Dear Chimera users, I cannot find a way to search the chimera-users archive, so I appologize if this has been asked already. I wish to alter some volume data in specific ways; delete (zero out) all volume values that do not meet certain density criteria. The following code modifies the matrix values, but I can't figure out how to update the map that is being displayed in the volume viewer. I would like to be able to do something like: opened[0].full_matrix = H Then I would only see the swath that I "selected" with the following code. # ------------------------------------------------------------------------ source = '1R0A_antigen_6A_8s_0.425f_inv.mrc' opened = chimera.openModels.open(source) em = opened[0] H = em.full_matrix() s = H.shape for k in range(0,s[2]-1): for i in range(0,s[0]-1): for j in range(0,s[1]-1): if(H[i,j,k] >= -.28) and (H[i,j,k] <= -0.001): H[i,j,k] = H[i,j,k]+1 else: H[i,j,k] = 0 # ------------------------------------------------------------------------ Thank you, -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University
Hi Michael, You can search the archive by going to the Chimera home page and clicking the quick link "Contact Us" on the lefthand side, which gets you here (where there is a search field): <http://www.cgl.ucsf.edu/chimera/docs/feedback.html> I don't know about python, but here is a summary of the "user interface" ways to modify data: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> In your case, I'm thinking you could show an isosurface at the density value you want as your cutoff (with Volume Viewer or the "volume" command), then use the "mask" command to generate a new map with values only inside the surface, zero elsewhere. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> 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 Feb 1, 2010, at 6:26 PM, Michael Zimmermann wrote:
Dear Chimera users, I cannot find a way to search the chimera-users archive, so I appologize if this has been asked already. I wish to alter some volume data in specific ways; delete (zero out) all volume values that do not meet certain density criteria. The following code modifies the matrix values, but I can't figure out how to update the map that is being displayed in the volume viewer.
I would like to be able to do something like: opened[0].full_matrix = H Then I would only see the swath that I "selected" with the following code.
# ------------------------------------------------------------------------ source = '1R0A_antigen_6A_8s_0.425f_inv.mrc' opened = chimera.openModels.open(source) em = opened[0] H = em.full_matrix() s = H.shape for k in range(0,s[2]-1): for i in range(0,s[0]-1): for j in range(0,s[1]-1): if(H[i,j,k] >= -.28) and (H[i,j,k] <= -0.001): H[i,j,k] = H[i,j,k]+1 else: H[i,j,k] = 0
# ------------------------------------------------------------------------
Thank you,
-- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Michael, Your code almost does the job. The line H = em.full_matrix() gets the actual data array that Chimera is using, not a copy of it. So your loop is modifying the only copy of the data in memory. But there is a problem with this. Chimera currently does not support modifying map values that come from a file. (It only reads parts of the map from the file on-demand, and later deletes them from memory when not needed. This caching can't handle modifying values.) You have to make an in-memory copy of the map to do that. So do this. emc = em.writable_copy() H = emc.full_matrix() # Your thresholding code here. emc.data.values_changed() That last "values_changed()" call will cause the graphics and histogram to update. To save the map to a file: emc.write_file('newfile.mrc') The "vop" (volume operation ) command should do this simple thresholding though it currently doesn't. I've added that to our feature request list. http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html Elaine's tricky masking suggestion would probably work. Make two contour surfaces (ctrl click on histogram to make second one. Then use the mask command to zero everything outside of those. Then use "vop scale" to shift the map as you have in your code. Tom -------- Original Message -------- Subject: [Chimera-users] alter volume data with python From: Michael Zimmermann <michaelz@iastate.edu> To: chimera users <chimera-users@cgl.ucsf.edu> Date: 2/1/10 6:26 PM
Dear Chimera users,
I cannot find a way to search the chimera-users archive, so I appologize if this has been asked already. I wish to alter some volume data in specific ways; delete (zero out) all volume values that do not meet certain density criteria. The following code modifies the matrix values, but I can't figure out how to update the map that is being displayed in the volume viewer.
I would like to be able to do something like: opened[0].full_matrix = H Then I would only see the swath that I "selected" with the following code.
# ------------------------------------------------------------------------ source = '1R0A_antigen_6A_8s_0.425f_inv.mrc' opened = chimera.openModels.open(source) em = opened[0] H = em.full_matrix() s = H.shape for k in range(0,s[2]-1): for i in range(0,s[0]-1): for j in range(0,s[1]-1): if(H[i,j,k] >= -.28) and (H[i,j,k] <= -0.001): H[i,j,k] = H[i,j,k]+1 else: H[i,j,k] = 0
# ------------------------------------------------------------------------
Thank you,
participants (3)
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Elaine Meng -
Michael Zimmermann -
Tom Goddard