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
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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>
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Reply to this item at:
<http://gna.org/bugs/?7596>
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[bug #7596] Error using pdb.create_tensor_pdb() on amd64 Linux