[PyMOL] pisa
protein 1b8e says its a dimer by its pdb file info as: BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 REMARK 350 BIOMT1 2 -1.00 0.00 0.000.0 REMARK 350 BIOMT2 2 0.00 1.00 0.000.0 REMARK 350 BIOMT3 2 0.00 0.00 -1.00 33.43000 when i feed the same into pisa..it says no assemblies are possible... i can't make out...can ny1 help.. Regards, Kanika -- 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
Re: [PyMOL] pisa
Why do you expect PISA to agree with author assigned biological units? Read the paper and see if there's a reason the authors made the assignment. If you really don't understand why things might be different, read the intro to the ProtCID paper. -David On Mar 3, 2011, at 6:37 AM, kanika sharma ksharma...@gmail.com wrote: protein 1b8e says its a dimer by its pdb file info as: BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT2 1 0.00 1.00 0.000.0 REMARK 350 BIOMT3 1 0.00 0.00 1.000.0 REMARK 350 BIOMT1 2 -1.00 0.00 0.000.0 REMARK 350 BIOMT2 2 0.00 1.00 0.000.0 REMARK 350 BIOMT3 2 0.00 0.00 -1.00 33.43000 when i feed the same into pisa..it says no assemblies are possible... i can't make out...can ny1 help.. Regards, Kanika -- 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 -- 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
Re: [PyMOL] pisa
ya,i get it... Thanks... On Thu, Mar 3, 2011 at 5:58 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Kanika, REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC It says 'author determined'. It doesn't say how, though. But look at the following: # Get the molecule fetch 1b8e,async=0 # Create a copy create 1b8e_copy,1b8e # Color it color hotpink, 1b8e_copy # Transform the copy according to the BIOMT record alter_state 1,1b8e_copy,(x,z)=(-x,33.43-z) # Set both units in view orient # Now look at the symmetry operation symexp A=1b8e,all,2 # Remove the transformed unit: disable 1b8e_copy ### That shows that the dimer state is most probably inferred from the crystal. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
Re: [PyMOL] select clipped atoms
Hello Tsjerk, I can use the function and commands. print clipped(clipsed) - but not print clipped(3lzt) - shows the indices of the atoms between the clipping planes Tsjerk Wassenaar wrote: Hi Johannes, Coincidentally, I found myself in need of the same functionality the other day. I came up with this: from pymol import cmd def clipped_by(at,v): x,y,z = at.coord nz = v[2]*(x-v[12])+v[5]*(y-v[13])+v[8]*(z-v[14])-v[11] return nz v[15] and nz v[16] ATTENTION: The rotation matrix is in column-major order http://en.wikipedia.org/wiki/Column-major#Column-major_order - that's understandable. Hence by multiplying with v[2], v[5] and v[8], you multiply the third column - not row! - with the coordinate vector, in order to get the rotated z-component. The matrix seems to be transposed. For me that is very unusual. In my R script, I made ordinary matrix multiplication and got erroneous results. def clipped(selection=all,state=1): v = cmd.get_view() return [ i.id for i in cmd.get_model(selection,state).atom if clipped_by(i,v) ] The function 'clipped' returns a list of IDs for atoms from a given selection that are outside the clipping planes. You can use it like: The function returns the atoms inside the planes. run clipped.py fetch 3lzt,async=0 clip near,-30 cmd.select_list(clipsed,3lzt,clipped(3lzt)) orient hide show spheres, not clipsed Hence show spheres, clipsed reproduces the selection by a previous slab. Thank you very much. Johannes On Wed, Mar 2, 2011 at 5:27 PM, 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 (\ 1.0,0.0,0.0,\ 0.0,1.0,0.0,\ 0.0,0.0,1.0,\ 0.0,0.0, -320.337890625,\ 74.147140503, 74.174217224, 74.123344421,\ 317.145324707, 323.530487061, -20.0 ) 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
Re: [PyMOL] select clipped atoms
Hi Johannes, I can use the function and commands. print clipped(clipsed) - but not print clipped(3lzt) - shows the indices of the atoms between the clipping planes print clipped(3lzt) should print the indices of atoms that are clipped off by the clipping planes. That works for me, but in terms of the lines I sent, you may want to first save the clipping selection to a variable. ATTENTION: The rotation matrix is in column-major order - that's understandable. Hence by multiplying with v[2], v[5] and v[8], you multiply the third column - not row! - with the coordinate vector, in order to get the rotated z-component. The matrix seems to be transposed. For me that is very unusual. In my R script, I made ordinary matrix multiplication and got erroneous results. Well, the transpose is just the reverse rotation. It's merely a matter of what the programmer had in mind when writing it :) In your R script, you could just have tried t(R) %*% x in stead of R %*% x ;) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
