From: Sampson, Jared <Jared.Sampson@ny...>  20101214 18:56:43

Hello all  I'm trying to calculate the elbow angle of an Fab locally (i.e. without uploading to a server) and decided to try it in PyMOL. I got stuck, and thought maybe someone much wiser than I might be able to shed some light on the error(s) of my ways. I've been trying to use some of the functions in transformations.py by Christoph Gohlke (quite a thorough toolset!); what I have so far is the following .pml script: run transformations.py import numpy import transformations fetch 3ghe, async=0 # break the fab into 4 pieces create vl, chain L and resi 1107 create vh, chain H and resi 1113 create cl, chain L and !vl create ch, chain H and !vh # align the pieces super vl,vh super cl,ch python # get the transformation matrices mat_v = cmd.get_object_matrix("vl") mat_c = cmd.get_object_matrix("cl") # turns Pymol's output into a 4x4 python array def mat_to_R(mat): R = [[mat[0],mat[1],mat[2],mat[3]], [mat[4],mat[5],mat[6],mat[7]], [mat[8],mat[9],mat[10],mat[11]], [mat[12],mat[13],mat[14],mat[15]]] return R Rv = mat_to_R(mat_v) Rc = mat_to_R(mat_c) # calculate the axis & angle angle_v,direction_v,point_v = transformations.rotation_from_matrix(Rv) angle_c,direction_c,point_c = transformations.rotation_from_matrix(Rc) # calculate the elbow angle elbow = numpy.degrees(numpy.dot(direction_v,direction_c)) print "Elbow angle:",elbow python end I'm getting the following error, but I'm not sure how to address it: Traceback (most recent call last): File "/sw64/lib/pymolpy26/modules/pymol/parser.py", line 155, in parse exec(py_block,self.pymol_names,self.pymol_names) File "<string>", line 19, in <module> File "transformations.py", line 348, in rotation_from_matrix raise ValueError("no unit eigenvector corresponding to eigenvalue 1") ValueError: no unit eigenvector corresponding to eigenvalue 1 Any help would be greatly appreciated! Thanks, Jared  Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 2122637898  This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= 