Hi Johannes, My guess is that you missed that get_view[0:8] is a _column-major_ rotation matrix. Transpose it before using it.
I decided to take a look at this problem for preparation of better clipping planes in PyMOL. I got it to work in PyMOL using Python, after much fussing about. Here's what I did: * center the molecule in the model space * rotate by the transpose of the rotation matrix. * add the model-based origin of rotation back to the coordinates * compare the z-values to the z-values of the clipping planes. I'll clean up the code and post it tomorrow on the wiki if I remember. I made a few other convenience functions for placing pseudoatoms at the origin or rotation, camera center, etc. Last, atom labels have an offset, so will disappear at a different time than their corresponding atoms; also, if you cannot see the atom, it could still be shown--it could be very slightly inside the slab, but hinted away for a better viewing experience. Cheers, -- Jason On Wed, Mar 2, 2011 at 11:27 AM, Johannes Wollbold <jwollb...@gmx.de> wrote: > Hi, > > I implemented the coordinate transformation and the selection of atoms > outside PyMol, in R. In principle it works, but there seems to be some > error, since too many atoms are selected, corresponding roughly, but not > completely to an enlarged clipping corridor between the planes defined by > get_view, matrix elements (6,1) and (6,2). Or could it be that not the > complete slab is visualized in PyMol? However, the missing atoms are > completely shadowed. > > Do I understand the rows of the view matrix well (see > http://www.pymolwiki.org/index.php/Get_View), by computing the following > coordinate transformation?: > 1) Translation of the original pdb coordinates by subtracting row 5 of the > view matrix (translation of the coordinate origin to the rotation center). > 2) Rotation of the coordinates by rows 1-3 of the view matrix. > 3) Test: view[4,3] + view[6,1]) <= z <= view[4,3] + view[6,2]. > > Sorry for this simple question of affine geometry, but I hope I did not make > a logical mistake in this domain... > > Regards > Johannes > > > Tsjerk Wassenaar wrote: > > Hi Johannes, > > It's not that hard. The clipping planes are defined by the z coordinate (in > the viewing matrix). So you can get the atoms for a selection, transform to > get the new z coordinate only, and check whether it's in between the planes: > > m = cmd.get_model(selection).atom > v = cmd.get_view() > m = [ i for i in m if clipped(i,v) ] > > So clipped should do the transform and check whether the atom is clipped. > The trick then is to turn m back into a selection. > > Hope it helps, > > Tsjerk > > On Feb 25, 2011 5:18 PM, "Johannes Wollbold" <jwollb...@gmx.de> wrote: > > Jason Vertrees wrote: > Having said this, you can however, can get the > clipping information > from P... > > Hi Jason, > > thank you again for the hint. First I looked if I can select atoms > according to their coordinates, or store new coordinates after a > rotation / shift. But implicitly you already said that such > functionalities are not yet implemented. If clipping is performed with > the original camera view, the task is simple. get_view gives the output > (see above link to the help page): > > set_view (\ > 1.000000000, 0.000000000, 0.000000000,\ > 0.000000000, 1.000000000, 0.000000000,\ > 0.000000000, 0.000000000, 1.000000000,\ > 0.000000000, 0.000000000, -320.337890625,\ > 74.147140503, 74.174217224, 74.123344421,\ > 317.145324707, 323.530487061, -20.000000000 ) > > According to (4,3), the camera is shifted by -320 A in z direction only. > Since (6,1) and (6,2) indicate the camera distances of the slab planes, > I can select, in the pdb file, the atoms with (74 - 320 + 317 ) <= z <= > (74 - 320 + 323). > > For different views, coordinate transformations with the rotation matrix > of the first 3 lines are needed. This should not be very difficult, but > perhaps somebody has already a solution? > > Best regards > Johannes > >> On Thu, Feb 24, 2011 at 3:50 AM, Johannes Wollbold <jwollb...@gmx.de> >> wrote: > >> Hello, >> >>... > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. 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