Hi Smith, and everybody who tried to help you so far,
Short answer: copy and paste this into the PyMOL command line, it will save the
view-transformed object to "transformed.pdb" in your home folder.
cv=list(cmd.get_view())
cmd.transform_selection("all", \
cv[0:3]+[0.0]+ \
cv[3:6]+[0.0]+ \
cv[6:9]+[0.0]+ \
cv[12:15]+[1.0], transpose=1)
cmd.save('~/transformed.pdb')
To comment on the many emails that have been posted so far:
1) I think you haven't used the script correct. Instead of "run
save_trannsforme.py all, newpdb.pdb", you have to do "run save_transformed.py",
followed by "save_transformed all, newpdb.pdb"
2) The script is actually wrong (missing transpose=1)
3) A correct solution has been posted for example here:
https://sourceforge.net/p/pymol/mailman/message/27824450/
Hope that helps.
Cheers,
Thomas
On 28 Nov 2015, at 02:52, Jordan Willis <[email protected]> wrote:
> 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 <[email protected]> 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" <[email protected]> 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 <[email protected]> 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
>>>
>>> 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, 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 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" <[email protected]> wrote:
>>> very possible, can you send me the script?
>>>> On Nov 27, 2015, at 10:58 PM, Smith Liu <[email protected]> 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" <[email protected]> wrote:
>>>> try running
>>>>
>>>>
>>>> find ~/ -name “newpdb.pdb”
>>>>
>>>>
>>>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <[email protected]> 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" <[email protected]>
>>>>> 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 <[email protected]> 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" <[email protected]> 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
>>>>> 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 <[email protected]> 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" <[email protected]> wrote:
>>>>> http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures
>>>>>
>>>>>
>>>>> Andreas
>>>>>
>>>>>
>>>>> On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <[email protected]> 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" <[email protected]>
>>>>> 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 <[email protected]> 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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