Hi Smith,
It will be in whatever folder pymol is launched from. If you launched pymol
from a specific place, it will be that folder. If not, it might be in the
system files for pymol, which will depend on your operating system and
architecture.
Shane
Shane Caldwell
McGill University
On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smith_liu...@163.com> wrote:
> Dear All，
>
> Once a molecule displayed in pymol, first I input command "orient", then I
> input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the
> oriented newpdb.pdb.
>
> Will you please show me how to get the oriented newpdb.pdb?
>
> Smith
>
>
>
>
>
> At 2015-11-26 18:58:48, "Spencer Bliven" <spencer.bli...@gmail.com> wrote:
>
> 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
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>>
>>>
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>>> Give your users amazing mobile app experiences with Intel(R) XDK.
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>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
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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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>
>
>
>
>
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