Smith–
The code is intended to be saved to a file ("save_transformed.py") and then
loaded into pymol using `run /path/to/save_transformed.py`. There's some
general info on running pymol scripts: Simple_Scripting
<http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts
<http://pymolwiki.org/index.php/Running_Scripts>
The script defines a new command which can be run e.g. `save_transformed
<object>, <file>`. You don't have to replace anything in the script
yourself.
Note that the save_transformed command modifies the object it's run on, so
you might want to run it on a backup copy by first calling `create
<object>_backup, <object>`
-Spencer
On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smith_liu...@163.com> wrote:
> Dear All,
>
> For get view, we get something like
>
> set_view (\
> 0.999876618, -0.000452542, -0.015699286,\
> 0.000446742, 0.999999821, -0.000372844,\
> 0.015699454, 0.000365782, 0.999876678,\
> 0.000000000, 0.000000000, -150.258514404,\
> 11.842411041, 20.648729324, 8.775371552,\
> 118.464958191, 182.052062988, 0.000000000 )
>
> For save trasformed pdb file, we need sonething like
>
> ttt = [m[0], m[1], m[2], 0.0,
> m[3], m[4], m[5], 0.0,
> m[6], m[7], m[8], 0.0,
> 0.0, 0.0, 0.0, 1.0]
> Will you please show me how to replace m[0], m[1].... from what we get by
> get_view? Which item is which item?
>
> In addition, for the save_transformed.py, the last sentence is
> "cmd.extend('save_transformed',save_transformed)". Should we replace the
> second save_transformed with something, for example *.pdb? Ortherwise how
> to get the output modified PDB?
>
>
> I am looking forward to getting a reply from you.
>
> Smith
>
>
>
>
>
>
>
>
>
> At 2015-11-26 14:24:15, "Andreas Forster" <docandr...@gmail.com> wrote:
>
> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>
>
> Andreas
>
>
> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smith_liu...@163.com> wrote:
>
>> Dear Shane,
>>
>> get_view is a nice command. Is any way to change the original PDB based
>> on what we get by set_view to get the new pdb?
>>
>> Smith
>>
>>
>>
>>
>>
>>
>> At 2015-11-26 03:54:32, "Shane Caldwell" <shane.caldwel...@gmail.com>
>> wrote:
>>
>> Hi Smith,
>>
>> You can type
>>
>> >get_view
>>
>> and copy the output into a txt file for later use. The output set_view
>> command will return the window to the same camera settings
>>
>> Shane
>>
>> Shane Caldwell
>> McGill University
>>
>> On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smith_liu...@163.com> wrote:
>>
>>> Dear All,
>>>
>>> Suppose the original PDB was not oriented. Once we have it oriented by
>>> pymol, is any way we can save the new PDB oriented?
>>>
>>> Smith
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
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>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
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>>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
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