I have implemented a user function for creating a PDB representation of
the Brownian rotational diffusion tensor. The changes have been made to
the 'tensor_pdb' branch of the repository. The user function is called
'pdb.create_tensor_pdb()'.
Unfortunately Molmol refuses to recognise PDB CONECT
Hi,
Simultaneously with the work with the diffusion tensor PDB
representation (i.e. the code is in the 'tensor_pdb' branch), I have
implemented rudimentary support for PyMOL. The following user functions
are now available:
pymol.view()# Launches PyMOL opening the loaded PDB file.
On Tue, 2006-10-31 at 15:38 +1100, Andrew Perry wrote:
(responding to essentially the entire thread)
I would strongly prefer a separate directory tree of files to
prevent
clutter. I've seen many projects take this approach where the
tests
are
On Wed, 2006-11-01 at 02:11 +1100, Edward d'Auvergne wrote:
pymol.cartoon() doesn't work for me. The commands go to pymol (they
appear in the tcl gui at least) but have no apparent effect. Just doing:
hide everything
show cartoon
on the pymol cmd line has the expected effect.
Edward d'Auvergne wrote:
It would be better if Molmol simply recognised the CONECT records.
Maybe we can ask them to add the basic feature - I'm sure many people
would be happy if their organic molecules were correctly loaded into
Molmol without having to do any additional work.
The problem
pymol.cartoon() doesn't work for me. The commands go to pymol (they
appear in the tcl gui at least) but have no apparent effect. Just doing:
hide everything
show cartoon
on the pymol cmd line has the expected effect.
This could be a PyMOL version issue. Which version are you
On 10/31/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Two comments
1. we need to be able to run the unittests woithou the gui sometimes ;-)
(I tend to view qa lot of gui stuff for calculations as 'sugar' command
lines are often quicker easier and more informative)
Good point. The test-suite
Edward d'Auvergne wrote:
On 11/1/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Edward d'Auvergne wrote:
It would be better if Molmol simply recognised the CONECT records.
Maybe we can ask them to add the basic feature - I'm sure many people
would be happy if their organic molecules were
On Wed, 2006-11-01 at 04:07 +1100, Edward d'Auvergne wrote:
Is the '[:-4]' in 'self.relax.data.pdb[self.run].file_name[:-4]' still
needed? This just chops off the text '.pdb' from the file name.
Opps...
Fixed
Edward
On 11/1/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Author:
On 11/1/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Edward d'Auvergne wrote:
2. I think the unit_test folder will need to be a mirror of the relax
source tree otherwise there will be name space clashes...
Could the files be named something like
'test_specific_fns_model_free.py'?
On 11/1/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Edward d'Auvergne wrote:
It's starting to shape up and it's looking good. The unit tests
framework can now evolve from your 'testfloat' class. Do you think
the unit test code follow the relax convention of the first letter of
the class
Edward d'Auvergne wrote:
2. I think the unit_test folder will need to be a mirror of the relax
source tree otherwise there will be name space clashes...
Could the files be named something like
'test_specific_fns_model_free.py'? That would avoid many directories.
I'm not worried about
Edward d'Auvergne wrote:
It's starting to shape up and it's looking good. The unit tests
framework can now evolve from your 'testfloat' class. Do you think
the unit test code follow the relax convention of the first letter of
the class being uppercase, using underscores between words in
That was simple, I didn't know about the 'basename()' and 'splitext()'
os functions. I'll merge all of the changes that have occurred within
the 1.3 line since the creation of the 'tensor_pdb' branch and then
incorporate this function. Another thing for tomorrow (unless you
would like to do it
On Wed, 2006-11-01 at 03:08 +1100, Edward d'Auvergne wrote:
Oh, and one last thought. It would be nice to automatically scale the
tensor size for the size of the protein, so we don't have to do
trial-and-error adjustments of the scaling factor. The current fixed
default scaling
2. I think the unit_test folder will need to be a mirror of the relax
source tree otherwise there will be name space clashes...
Could the files be named something like
'test_specific_fns_model_free.py'? That would avoid many directories.
I'm not worried about complexity with the test
On 11/1/06, Douglas Kojetin [EMAIL PROTECTED] wrote:
Is there sample data included with relax so we can view this new
feature?
A simple way is to test this is invent stuff - that's what I did when
I was creating this code. I then applied it to real data later. For
example I used the
Edward d'Auvergne wrote:
On 10/31/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Two comments
1. we need to be able to run the unittests woithou the gui sometimes ;-)
(I tend to view qa lot of gui stuff for calculations as 'sugar' command
lines are often quicker easier and more informative)
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 -
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