URL: <http://gna.org/bugs/?7596> Summary: Error using pdb.create_tensor_pdb() on amd64 Linux Project: relax Submitted by: None Submitted on: Wednesday 11/01/2006 at 03:28 CET Category: None Priority: 5 - Normal Severity: 3 - Normal Status: None Privacy: Public Assigned to: None Originator Name: Originator Email: james.horne@xxxxxxxxxxxxxxxxx Open/Closed: Open Release: Other (missing version) Operating System: GNU/Linux _______________________________________________________ Details: Running relax with a script from the branches/tensor_pdb version of relax (2722) and the attached script causes the error pasted below. This was run on an Opteron processor with Gentoo Linux kernel 2.6.14, Numeric-23.7 and ScientificPython-2.4.9 and Python-2.4.2. The same script run in a 32 bit chroot environment (same OS in 32 bit mode; same kernel, Numeric-23.6, ScientificPython 2.4.6 and Python2.3.4) runs without error and produces lovely diagrams in PyMol. I don't have a clue if this is an error of my 64 bit system setup or relax but perhaps others have encountered this issue before. --------------------------------------Error trace--------------------------------------------------------- relax> pdb.create_tensor_pdb(run='tensor', scale=1.7999999999999999e-06, file='red_trx_tensor.pdb', dir=None, force=1) Calculating the center of mass. Total mass: M = 10442.408100000024 Center of mass: R = array([ -6.53186368, -26.18782042, 37.27497538]) Generating the unique axis of the diffusion tensor. Scaling factor: 1.7999999999999999e-06 Dpar vector (scaled + shifted to R): array([-12.07457919, -14.60142721, 50.52065598]) Generating the geometric object. Creating the uniform vector distribution. Traceback (most recent call last): File "./relax", line 458, in ? Relax() File "./relax", line 170, in __init__ self.interpreter.run() File "/home/hjh/relax_tensor_pdb/prompt/interpreter.py", line 216, in run run_script(intro=self.relax.intro_string, local=self.local, script_file=self.relax.script_file, quit=1) File "/home/hjh/relax_tensor_pdb/prompt/interpreter.py", line 391, in run_script console.interact(intro, local, script_file, quit) File "/home/hjh/relax_tensor_pdb/prompt/interpreter.py", line 343, in interact_script execfile(script_file, local) File "tensor_pdb.py", line 16, in ? pdb.create_tensor_pdb(name, file=tensor_file, force=1) File "/home/hjh/relax_tensor_pdb/prompt/pdb.py", line 113, in create_tensor_pdb self.__relax__.generic.pdb.create_tensor_pdb(run=run, scale=scale, file=file, dir=dir, force=force) File "/home/hjh/relax_tensor_pdb/generic_fns/pdb.py", line 349, in create_tensor_pdb vector = dot(self.relax.data.diff[self.run].rotation, vectors[index]) File "/home/hjh/relax_tensor_pdb/data.py", line 349, in __getattr__ rotation = identity(3, Float64) File "/usr/lib64/python2.4/site-packages/Numeric/Numeric.py", line 604, in identity return resize(array([1]+n*[0],typecode=typecode), (n,n)) File "/usr/lib64/python2.4/site-packages/Numeric/Numeric.py", line 398, in resize return reshape(a, new_shape) ValueError: total size of new array must be unchanged _______________________________________________________ Carbon-Copy List: CC Address | Comment ------------------------------------+----------------------------- Available only the item webpage | Originator Email _______________________________________________________ File Attachments: ------------------------------------------------------- Date: Wednesday 11/01/2006 at 03:28 CET Name: tensor_pdb.py Size: 670B By: None inut script for relax diffusion tensor mapping onto a pdb structure <http://gna.org/bugs/download.php?file_id=1456> _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?7596> _______________________________________________ Message sent via/by Gna! http://gna.org/