On Wed, Jul 20, 2011 at 5:21 PM, Thomas Holder
<spel...@users.sourceforge.net> wrote:
>> Thanks, but I still failed to get this new pdb.
>>
>> File -- Save molecular -->
>>
>> I wish the present coordinate will be saved as a new pdb after rotation.
>
> I guess with present coordinate you mean what you see on screen. To get this
> you need to transform the atom coordinates by current camera orientation
> before saving to file.
>
> This python code will do that:
>
> def transform_by_camera_rotation():
> view = list(cmd.get_view())
> M = view[0:3] + [-view[12]] + \
> view[3:6] + [-view[13]] + \
> view[6:9] + [-view[14]] + \
> view[12:15] + [1.]
> cmd.transform_selection('(all)', M, transpose=1)
> cmd.set_view([1,0,0,0,1,0,0,0,1] + view[9:])
> cmd.extend('transform_by_camera_rotation', transform_by_camera_rotation)
Thanks first,
but here comes another question,
once I touched a transform_by_camera_rotation.py and copy those inside
it as following,
$ more transform_by_camera_rotation.py
#/usr/bin/python
def transform_by_camera_rotation():
view = list(cmd.get_view())
M = view[0:3] + [-view[12]] + \
view[3:6] + [-view[13]] + \
view[6:9] + [-view[14]] + \
view[12:15] + [1.]
cmd.transform_selection('(all)', M, transpose=1)
cmd.set_view([1,0,0,0,1,0,0,0,1] + view[9:])
cmd.extend('transform_by_camera_rotation', transform_by_camera_rotation)
>
> Example:
>
> fetch 2xwu
> orient
> transform_by_camera_rotation
PyMOL>transform_by_camera_rotation
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line
464, in parse
exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
File "<string>", line 1, in <module>
NameError: name 'transform_by_camera_rotation' is not defined
I don't know how achieve this part. Thanks again with best regards,
> save /tmp/withneworientation.pdb
>
> Cheers,
> Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
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