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Re: [PyMOL] save_transformed.py
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From: Jordan W. <jwi...@gm...> - 2015-11-28 07:52:59
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Yes, but what you are describing, saving a new view is your purpose. All orient does is move the camera. It does not do anything to the x,y,z coordinates of the PDB.
> On Nov 27, 2015, at 11:49 PM, Smith Liu <smi...@16...> wrote:
>
> Dear Jordan,
>
> To save a new view is not my purpose, my purpose is to save a new set of PDB. For example， if the original PDB does not orient well by pymol by default, first I input "orient", and I want to save a set of new pdb, when I display by pymol the new pdb, it will display as "oriented“. Is any way we can get this oriented pdb?
>
> Smith
>
>
>
>
>
> At 2015-11-28 15:37:10, "Jordan Willis" <jwi...@gm...> wrote:
> 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 <smi...@16... <mailto:smi...@16...>> 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" <jwi...@gm... <mailto:jwi...@gm...>> wrote:
>> very possible, can you send me the script?
>>> On Nov 27, 2015, at 10:58 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> 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" <jwi...@gm... <mailto:jwi...@gm...>> wrote:
>>> try running
>>>
>>>
>>> find ~/ -name “newpdb.pdb”
>>>
>>>
>>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <smi...@16... <mailto:smi...@16...>> 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" <sha...@gm... <mailto:sha...@gm...>> 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 <smi...@16... <mailto:smi...@16...>> 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" <spe...@gm... <mailto:spe...@gm...>> 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 <smi...@16... <mailto:smi...@16...>> 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" <doc...@gm... <mailto:doc...@gm...>> 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 <smi...@16... <mailto:smi...@16...>> 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" <sha...@gm... <mailto:sha...@gm...>> 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 <smi...@16... <mailto:smi...@16...>> 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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