get view takes in camera coordinates. You can’t open a PDB and it have know
anything about the camera view. You will have to grab the view, save it
somewhere, and then load it. You can’t code a view change within the PDB.
> On Nov 27, 2015, at 11:27 PM, Smith Liu <smith_liu...@163.com> wrote:
>
> Dear Jordan,
>
> My purpose is, once you move a molecule in pymol, I want to save a new pdb,
> when we open the new pdb, pymol will display the new position as default.
>
> The script is
>
> "# Adds the command save_transformed
> # Usage: save_transformed object, file
> def save_transformed(object,file):
> m = cmd.get_view(0)
> 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]
> cmd.transform_object(object,ttt)
> cmd.save(file,object)
> cmd.extend('save_transformed',save_transformed)"
>
> shown in http://pymolwiki.org/index.php/Modeling_and_Editing_Structures
> <http://pymolwiki.org/index.php/Modeling_and_Editing_Structures>
>
> Here I notice that once load a pdb, you move it a little, then you input
> "get_view", you will get the matrix like
> 0.448818117, 0.886667669, -0.111277729
> -0.889764965, 0.454960942, 0.036454394
>
> which should be the m[0] to m[5] in the above script.
>
> In addition, in http://www.pymolwiki.org/index.php/Transform_odb
> <http://www.pymolwiki.org/index.php/Transform_odb>, there is also a
> transcript. For matrix it uses *.odb file. Is this *.odb same as the
> get_view matrix, if not, can we convert get_view matrix to *.odb?
>
> Besides, in http://www.pymolwiki.org/index.php/Transform_selection
> <http://www.pymolwiki.org/index.php/Transform_selection> there is another
> script.
>
> I do not know how to use this scripts to realize my purpose.
>
> Smith
>
>
>
>
>
>
>
>
> At 2015-11-28 15:07:18, "Jordan Willis" <jwillis0...@gmail.com> wrote:
> very possible, can you send me the script?
>> On Nov 27, 2015, at 10:58 PM, Smith Liu <smith_liu...@163.com
>> <mailto:smith_liu...@163.com>> wrote:
>>
>> By Jordan,
>>
>> by
>>
>> find ~/ -name “newpdb.pdb” or by
>>
>> find / -name “newpdb.pdb”
>>
>> still does not work. Is any possibility the original "save_transformed.py"
>> does not work?
>>
>>
>> Smith
>>
>>
>>
>>
>>
>> At 2015-11-28 13:11:25, "Jordan Willis" <jwillis0...@gmail.com
>> <mailto:jwillis0...@gmail.com>> wrote:
>> try running
>>
>>
>> find ~/ -name “newpdb.pdb”
>>
>>
>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <smith_liu...@163.com
>>> <mailto:smith_liu...@163.com>> wrote:
>>>
>>>
>>> Dear All,
>>>
>>> Osvaldo is new here for this question, so I repeat it a little. By pymol I
>>> open a pdb and orient it and I want to save the oriented pdb. First I input
>>> command "orient" after load the pdb, then I input command "run
>>> save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb
>>> by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I
>>> cannot find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL
>>> 1.6.X.
>>>
>>> I am looking forward to getting a reply from you on how to get the
>>> oriented pdb, which should be different from the original PDB I load.
>>>
>>> Smith
>>>
>>>
>>>
>>>
>>>
>>>
>>> At 2015-11-28 00:44:07, "Shane Caldwell" <shane.caldwel...@gmail.com
>>> <mailto:shane.caldwel...@gmail.com>> wrote:
>>> 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
>>> <mailto: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
>>> <mailto: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
>>> <mailto: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
>>> <mailto:docandr...@gmail.com>> wrote:
>>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>> <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
>>> <mailto: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
>>> <mailto: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
>>> <mailto: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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