Dear Thomas,
I do not know I still do something wrong.
First I load a PDB in pymol, then I input orient (with orient input the
molecule really moved significantly in display), then I input
transform_by_camera_rotation, then I input save /tmp/withneworientation.pdb,
the withneworientation.pdb was really saved, but the newly saved
withneworientation.pdb has the all atom orientations (x,y,z) exactly same as
those of the original PDB I initially input to the pymol for the process I
obtained the withneworientation.pdb.
Smith
At 2015-11-30 08:08:52, "Thomas Holder" <thomas.hol...@schrodinger.com> wrote:
>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 <jwillis0...@gmail.com> 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 <smith_liu...@163.com> 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" <jwillis0...@gmail.com> 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 <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
>>>>
>>>> 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" <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> 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> wrote:
>>>>> try running
>>>>>
>>>>>
>>>>> find ~/ -name “newpdb.pdb”
>>>>>
>>>>>
>>>>>> On Nov 27, 2015, at 9:08 PM, Smith Liu <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>
>>>>>> 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> 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
>>>>>> 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
>
>--
>Thomas Holder
>PyMOL Principal Developer
>Schrödinger, Inc.
>
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