75 and you probably want to try other values. You can add a gridSpacing parameter to get smoother appearance (defaults to 1/3 resolution). This command is not yet documented. It has been in Chimera builds for a few days but you should try tonight's build (if it succeeds) because I forgot to include some C++ optimization in earlier builds. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom

Hi Tom, Thanks for the update. I've installed the new build and got an error message when trying to run the molmap command. I generated a bug report that you can look at. James Tom Goddard wrote:
Hi James,
I just added a Chimera command molmap to make a density map from an atomic model. It sums Gaussians for each atom. If your pseudo-atom saxs model is opened as model id 0 you would run it like
molmap #0 3.75
and it will create the map and display it with volume viewer. Here the resolution is 3.75 and you probably want to try other values. You can add a gridSpacing parameter to get smoother appearance (defaults to 1/3 resolution). This command is not yet documented. It has been in Chimera builds for a few days but you should try tonight's build (if it succeeds) because I forgot to include some C++ optimization in earlier builds.
http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
Tom
-- James Fethiere, Ph.D. Institut de Recherche en Immunologie et Cancerologie Pavillon Marcelle Coutu, University de Montreal 2900 edouard-montpetit Montreal, Qc H3t 1J4 Tel: 514-343-6111 ext. 0918/0919 Fax: 514-343-5839 james.fethiere@umontreal.ca

Hi James, Last night's Chimera build still did not have the needed C++ code for the molmap command because I included it around 9 pm after the builds had already finished. This is why you get the error using molmap. The code will be complete in tonight's builds. Sorry for the misinformation in the previous message. Tom
participants (3)
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Elaine Meng
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James Fethiere
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Tom Goddard