Hi Ben, I just added an option to MD Movie to allow atomic radii to be factored in. The two options (other than the previous behavior which is also available) is to increment all grid cells within the atomic radii uniformly, or to increment those closer to the atomic center more. The latter is a very simple scheme in that the "outermost" cells are incremented by 1, the next layer by 2, the next by 3, etc. with the center cell getting the highest increment. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 31, 2012, at 9:49 AM, Tom Goddard wrote:

Hi Ben,

The MD occupancy map can only record the center positions of atoms. After it is calculated you can use Gaussian filtering, for example,

vop gaussian #1 sdev 6.5

to convolve the occupancy map with a Gaussian. Equivalently you could use the Volume Filter dialog (menu Tools / Volume Data). Of course both of these are not quite the same as putting a Gaussian at the atom center positions and then accumulating because the above procedure first discretizes the center positions by recording them in the occupancy grid before we apply the Gaussian. But the difference will be small if the grid size is fine. We don't currently offer any other kernels such as a sphere.

Tom

...

Hi list,

I am using the MD->occupancy tool to produce occupancy densities of a very coarse grained model (I have a few spheres, with big radii : approximatively 10 spheres with 10A radius each). My problem is that the density is computed only for the center of each sphere, which tells me where the center stands. To have a better feeling of the space occupied by each sphere I'd rather like a density computed for the whole sphere (updating each cell of the grid by either incrementing if the cell is covered by the sphere, or why not with any type of kernel centered on the sphere and depending on the sphere's radius.). Can I do that with Chimera ? And if so, How ?

thanks

--Ben

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Hi Ben, Yes, you would have to get a daily build dated after when the change was made. Occasionally the build will fail and there might not be a new one every single day. You would need to wait for the next successful build for your type of computer. There are many ways to set radii. I'll list several; option (D) might be easiest... An advantage of Chimera is that you don't have to use the B-factor column every time you want to assign some values to atoms. It can read a separate "attribute definition" file, and you can have multiple custom attributes; rather than reading in multiple PDB files of the same structure with different values in the B-factor column, you could just load the structure once and then load several different attributes using separate definition file(s). In this case, you would have to use atom atribute name "radius". That's option (A). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile> (B) there is also a "setattr" command to set one value at a time. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> (C) for VDW radii specifically, there is also a "vdwdef" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> (D) if you already have those PDB files with B-factor field used for radius, you could just equivalence "radius" to your existing "bfactor" values using "Attribute Calculator" (under Tools... Structure Analysis). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html> Start that tool, Calculate attribute "radius" (omit quotes please) for atoms. Set Formula to atom.bfactor, uncheck all the checkboxes except for maybe "Show calculation results in Reply Log" if you want to verify the assignments, then Apply. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 2, 2012, at 7:51 AM, Benjamin SCHWARZ wrote:

1. (newby question, sorry) I guess if I want to access that I'll have to download the latest night build ? 2. In my case I play with fake Calpha PDB files, with radii stored in the B factor… I guess I'll have to change the radii of my fake atoms manually in chimera. How can I do that ?